# BugSigDB 2024-10-04_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
BSDB ID,Study,Study design,PMID,DOI,URL,Authors list,Title,Journal,Year,Keywords,Experiment,Location of subjects,Host species,Body site,UBERON ID,Condition,EFO ID,Group 0 name,Group 1 name,Group 1 definition,Group 0 sample size,Group 1 sample size,Antibiotics exclusion,Sequencing type,16S variable region,Sequencing platform,Statistical test,Significance threshold,MHT correction,LDA Score above,Matched on,Confounders controlled for,Pielou,Shannon,Chao1,Simpson,Inverse Simpson,Richness,Signature page name,Source,Curated date,Curator,Revision editor,Description,Abundance in Group 1,MetaPhlAn taxon names,NCBI Taxonomy IDs,State,Reviewer
bsdb:1/1/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae",2|1239|91061;2|1224|1236;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3085636|186803|189330;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|995019|40544;2|201174|1760|2037;2|201174|1760|2037|2049;2|1224|28216|80840|506;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|909932|1843489|31977;2|1224|1236|91347;2|201174|1760|85007|1653;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817,Complete,Fatima
bsdb:1/1/2,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Cyanobacteriota",2|1239|526524|526525|2810280|100883;2|1117,Complete,Shaimaa Elsafoury
bsdb:1/2/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Hyperplastic Polyp,EFO:1000299,controls,hyperplastic polyp cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,40,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae",2|1239|186801|3085636|186803|207244;2|1239|91061|186826|33958|2759736|57037,Complete,Shaimaa Elsafoury
bsdb:1/2/2,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Hyperplastic Polyp,EFO:1000299,controls,hyperplastic polyp cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,40,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1224|1236;2|1239|526524|526525|2810280|100883;2|1224|1236|91347,Complete,Shaimaa Elsafoury
bsdb:1/3/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Colon Sessile Serrated Adenoma/Polyp,EFO:1000189,controls,Sessile serrated adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,33,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|1239|526524;2|1224|1236,Complete,Shaimaa Elsafoury
bsdb:1/4/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Proximal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,87,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|201174|1760|2037;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300;2|1239|186801|186802|31979|1485;2|976|200643|171549|171551|836;2|1239|91061;2|1239|91061|186826;2|1239|1737404|1737405|1570339|162289;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|1853231|283168;2|1239|909932|1843489|31977;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|189330;2|1224|28216|80840|995019|40544;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|506;2|1224|1236|91347;2|1224|1236;2|976|200643|171549|1853231,Complete,Shaimaa Elsafoury
bsdb:1/4/2,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Proximal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,87,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",decreased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,2|1239|526524|526525|2810280|100883,Complete,Shaimaa Elsafoury
bsdb:1/5/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Distal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,55,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,"Fatima,Merit,WikiWorks,Lwaldron,Davvve","Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10, are included in the table.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Synergistota,k__Bacteria|p__Synergistota",2|1239|186801|3082768|990719;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|544448|31969;2|508458;2|508458,Complete,Fatima
bsdb:1/6/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Non-advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,121,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|201174|1760|2037|2049|1654;2|976|200643|171549|1853231|283168;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|189330;2|1239|909932|1843489|31977;2|1224|28216|80840|995019|40544;2|1224|28216|80840|506;2|1239|909932|1843488|909930|33024,Complete,Shaimaa Elsafoury
bsdb:1/7/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,22,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental Table S7 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae",2|201174|1760|2037;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836;2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|135625|712|724;2|201174|1760|85007|1653,Complete,Shaimaa Elsafoury
bsdb:1/7/2,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,22,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Table S7 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria",2|976|200643|171549|2005519;2|1117;2|1239|186801|3082768|990719;2|1239|186801|3085636|186803|140625;2|1239|186801|3085636|186803|28050;2|1224|28211,Complete,Shaimaa Elsafoury
bsdb:2/1/1,Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 1,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,normal adjacent tissues,squamous cell carcinoma tissues,tissues with evidence of squamous cell carcinoma,121,121,NA,16S,1234,Sanger,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3 +text,10 January 2021,Nidhi Saini,WikiWorks,Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1570339|543311,Complete,Shaimaa Elsafoury
bsdb:2/1/2,Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 1,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,normal adjacent tissues,squamous cell carcinoma tissues,tissues with evidence of squamous cell carcinoma,121,121,NA,16S,1234,Sanger,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174;2|201174|1760;2|201174|1760|2037;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
bsdb:2/2/1,Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 2,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,T0-T2 low tumor stages patients,T3-T4 high tumor stages patients,Not stated,NA,NA,NA,16S,1234,Sanger,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",increased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,2|1239|1737404|1737405|1570339|543311,Complete,Shaimaa Elsafoury
bsdb:2/2/2,Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 2,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,T0-T2 low tumor stages patients,T3-T4 high tumor stages patients,Not stated,NA,NA,NA,16S,1234,Sanger,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota",2|201174|1760|2037|2049|1654;2|201174,Complete,Shaimaa Elsafoury
bsdb:3/1/1,Study 3,case-control,27015276,10.1371/journal.pone.0152126,NA,"Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB , Goedert JJ","Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations",PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,adenocarcinoma of colon and rectum patients,Not stated,89,42,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Fecal microbes independently associated with colorectal cancer,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836,Complete,Shaimaa Elsafoury
bsdb:3/1/2,Study 3,case-control,27015276,10.1371/journal.pone.0152126,NA,"Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB , Goedert JJ","Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations",PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,adenocarcinoma of colon and rectum patients,Not stated,89,42,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Nidhi Saini,WikiWorks,Fecal microbes independently associated with colorectal cancer,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:4/1/1,Study 4,case-control,27625705,10.1186/s13099-016-0124-2,NA,"Aly AM, Adel A, El-Gendy AO, Essam TM , Aziz RK",Gut microbiome alterations in patients with stage 4 hepatitis C,Gut pathogens,2016,"Gastro-intestinal tract, High-throughput sequencing, Infectious diseases, Liver disease, Microbiome, Next-generation sequencing, Virology",Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Hepatitis,HP:0012115,male healthy controls,HCV stage 4 male patients,Not stated,8,6,3 months,16S,4,Illumina,LEfSe,0.1,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Table 2 and Fig 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants  (non-parametric t test). All participants were male.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota",2|1224|1236|2887326|468|469;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|1239|909932|1843488|909930|33024;2|1224|1236|72274;2|1224|1236|2887326|468;2|976|200643|171549;2|976|200643;2|976,Complete,Shaimaa Elsafoury
bsdb:4/1/2,Study 4,case-control,27625705,10.1186/s13099-016-0124-2,NA,"Aly AM, Adel A, El-Gendy AO, Essam TM , Aziz RK",Gut microbiome alterations in patients with stage 4 hepatitis C,Gut pathogens,2016,"Gastro-intestinal tract, High-throughput sequencing, Infectious diseases, Liver disease, Microbiome, Next-generation sequencing, Virology",Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Hepatitis,HP:0012115,male healthy controls,HCV stage 4 male patients,Not stated,8,6,3 months,16S,4,Illumina,LEfSe,0.1,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Table 2 and Fig 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants  (non-parametric t test). All participants were male.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Lentisphaerota",2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263;2|976|200643|171549|1853231|574697;2|201174;2|201174|1760;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|976|200643|171549|171551;2|544448|31969;2|544448;2|1224|1236|135622|267888|53246;2|1224|1236|135622|267888;2|1224|1236|135623;2|1239|909932|1843489|31977|39948;2|256845|1313211|278082|255528;2|256845|1313211|278082;2|256845,Complete,Shaimaa Elsafoury
bsdb:5/1/1,Study 5,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman AA, Kim HB, Reilly CS, Wendt C , Isaacson RE",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,NA,Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Chronic obstructive pulmonary disease,EFO:0000341,controls,Chronic obstructive pulmonary disease,Patients who have Chronic obstructive pulmonary disease,10,22,2 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Lwaldron,Fatima,WikiWorks",Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",2|1239|91061|186826|186827|46123;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1239|91061|186826|186827;2|1224|1236|135624|84642;2|1224|1236|135624;2|1224|1236|135624|84642|642;2|1239|186801|3085636|186803|653683;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|1239|186801|3085636|186803|830;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|976|117743|200644|49546|1016;2|1239|186801|3085636|186803|43996;2|1239|909932|909929|1843491|82202;2|201174|84998|84999|84107;2|201174|84998|1643822|1643826|84162;2|200940|3024418|213118|213119;2|200940|3024418|213118;2|200940|3031451|3024411|213121|893;2|1239|909932|1843489|31977|39948;2|976|200643|171549|2005520|156973;2|29547;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|52228;2|1239|186801|3085636|186803;2|1239|91061|186826;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|201174|1760|85006|1268;2|1224|28211|356|119045|186650;2|1224|28216|206351|481;2|1224|28216|206351;2|201174|1760|85009|85015|1839;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|265975;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|1224|28211|204441;2|201174|1760|85006|1268|32207;2|1239|909932|909929|1843491|970;2|1224|1236|91347|1903411|613;2|1239|526524|526525|128827|123375;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|201174|84998|84999,Complete,Fatima
bsdb:5/1/2,Study 5,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman AA, Kim HB, Reilly CS, Wendt C , Isaacson RE",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,NA,Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Chronic obstructive pulmonary disease,EFO:0000341,controls,Chronic obstructive pulmonary disease,Patients who have Chronic obstructive pulmonary disease,10,22,2 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,WikiWorks,Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus|s__Candidatus Blastococcus massiliensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Thermoactinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter",2|1239|186801|186802|31979|1485;2|201174|1760|1643682|85030|38501|1470358;2|201174|1760|1643682|85030|88138;2|201174|1760|1643684|85031;2|1239|91061|1385|186824|2023;2|1239|91061|1385|186824;2|1224|1236|91347|543|544;2|201174|1760|85006|1268|1663,Complete,Shaimaa Elsafoury
bsdb:5/2/1,Study 5,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman AA, Kim HB, Reilly CS, Wendt C , Isaacson RE",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,NA,Experiment 2,United States of America,Homo sapiens,Lung,UBERON:0002048,Chronic obstructive pulmonary disease,EFO:0000341,moderate Chronic obstructive pulmonary disease,Severe,Patients who have severe Chronic obstructive pulmonary disease,8,14,2 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pontibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|1224|1236|135624;2|200940|3024418|213118;2|1224|1236|135624|84642;2|200940|3031451|3024411|213121;2|201174|1760|85009|85015|1839;2|1239|91061|1385|186817|289201;2|1239|186801|186802|31979|1485;2|1224|28211|356|119045|186650;2|1224|1236|135624|84642|642,Complete,Shaimaa Elsafoury
bsdb:6/1/1,Study 6,prospective cohort,28467925,10.1016/j.cmet.2017.04.001,NA,"Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC , Nelson KE",Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease,Cell metabolism,2017,"NASH, biomarker, cirrhosis, fatty liver, fibrosis, hepatic steatosis, hepatitis, liver disease, microbiome, non-invasive",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,mild/moderate fibrosis,advanced fibrosis,"Based on clinical, magnetic resonance, histology assessment; Mild/Moderate NAFLD: fibrosis 0-2. Advanced NAFLD: fibrosis 3-4",72,14,NA,WMS,NA,Illumina,Random Forest Analysis,0.05,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"Lwaldron,WikiWorks",relative abundances of top 4 phyla found in all samples and representative species from the first 3 phyla.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:7/1/1,Study 7,case-control,20603222,10.1016/j.anaerobe.2010.06.008,NA,"Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR , Green JA",Pyrosequencing study of fecal microflora of autistic and control children,Anaerobe,2010,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non-sibling control,severely autistic,"Cases were diagnosed with autistic spectrum disorder. Moreover, they were evaluated for autism and their diagnoses were validated based on impairment in social skills, impairment in language skills and verbal communication, sensory disturbances, repetitive stereotypical behaviors, and gastrointestinal disturbances.",8,11,within preceding month,16S,NA,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Table 2 + Table 3 +  Table 5 + Table 6 + Table 8,10 January 2021,Marianthi Thomatos,WikiWorks,Significant fecal microflora of autistic and control children,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkaliflexus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota",2|1239|526524|526525|2810281|191303;2|976|200643|171549|815|816;2|976|200643|1970189|558415|286729;2|200940|3031449|213115|194924|872;2|1239|186801|186802|216572|258514;2|976|200643|171549|2005525|375288;2|200940|3031449|213115|194924|872|901;2|200940|3031449|213115|194924|872|876;2|200940|3031449|213115|194924|872|58621;2|976|200643|171549|815|909656|821;2|976;2|1224,Complete,Shaimaa Elsafoury
bsdb:7/1/2,Study 7,case-control,20603222,10.1016/j.anaerobe.2010.06.008,NA,"Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR , Green JA",Pyrosequencing study of fecal microflora of autistic and control children,Anaerobe,2010,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non-sibling control,severely autistic,"Cases were diagnosed with autistic spectrum disorder. Moreover, they were evaluated for autism and their diagnoses were validated based on impairment in social skills, impairment in language skills and verbal communication, sensory disturbances, repetitive stereotypical behaviors, and gastrointestinal disturbances.",8,11,within preceding month,16S,NA,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,Table 2 + Table 3 +  Table 5 + Table 6 + Table 8,10 January 2021,Marianthi Thomatos,"Lwaldron,WikiWorks",Significant fecal microflora of autistic and control children,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",2|201174;2|1239|186801|3082720|3118656|114627;2|1239|186801|186802|216572|52784;2|1239|186801|3082720|3030910|109326;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1683;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|216572|253238;2|1239;2|1239|1737404|1737405|1570339|31983;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1243;2|1239|186801|186802|186806|113286;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|46255;2|1239|186801|186802|216572|1535,Complete,Fatima
bsdb:8/1/1,Study 8,case-control,20140211,10.1371/journal.pone.0009085,NA,"Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH , Jakobsen M",Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults,PloS one,2010,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Control,Diabetes Type 2,The diabetic group had elevated concentration of plasma glucose as determined by a fasting oral glucose tolerance test (OGTT),10,10,NA,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2 + Text,10 January 2021,Phyu Han,WikiWorks,Relative abundances (%) of bacteria were determined in feces from human adults with type 2 diabetes and non-diabetic adult (all are males),increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,2|1224|28216,Complete,Shaimaa Elsafoury
bsdb:8/1/2,Study 8,case-control,20140211,10.1371/journal.pone.0009085,NA,"Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH , Jakobsen M",Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults,PloS one,2010,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Control,Diabetes Type 2,The diabetic group had elevated concentration of plasma glucose as determined by a fasting oral glucose tolerance test (OGTT),10,10,NA,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2 + Text,10 January 2021,Phyu Han,WikiWorks,Relative abundances (%) of bacteria were determined in feces from human adults with type 2 diabetes and non-diabetic adult (all are males),decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia",2|1239;2|1239|186801,Complete,Shaimaa Elsafoury
bsdb:9/1/1,Study 9,case-control,29190829,10.1371/journal.pone.0188873,NA,"Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP , Kalari KR",A comprehensive analysis of breast cancer microbiota and host gene expression,PloS one,2017,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,Control,Breast Cancer,Patients with breast cancer,668,72,NA,16S,345,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 +text,10 January 2021,Phyu Han,"Lwaldron,WikiWorks",Species compositions of the Breast Caner and Non-cancerous Adjacent tissues,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus|s__Alkalihalobacillus alcalophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium muris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Furfurilactobacillus|s__Furfurilactobacillus rossiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium phlei,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium fortuitum",2|1239|91061|1385|186817|2675234|1445;2|201174|1760|85006|85020|43668|219301;2|1239|91061|186826|33958|2767882|231049;2|1224|1236|91347|543|590|28901;2|201174|1760|85007|1762|1866885|1771;2|201174|1760|85007|1762|1866885|1766,Complete,Fatima
bsdb:9/1/2,Study 9,case-control,29190829,10.1371/journal.pone.0188873,NA,"Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP , Kalari KR",A comprehensive analysis of breast cancer microbiota and host gene expression,PloS one,2017,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,Control,Breast Cancer,Patients with breast cancer,668,72,NA,16S,345,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3 +text,10 January 2021,Phyu Han,"Lwaldron,WikiWorks",Species compositions of the Breast Caner and Non-cancerous Adjacent tissues,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium barkeri",2|1224|1236|2887326|468|469|40216;2|1224|1236|91347|543|561|562;2|1224|28216|80840|119060|48736|329;2|201174|1760|85006|85023|33882|33917,Complete,Fatima
bsdb:10/1/1,Study 10,case-control,29234019,10.1038/s41598-017-17351-9,NA,"Curty G, Costa RL, Siqueira JD, Meyrelles AI, Machado ES, Soares EA , Soares MA",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,NA,Experiment 1,Brazil,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Normal tissue HIV patients,Cervical Intraepithelial Lesion HIV patients,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health. this were also patients with cervical intraepithelial lesions,42,38,NA,16S,3456,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Phyu Han,WikiWorks,Bacteria that presented higher relative abundance in cervical lesions using LEfse,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,2|1239|186801|3085636|186803|437755,Complete,Shaimaa Elsafoury
bsdb:10/2/1,Study 10,case-control,29234019,10.1038/s41598-017-17351-9,NA,"Curty G, Costa RL, Siqueira JD, Meyrelles AI, Machado ES, Soares EA , Soares MA",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,NA,Experiment 2,Brazil,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Normal tissue HIV patients,Cervical Intraepithelial Lesion HIV patients,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health.,42,38,NA,16S,3456,Illumina,LEfSe,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,Davvve",Bacteria that presented higher relative abundance in cervical lesions using LEfse protocol,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas|s__Caldimonas thermodepolymerans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",2|1239|91061|186826|186827|1375;2|201174|1760|85004|31953|1678|1681;2|1224|28216|80840|2975441|196013|215580;2|201174|1760|85004|31953|2701|2702,Complete,Shaimaa Elsafoury
bsdb:11/1/1,Study 11,time series / longitudinal observational,29234019,10.1038/s41598-017-17351-9,NA,"Curty G, Costa RL, Siqueira JD, Meyrelles AI, Machado ES, Soares EA , Soares MA",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,NA,Experiment 1,Brazil,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,HIV pateints with normal tissue at 6 months,HIV patients with lesion at 12 months,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health.,5,5,NA,16S,3456,Illumina,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Gardnerella vaginalis abundance longitudinal analysis at six and twelve months postpartum in paired samples,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,2|201174|1760|85004|31953|2701|2702,Complete,Shaimaa Elsafoury
bsdb:12/1/1,Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 1,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV clearance,HPV persistent,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",15,16,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Phyu Han,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,2|976|200643|171549|2005525|375288|387661,Complete,Shaimaa Elsafoury
bsdb:12/2/1,Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 2,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV negative,HPV clearance,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",10,15,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Phyu Han,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2790998|2129|2130,Complete,Shaimaa Elsafoury
bsdb:12/3/1,Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 3,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV presistent and clearance,HPV negative,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",31,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Phyu Han,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,Shaimaa Elsafoury
bsdb:12/4/1,Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 4,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV presistent and negative,HPV clearance,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",26,15,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,2|1239|186801|3085636|186803|28050|39485,Complete,Shaimaa Elsafoury
bsdb:13/1/1,Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Cervical Intraepithelial Neoplasis -1,Cervical Intraepithelial Neoplasis +2,NA,126,40,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Phyu Han,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to Cervical Intraepithelial Neoplasia (CIN) status,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus",2|1239|91061|186826|33958|1578|47770;2|976|200643|171549|815|816|817;2|1239|91061|186826|1300|1301|1311;2|29547|3031852|213849|72294|194|827,Complete,Shaimaa Elsafoury
bsdb:13/1/2,Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Cervical Intraepithelial Neoplasis -1,Cervical Intraepithelial Neoplasis +2,NA,126,40,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Phyu Han,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to Cervical Intraepithelial Neoplasia (CIN) status,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium damselae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae",2|1224|1236|135623|641|657|38293;2|1239|91061|186826|33958|1578|109790;2|201174|84998|84999|1643824|2767327|82135,Complete,Shaimaa Elsafoury
bsdb:13/2/1,Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 2,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV -ve among pateints with Cervical Intraepithelial Neoplasia different severity status,HPV +ve,NA,130,36,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to HPV infection,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",2|1239|91061|186826|1300|1301|1311;2|976|200643|171549|815|816|817;2|1224|1236|72274|135621|2901164|316;2|1239|186801|3082720|186804|1257|1261,Complete,Shaimaa Elsafoury
bsdb:13/2/2,Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 2,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV -ve among pateints with Cervical Intraepithelial Neoplasia different severity status,HPV +ve,NA,130,36,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to HPV infection,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,2|1239|91061|186826|33958|1578|1584,Complete,Shaimaa Elsafoury
bsdb:14/1/1,Study 14,case-control,28875948,10.1088/1752-7163/aa7c24,NA,"Seerangaiyan K, van Winkelhoff AJ, Harmsen HJM, Rossen JWA , Winkel EG",The tongue microbiome in healthy subjects and patients with intra-oral halitosis,Journal of breath research,2017,NA,Experiment 1,Netherlands,Homo sapiens,Superior surface of tongue,UBERON:0007371,Halitosis,HP:0100812,Control,Oral Halitosis,"IOH patient group was selected based on an organoleptic score of >= 2 from the mouth and nose =< 1, having a VSC level > 160 ppb, and H2S > 4 nmol/ L (96 ppb) and CH3SH > 0.5 nmol/L (12 ppb) and a DPSI of =< 2",5,10,3 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Phyu Han,WikiWorks,Significant differentially abundant OTU of intr-aoral halitosis and Control,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|135625|712|416916|739;2|29547|3031852|213849|72294|194;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|39948;2|1239|186801|3082720|186804|1257;2|1239|909932|909929|1843491|970;2|32066|203490|203491|1129771|32067;2|1239|186801|186802|186807|2740;2|1239|186801|186802;2|1239|1737404|1737405|1570339|543311;2|203691|203692|136|2845253|157;2|976|117743|200644|49546|1016;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:14/1/2,Study 14,case-control,28875948,10.1088/1752-7163/aa7c24,NA,"Seerangaiyan K, van Winkelhoff AJ, Harmsen HJM, Rossen JWA , Winkel EG",The tongue microbiome in healthy subjects and patients with intra-oral halitosis,Journal of breath research,2017,NA,Experiment 1,Netherlands,Homo sapiens,Superior surface of tongue,UBERON:0007371,Halitosis,HP:0100812,Control,Oral Halitosis,"IOH patient group was selected based on an organoleptic score of >= 2 from the mouth and nose =< 1, having a VSC level > 160 ppb, and H2S > 4 nmol/ L (96 ppb) and CH3SH > 0.5 nmol/L (12 ppb) and a DPSI of =< 2",5,10,3 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Phyu Han,"Merit,WikiWorks",Significant differentially abundant OTU of intra-oral halitosis and Control,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|1236|135625|712|416916;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|437755;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186807|2740;2|32066|203490|203491|1129771|32067,Complete,Shaimaa Elsafoury
bsdb:15/1/1,Study 15,"cross-sectional observational, not case-control",28932201,10.3389/fphys.2017.00675,NA,"Zheng J, Xiao X, Zhang Q, Mao L, Yu M, Xu J , Wang T",The Placental Microbiota Is Altered among Subjects with Gestational Diabetes Mellitus: A Pilot Study,Frontiers in physiology,2017,"16S rRNA gene, clinical characteristics, gestational diabetes mellitus, microbiota, placenta",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Gestational diabetes,EFO:0004593,controls,Gestational diabetes mellitus,"GDM was diagnosed when the fasting plasma glucose ≥5.1 mmol/L or 1 h post-OGTT glycemia ≥10.0 mmol/L or 2 h post-OGTT glycemia ≥8.5 mmol/L, according to the criteria set by International Association of Diabetes and Pregnancy Study Groups (IADPSG)",10,10,9 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2+ Figure 4+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Phlotypes in placental microbiota significantly different between GDM and NDM groups,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae",2|1224;2|1224|28216|206389|2008794|33057;2|1224|28216|80840;2|1224|28211|356;2|1224|28216|80840|506,Complete,Shaimaa Elsafoury
bsdb:15/1/2,Study 15,"cross-sectional observational, not case-control",28932201,10.3389/fphys.2017.00675,NA,"Zheng J, Xiao X, Zhang Q, Mao L, Yu M, Xu J , Wang T",The Placental Microbiota Is Altered among Subjects with Gestational Diabetes Mellitus: A Pilot Study,Frontiers in physiology,2017,"16S rRNA gene, clinical characteristics, gestational diabetes mellitus, microbiota, placenta",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Gestational diabetes,EFO:0004593,controls,Gestational diabetes mellitus,"GDM was diagnosed when the fasting plasma glucose ≥5.1 mmol/L or 1 h post-OGTT glycemia ≥10.0 mmol/L or 2 h post-OGTT glycemia ≥8.5 mmol/L, according to the criteria set by International Association of Diabetes and Pregnancy Study Groups (IADPSG)",10,10,9 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2+ Figure 4+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Phlotypes in placental microbiota significantly different between GDM and NDM groups,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sulfuricellaceae|g__Sulfuricella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Acidobacteriota|c__Holophagae|o__Holophagales,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales,k__Bacteria|p__Ignavibacteriota|c__Ignavibacteria|o__Ignavibacteriales,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Acidobacteriota|c__Holophagae|o__Holophagales|f__Holophagaceae|g__Geothrix,k__Bacteria|p__Ignavibacteriota|c__Ignavibacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae",2|976;2|67819;2|1239|91061|1385|186822|55080;2|1224|28216|32003|2772226|935200;2|1239|91061|186826|33958|1578;2|1224|1236|135614|1775411|231454;2|976|200643|171549;2|1239|526524|526525;2|57723|533205|574975;2|1224|2008785|119069;2|1134404|795747|795748;2|1090;2|976|200643;2|57723|533205|574975|574976|44675;2|1134404|795747;2|1239|91061|186826|33958;2|1224|2008785|119069|206349;2|1239|91061|1385|186822,Complete,Shaimaa Elsafoury
bsdb:16/1/1,Study 16,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,normal chow diet,high fat diet,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6B + Data S1,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|3085636|186803|31980;2|976|200643|171549|171552;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|248744;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|572511,Complete,Shaimaa Elsafoury
bsdb:16/1/2,Study 16,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,normal chow diet,high fat diet,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6B + Data S1,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|1239|186801|3082720|3030910|109326;2|976|200643|171549|1853231|574697;2|1239|186801|3082768|990719;2|29547|3031852|213849|72293|209;2|1239|186801|3082768|990719|990721;2|200940|3031449|213115|194924|35832;2|544448;2|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
bsdb:16/2/1,Study 16,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,high fat diet,high fat diet + melatonin,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figure 6B + Data S1,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Antricoccaceae|g__Antricoccus",2|1224|1236|91347|1903414|583;2|976|200643|171549|1853231|283168;2|29547|3031852|213849|72293|209;2|1239|186801|3082720|3030910|109326;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924;2|976|200643|171549|1853231|574697;2|74201|203494|48461|1647988|239934;2|201174|1760|1643682|2805401|1920251,Complete,Shaimaa Elsafoury
bsdb:16/2/2,Study 16,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,high fat diet,high fat diet + melatonin,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figure 6B + Data S1 + Figure 7,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter marmotae",2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|244127;2|29547|3031852|213849|72293|209|152490,Complete,Shaimaa Elsafoury
bsdb:17/1/1,Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment active Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,36,40,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 1,10 January 2021,Fatima Zohra,WikiWorks,Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and generalized anxiety disorder groups,increased,"k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|32066;2|976;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|815|816;2|1239|186801|186802|216572|946234;2|32066|203490;2|32066|203490|203491|203492;2|32066|203490|203491;2|1239|186801|3085636|186803|1432051;2|1239|526524|526525|2810280|1505663;2|1239|526524|526525|128827|1522;2|976|200643|171549|815;2|976|200643|171549;2|976|200643,Complete,Shaimaa Elsafoury
bsdb:17/1/2,Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment active Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,36,40,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 1,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and generalized anxiety disorder groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1224|28216|80840|506;2|1224|28216;2|200940|3031449|213115|194924|35832;2|1224|28216|80840;2|1239|186801|186802|3085642|580596;2|1239|186801|3082768|990719;2|1239|186801;2|201174|84998|84999|84107;2|201174|84998|84999;2|28221;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|1239|186801|186802|186807;2|1239|186801|3085636|186803|46205;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:17/2/1,Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment naiive Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,17,12,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and treatment naiive generalized anxiety disorder groups,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota",2|1239|91061|186826|33958|1578;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|815|816;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|976|200643|171549|815;2|976|200643|171549;2|976|200643;2|976;2|1224|1236|91347|543;2|1224|1236|91347;2|976|200643|171549|2005525|375288;2|1239|91061|186826|33958;2|1239|526524|526525|2810280|1505663;2|1239|186801|3085636|186803|2316020|33039;2|1239|526524|526525|128827|1522;2|1239|186801|186802|216572|946234;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066,Complete,Shaimaa Elsafoury
bsdb:17/2/2,Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment naiive Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,17,12,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and treatment naiive generalized anxiety disorder groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|186801|186802|216572|244127;2|976|200643|171549|2005519|397864;2|1239|186801|186802|3085642|580596;2|976|200643|171549|1853231|574697;2|1239|186801|3082768|990719;2|1239|186801;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|186801|186802;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|437755;2|1239|186801|186802|541000;2|1224|28216|80840|75682|846;2|1224|28216|80840|75682;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186807;2|1239|186801|186802|186807|2740;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:18/1/1,Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 1,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6- Low Fat,Sv129- Low Fat,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Lwaldron,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Synergistota,k__Bacteria|p__Thermotogota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse",2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|830;2|1239|186801|3085636|186803|830|43305;2|200795;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|1649459|154046;2|1117;2|1239|186801|3085636|186803|189330;2|1239|91061|186826|81852|1350|1351;2|1239|186801|186802|186806|1730;2157|28890;2|1239|186801|186802|216572|216851;2|1239;2|32066;2|1239|186801|3085636|186803|658087;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2767887|1605;2|1239|186801|3085636|186803|248744|168384;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|351091;2|203682;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263;2|203691;2|1239|186801|186802|216572|292632;2|508458;2|200918;2|1239|186801|3085636|186803|1506553|89153;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|186802|31979|49082|49118,Complete,Chloe
bsdb:18/1/2,Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 1,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6- Low Fat,Sv129- Low Fat,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Fibrobacterota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",2|201174;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759;2|1090;2|65842;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|195950;2|74201;2|1239|526524|526525|128827|1573535|1735,Complete,Chloe
bsdb:18/2/1,Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 2,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat without enomithacin,Sv129-High Fat without enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse",2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|1649459|154046;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958|2767887|1605;2|1239|186801|3085636|186803|248744|168384;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|186802|31979|49082|49118,Complete,Fatima
bsdb:18/2/2,Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 2,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat without enomithacin,Sv129-High Fat without enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|203682;2|74201;2|1239|526524|526525|128827|1573535|1735,Complete,Fatima
bsdb:18/3/1,Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 3,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat with enomithacin,Sv129-High Fat with enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,9,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,WikiWorks,"Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Fibrobacterota",2|976|200643|171549|815|816;2|976;2|1117;2|1090;2|65842,Complete,Shaimaa Elsafoury
bsdb:18/3/2,Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 3,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat with enomithacin,Sv129-High Fat with enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,9,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,Kwekuamoo,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis",2|201174;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|1535;2|32066;2|1239|526524|526525|128827|1573535|1735;2|203682;2|74201;2|1239|186801|3082720|186804|2743582|89152,Complete,Fatima
bsdb:19/1/1,Study 19,"cross-sectional observational, not case-control",29352709,10.1016/j.schres.2018.01.002,NA,"Shen Y, Xu J, Li Z, Huang Y, Yuan Y, Wang J, Zhang M, Hu S , Liang Y",Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study,Schizophrenia research,2018,"16S rRNA sequencing, Biomarker, Brain-gut axis, Gut microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia,The patients were examined and diagnosed according to the ICD-10 by two trained psychiatric physicians.,53,64,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 4, S3",10 January 2021,Fatima Zohra,WikiWorks,"Microbial composition at phylum, genus and species level in healthy and schizophrenia cohorts",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1224|1236;2|1224;2|1224|1236|135624;2|1224|1236|135624|83763|83770;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|135624|83763;2|32066|203490;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|32066|203490|203491;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1224|1236|91347|543|544;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930|904;2|200940|3031449|213115|194924|872,Complete,Shaimaa Elsafoury
bsdb:19/1/2,Study 19,"cross-sectional observational, not case-control",29352709,10.1016/j.schres.2018.01.002,NA,"Shen Y, Xu J, Li Z, Huang Y, Yuan Y, Wang J, Zhang M, Hu S , Liang Y",Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study,Schizophrenia research,2018,"16S rRNA sequencing, Biomarker, Brain-gut axis, Gut microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia,The patients were examined and diagnosed according to the ICD-10 by two trained psychiatric physicians.,53,64,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 4, S3",10 January 2021,Fatima Zohra,WikiWorks,"Microbial composition at phylum, genus and species level in healthy and schizophrenia cohorts",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511;2|1224|28216|80840|506;2|1239|186801|186802;2|1239|186801;2|1239;2|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:20/1/1,Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Non-NASH,NASH,"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular inflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",22,35,2 months,16S,4,Illumina,Logistic Regression,0.1,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 1,Table 2 + text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant Abundance of Gut Microbiome Taxa in Patients With NASH and Without NASH,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:20/1/2,Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Non-NASH,NASH,"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular inflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",22,35,2 months,16S,4,Illumina,Logistic Regression,0.1,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 2,Table 2 + text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant Abundance of Gut Microbiome Taxa in Patients With NASH and Without NASH,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Shaimaa Elsafoury
bsdb:20/2/1,Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,mild fibrosis (F 0-1),significant fibrosis (F>2),"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular nflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",30,27,2 months,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant Abundance of Gut Microbiome Taxa in Patients With Significant F 2 Fibrosis and No/Mild Fibrosis (F0/F1 Stage),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|216572|1263;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:20/2/2,Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,mild fibrosis (F 0-1),significant fibrosis (F>2),"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular nflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",30,27,2 months,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant  Abundance of Gut Microbiome Taxa in Patients With Significant F 2 Fibrosis and No/Mild Fibrosis (F0/F1 Stage),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
bsdb:21/1/1,Study 21,"cross-sectional observational, not case-control",25763184,10.1186/s40168-015-0072-y,NA,"Ross MC, Muzny DM, McCormick JB, Gibbs RA, Fisher-Hoch SP , Petrosino JF",16S gut community of the Cameron County Hispanic Cohort,Microbiome,2015,NA,Experiment 1,United States-Mexico Border,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Human Microbiome Project samples,Cameron County Hispanic Cohort samples,NA,213,63,NA,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.02,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance comparision between Cameron County Hispanic Cohort (CCHC) and Human microbiome project (HMP) subject stool samples,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1239;2|201174;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977;2|201174|84998|84999|84107;2|1239|186801|186802|541000;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|841;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|39948,Complete,Shaimaa Elsafoury
bsdb:21/1/2,Study 21,"cross-sectional observational, not case-control",25763184,10.1186/s40168-015-0072-y,NA,"Ross MC, Muzny DM, McCormick JB, Gibbs RA, Fisher-Hoch SP , Petrosino JF",16S gut community of the Cameron County Hispanic Cohort,Microbiome,2015,NA,Experiment 1,United States-Mexico Border,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Human Microbiome Project samples,Cameron County Hispanic Cohort samples,NA,213,63,NA,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.02,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance comparision between Cameron County Hispanic Cohort (CCHC) and Human microbiome project (HMP) subject stool samples,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976;2|976|200643|171549|815;2|976|200643|171549|171550;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:22/1/1,Study 22,"cross-sectional observational, not case-control",28429209,10.1007/s10517-017-3700-7,NA,"Petrov VA, Saltykova IV, Zhukova IA, Alifirova VM, Zhukova NG, Dorofeeva YB, Tyakht AV, Kovarsky BA, Alekseev DG, Kostryukova ES, Mironova YS, Izhboldina OP, Nikitina MA, Perevozchikova TV, Fait EA, Babenko VV, Vakhitova MT, Govorun VM , Sazonov AE",Analysis of Gut Microbiota in Patients with Parkinson's Disease,Bulletin of experimental biology and medicine,2017,"16S rRNA sequencing, Parkinson’s disease, gut microbiota",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's,NA,66,89,NA,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the content of bacterial taxa in PD patients and control subjects at the genus and species level,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella hongkongensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans",2|1239|91061|186826|33958|1578;2|1239|186801|3082768|990719|990721;2|1239|186801|3082768|990719|270497;2|1239|186801|186802|216572|119852;2|201174|1760|85004|31953|1678;2|1239|186801|3082768|990719|990721|626937;2|1239|186801|3082768|990719|990721|270498;2|1239|91061|186826|33958|2742598|97478;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|100175|100176,Complete,Shaimaa Elsafoury
bsdb:22/1/2,Study 22,"cross-sectional observational, not case-control",28429209,10.1007/s10517-017-3700-7,NA,"Petrov VA, Saltykova IV, Zhukova IA, Alifirova VM, Zhukova NG, Dorofeeva YB, Tyakht AV, Kovarsky BA, Alekseev DG, Kostryukova ES, Mironova YS, Izhboldina OP, Nikitina MA, Perevozchikova TV, Fait EA, Babenko VV, Vakhitova MT, Govorun VM , Sazonov AE",Analysis of Gut Microbiota in Patients with Parkinson's Disease,Bulletin of experimental biology and medicine,2017,"16S rRNA sequencing, Parkinson’s disease, gut microbiota",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's,NA,66,89,NA,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the content of bacterial taxa in PD patients and control subjects at the genus and species level,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus|s__Candidatus Stoquefichus massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",2|1239|186801|3085636|186803|189330;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851;2|976|200643|171549|815|909656|204516;2|1239|186801|3085636|186803|572511|536633;2|1239|526524|526525|128827|1470349|1470350;2|976|200643|171549|815|909656|310298;2|1239|186801|186802|216572|1263|40519;2|1239|186801|3085636|186803|189330|88431;2|976|200643|171549|815|909656|357276;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|815|909656|310297;2|1239|186801|3085636|186803|33042|33043,Complete,Shaimaa Elsafoury
bsdb:23/1/1,Study 23,case-control,29051531,10.1038/s41598-017-13601-y,NA,"Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB , Rey FE",Gut microbiome alterations in Alzheimer's disease,Scientific reports,2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healhty controls,Alzheimer's,NA,25,25,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,unchanged,NA,Signature 1,Figure 2+figure 1,10 January 2021,Fatima Zohra,"Kwekuamoo,Merit,WikiWorks",Bacterias differentially represented in faeces from AD participants compared to controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|171550|239759;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|91061|1385|539738|1378;2|1239|909932|1843488|909930|33024;2|200940|3031449|213115|194924|35832;2|976|200643|171549|171550;2|976|200643|171549,Complete,Shaimaa Elsafoury
bsdb:23/1/2,Study 23,case-control,29051531,10.1038/s41598-017-13601-y,NA,"Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB , Rey FE",Gut microbiome alterations in Alzheimer's disease,Scientific reports,2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healhty controls,Alzheimer's,NA,25,25,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,unchanged,NA,Signature 2,Figure 2+figure 1,10 January 2021,Fatima Zohra,"Fatima,Kwekuamoo,WikiWorks",Bacterias differentially represented in faeces from AD participants compared to controls,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|201174;2|201174|84998|1643822|1643826|447020;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1239;2|1239|186801|186802|541000;2|1239|186801|3082720|186804;2|1239|526524|526525|2810281;2|1239|186801;2;2|1239|186801|3082720|3030910|86331,Complete,Fatima
bsdb:24/1/1,Study 24,case-control,30204780,10.1371/journal.pone.0203503,NA,"Wang T, Yu L, Xu C, Pan K, Mo M, Duan M, Zhang Y , Xiong H",Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Chronic fatigue syndrome,EFO:0004540,Healthy controls,Chronic Fatigue patients,NA,45,46,2 months for healthy control only,16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3b,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalibacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1239|91061|1385|186817|331654;2|976|200643|171549|815;2|976|200643|171549|815|816;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|29547;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378,Complete,Fatima
bsdb:24/1/2,Study 24,case-control,30204780,10.1371/journal.pone.0203503,NA,"Wang T, Yu L, Xu C, Pan K, Mo M, Duan M, Zhang Y , Xiong H",Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Chronic fatigue syndrome,EFO:0004540,Healthy controls,Chronic Fatigue patients,NA,45,46,2 months for healthy control only,16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3b,10 January 2021,Shaimaa Elsafoury,WikiWorks,LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236;2|1239|909932|1843489|31977;2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712|724;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1224|1236|2887326|468|475;2|1224|1236|72274|135621|351;2|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
bsdb:25/1/1,Study 25,prospective cohort,23153041,10.1186/gb-2012-13-11-r101,NA,"Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J , Timmerman HM",Microbiome dynamics of human epidermis following skin barrier disruption,Genome biology,2012,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,Female,Psoriasis Male,"tape stripping method involves the repeated application of adhesive tape to the skin surface, thereby removing stratum corneum layers, it creates a superficial wound showing slight skin irritation (erythema) and loss of barrier function (transepidermal water loss)",6,6,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 4,10 January 2021,WikiWorks,WikiWorks,Difference in microbial community composition of upper buttok skin between males and females,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tepidibacteraceae|g__Sporacetigenium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|186827;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|31979;2|1239|1737404|1737405|1570339|150022;2|1239|186801|3082720|186804;2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465;2|1239|186801|3082720|3120162|360541;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|1760|2037;2|201174|1760|85006|85020;2|201174|1760|85006|85020|43668;2|201174|1760|85006|1268|32207;2|201174;2|201174|1760;2|201174|1760|85006|85023;2|201174|1760|85006|85023|33882;2|201174|1760|85006|145357|57495;2|976|117743;2|976|117743|200644;2|976|117743|200644|49546;2|976|117743|200644|49546|1016;2|1224|1236|2887326|468|469;2|201174|1760|85006|85020|36739;2|1239|91061|186826|186827|171412,Complete,Shaimaa Elsafoury
bsdb:25/1/2,Study 25,prospective cohort,23153041,10.1186/gb-2012-13-11-r101,NA,"Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J , Timmerman HM",Microbiome dynamics of human epidermis following skin barrier disruption,Genome biology,2012,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,Female,Psoriasis Male,"tape stripping method involves the repeated application of adhesive tape to the skin surface, thereby removing stratum corneum layers, it creates a superficial wound showing slight skin irritation (erythema) and loss of barrier function (transepidermal water loss)",6,6,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 4,10 January 2021,WikiWorks,WikiWorks,Difference in microbial community composition of upper buttok skin between males and females,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|2701;2|1224;2|1224|1236;2|1224|1236|72274;2|1224|1236|2887326|468;2|1224|28211|356|212791;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696,Complete,Shaimaa Elsafoury
bsdb:26/1/1,Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Sex design,EFO:0001752,male,female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,39,36,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",2|200940|3031449|213115|194924|35832;2|976|200643|171549|815|816|47678,Complete,Shaimaa Elsafoury
bsdb:26/1/2,Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Sex design,EFO:0001752,male,female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,39,36,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,2|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
bsdb:26/2/1,Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male,BMI >33 female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,13,13,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 2 +Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:26/2/2,Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male,BMI >33 female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,13,13,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Figure2 + Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,2|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
bsdb:27/1/1,Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 pre HFD,foster mother wild-type pre HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|128827;2|1239|186801|186802|186807;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|946234;2|1239|526524|526525;2|1239|526524;2|976|200643|171549|1853231|574697;2|1239|186801|186802|541000;2|1239|186801|186802|3085642|580596;2|976|200643|171549|2005525|375288;2|1239;2|1239|186801;2|1239|186801|186802,Complete,Shaimaa Elsafoury
bsdb:27/1/2,Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 pre HFD,foster mother wild-type pre HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",2|976;2|976|200643;2|976|200643|171549;2|29547|3031852|213849;2|29547;2|1224;2|976|200643|171549|815;2|976|200643|171549|815|816;2|28221;2|200940|3031449|213115;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|976|200643|171549|2005519|397864;2|29547|3031852|213849|72293;2|29547|3031852|213849|72293|209;2|200940|3031449|213115|194924;2|976|200643|171549|1853231|283168;2|200940|3031449|213115|194924|872;2|1239|526524|526525|128827|174708;2|976|200643|171549|171550|28138;2|95818|2093818|2093825|2171986|1331051,Complete,Shaimaa Elsafoury
bsdb:27/2/1,Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 post HFD,foster mother wild-type post HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",increased,"k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria",2|256845|1313211|278082|255528|172900;2|256845|1313211|278081|566277|256846;2|256845|1313211|278082|255528;2|1239|526524|526525|128827;2|256845|1313211|278082;2|1239|186801|186802|31979|1485;2|1239|526524|526525;2|1239|526524;2|976|200643|171549|171550|28138;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|946234;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186807;2|1239|91061|186826;2|1239|91061;2|976|200643|171549|1853231|574697;2|1239|186801|186802|541000;2|1239|186801|3085636|186803;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239;2|1239|186801;2|1239|186801|186802;2|256845|1313211,Complete,Shaimaa Elsafoury
bsdb:27/2/2,Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 post HFD,foster mother wild-type post HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",decreased,"k__Bacteria|p__Campylobacterota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Pseudomonadota,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",2|29547;2|29547|3031852|213849;2|1224;2|28221;2|200940|3031449|213115;2|29547|3031852|213849|72293;2|29547|3031852|213849|72293|209;2|200940|3031449|213115|194924;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|95818|2093818|2093825|2171986|1331051,Complete,Shaimaa Elsafoury
bsdb:28/1/1,Study 28,case-control,27338587,10.1186/s40168-016-0171-4,NA,"Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE , Hanson MR",Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2016,"Beta-diversity, Chronic fatigue syndrome, Inflammation, Lipopolysaccharides, Microbial translocation, Microbiome, Myalgic encephalomyelitis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Healthy controls,CFS cases,"Subjects with ME/CFS were established patients of a ME/ CFS specialist, Susan Levine, M.D. and fit the Fukuda diag- nostic criteria",39,48,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,figure 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,taxonomy of differentially abundant microbiota between  ME/CFS and healthy individuals,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|186801|186802|216572|119852;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|1300|1357;2|1239|186801|186802|216572|244127;2|1239|526524|526525|2810280|100883,Complete,Shaimaa Elsafoury
bsdb:28/1/2,Study 28,case-control,27338587,10.1186/s40168-016-0171-4,NA,"Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE , Hanson MR",Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2016,"Beta-diversity, Chronic fatigue syndrome, Inflammation, Lipopolysaccharides, Microbial translocation, Microbiome, Myalgic encephalomyelitis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Healthy controls,CFS cases,"Subjects with ME/CFS were established patients of a ME/ CFS specialist, Susan Levine, M.D. and fit the Fukuda diag- nostic criteria",39,48,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,figure 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,taxonomy of differentially abundant microbiota between  ME/CFS and healthy individuals,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801|186802|186807|2740;2|1224|1236|135625|712|724;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1224|1236|135625|712|416916;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:29/1/1,Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Active Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,29,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,unchanged,Signature 1,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|186801|186802|216572|946234;2|976|200643|171549|1853231|574697;2|1224|1236|91347;2|1224|1236|91347|543;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|976|200643|171549|171550|239759;2|976|200643|171549|171550,Complete,Shaimaa Elsafoury
bsdb:29/1/2,Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Active Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,29,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,unchanged,Signature 2,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|39948;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|216572|1263;2|1224|1236|135625|712|724;2|1239|186801|3082720|186804;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,Shaimaa Elsafoury
bsdb:29/2/1,Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Responded Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,17,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Responded Major Depressive Disorder groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549|1853231|574697;2|976|200643|171549|171551,Complete,Shaimaa Elsafoury
bsdb:29/2/2,Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Responded Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,17,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Responded Major Depressive Disorder groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|186801|186802|216572|1263;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|1236|135625|712|724;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:30/1/1,Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Norweigan controls,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,17,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian controls and Belgian controls.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",2|1239|186801|3085636|186803|841;2|1239|526524|526525|128827|61170,Complete,Shaimaa Elsafoury
bsdb:30/1/2,Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Norweigan controls,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,17,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian controls and Belgian controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|976|200643|171549|171550|239759;2|976|200643|171549|2005519|397864;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:30/2/1,Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Norweigan controls,Norweigan CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,17,25,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian CFS patients and Norwegian controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor",2|976|200643|171549|171550|239759;2|1239|186801|186802|31979|420345,Complete,Shaimaa Elsafoury
bsdb:30/2/2,Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Norweigan controls,Norweigan CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,17,25,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian CFS patients and Norwegian controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus",2|1239|186801|3085636|186803|841;2|1239|526524|526525|128827|61170;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|84036,Complete,Shaimaa Elsafoury
bsdb:30/3/1,Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Belgian CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,18,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Belgian CFS patients and Belgian controls,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,2|1239|186801|186802|31979|420345,Complete,Shaimaa Elsafoury
bsdb:30/3/2,Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Belgian CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,18,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Belgian CFS patients and Belgian controls,decreased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,2|201174|84998|1643822|1643826|553372,Complete,Shaimaa Elsafoury
bsdb:31/1/1,Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,50,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Differentiately abundant mictobiota between CFS/ME and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis",2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|207244|105841;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|2719313|333367;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33038;2|1239|526524|526525|2810280|100883|100884,Complete,Fatima
bsdb:31/1/2,Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,50,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,Shaimaa Elsafoury,"Fatima,Lwaldron,WikiWorks",Differentiately abundant mictobiota between CFS/ME and healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803;2|976|200643|171549|2005525|375288|823;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|216851|1971605,Complete,Fatima
bsdb:31/2/1,Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients with IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,21,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between CFS/ME with IBS and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|1239|186801|3085636|186803|207244|105841;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|207244,Complete,Shaimaa Elsafoury
bsdb:31/2/2,Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients with IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,21,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,10 January 2021,Shaimaa Elsafoury,"Lwaldron,WikiWorks",Differentiately abundant mictobiota between CFS/ME with IBS and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|3085636|186803|572511|40520,Complete,Shaimaa Elsafoury
bsdb:31/3/1,Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients without IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,29,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,10 January 2021,Shaimaa Elsafoury,"Fatima,Lwaldron,WikiWorks",Differentiately abundant mictobiota between CFS/ME without IBS and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",2|1224|1236|72274|135621|351;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|2810280|100883|100884;2|1239|186801|3085636|186803|189330|88431;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|31979|1485|1506,Complete,Fatima
bsdb:31/3/2,Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients without IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,29,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3c,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between CFS/ME without IBS and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1239|186801|3085636|186803|33042|116085;2|976|200643|171549|2005525|375288|823;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330,Complete,Shaimaa Elsafoury
bsdb:32/1/1,Study 32,prospective cohort,28636668,10.1371/journal.pone.0179739,NA,"Borgo F, Riva A, Benetti A, Casiraghi MC, Bertelli S, Garbossa S, Anselmetti S, Scarone S, Pontiroli AE, Morace G , Borghi E","Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests",PloS one,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Controls,Aonerxia Nervosa patients,"The severity of eating disorder and psychopathology tests were assessed by means of the Symptom Checklist 90 (general psychopathology), Eating Disorder Inventory 2 (eating disorder), State Trait Anxiety Inventory (anxiety disorder) and Beck Depression Inventory (depressive symptoms). Psychologists and psychiatrists (all extensively trained in the use of the instruments) conducted clinical evaluations.",15,15,1 month,16S,NA,Illumina,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 +text,10 January 2021,Fatima Zohra,WikiWorks,Significant differential abundance in anorexia nervosa vs controls,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",2|1224;2|1224|1236|91347|543;2157|28890|183925|2158|2159|2172|2173,Complete,Shaimaa Elsafoury
bsdb:32/1/2,Study 32,prospective cohort,28636668,10.1371/journal.pone.0179739,NA,"Borgo F, Riva A, Benetti A, Casiraghi MC, Bertelli S, Garbossa S, Anselmetti S, Scarone S, Pontiroli AE, Morace G , Borghi E","Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests",PloS one,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Controls,Aonerxia Nervosa patients,"The severity of eating disorder and psychopathology tests were assessed by means of the Symptom Checklist 90 (general psychopathology), Eating Disorder Inventory 2 (eating disorder), State Trait Anxiety Inventory (anxiety disorder) and Beck Depression Inventory (depressive symptoms). Psychologists and psychiatrists (all extensively trained in the use of the instruments) conducted clinical evaluations.",15,15,1 month,16S,NA,Illumina,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 +text,10 January 2021,Fatima Zohra,WikiWorks,Significant differential abundance in anorexia nervosa vs controls,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|841;2|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
bsdb:33/1/1,Study 33,"cross-sectional observational, not case-control",26261039,10.1186/s12876-015-0330-2,NA,"Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, Shiraki K, Ito M, Takei Y , Takase K","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing",BMC gastroenterology,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,BMI ≥25 kg/m2,4,6,current use,16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 2, Table 4 & Table 5",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, using  Next generation sequencing",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",2|1239|186801|3085636|186803|572511|53443;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803|572511|40520,Complete,Fatima
bsdb:33/1/2,Study 33,"cross-sectional observational, not case-control",26261039,10.1186/s12876-015-0330-2,NA,"Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, Shiraki K, Ito M, Takei Y , Takase K","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing",BMC gastroenterology,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,BMI ≥25 kg/m2,4,6,current use,16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Table 2, Table 4 & Table 5",10 January 2021,Marianthi Thomatos,WikiWorks,"Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, using  Next generation sequencing",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacteroidota",2|1239|186801|186802|216572|946234|292800;2|976|200643|171549|815|816|871325;2|976|200643|171549|815|816|818;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|2719313|208479;2|976,Complete,Shaimaa Elsafoury
bsdb:34/1/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,32,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia",2|201174;2|201174|84998|84999;2|201174|84998|84999|84107;2|201174|84998,Complete,Shaimaa Elsafoury
bsdb:34/1/2,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,32,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:34/2/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low IL-6,Bipolar patients with high IL-6,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to inflammatory markers among bipolar patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:34/3/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low total cholesterol,Bipolar patients with high total cholesterol,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to lipid levels among bipolar patients,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:34/4/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 4,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low LDL,Bipolar patients with high LDL,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Shaimaa Elsafoury,WikiWorks,Microbiota composition in relation to lipid levels among bipolar patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:34/5/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 5,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low TRP,Bipolar patients with high TRP,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to tryptophan metabolites among bipolar patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|201174|84998|84999|84107;2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:34/6/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 6,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low TBARS level,Bipolar patients with high TBARS level,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to markers of oxidative stress among bipolar patients,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,2|1239|186801|186802|186806|1730,Complete,Shaimaa Elsafoury
bsdb:34/7/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 7,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low MDA level,Bipolar patients with high MDA level,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to markers of oxidative stress among bipolar patients,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:34/8/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 8,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low BMI,Bipolar patients with high BMI,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to BMI among bipolar patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061,Complete,Shaimaa Elsafoury
bsdb:34/9/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 9,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,no metabolic syndrome,Bipolar patients with metabolic syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to metabolic syndrome among bipolar patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|201174|84998|84999|84107,Complete,Shaimaa Elsafoury
bsdb:34/10/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 10,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthier bipolar patients,Bipolar patients with depressive syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to depressive syndrome among bipolar patients,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:34/10/2,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 10,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthier bipolar patients,Bipolar patients with depressive syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to depressive syndrome among bipolar patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|31979;2|1239|186801|3085636|186803|841,Complete,Shaimaa Elsafoury
bsdb:34/11/1,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 11,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,27,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC after exclusion obese and diabetic patients,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia",2|201174;2|201174|84998|84999;2|201174|84998|84999|84107;2|201174|84998,Complete,Shaimaa Elsafoury
bsdb:34/11/2,Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 11,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,27,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 1,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC after exclusion obese and diabetic patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:35/1/1,Study 35,case-control,30280027,10.7717/peerj.5649,NA,"Zhou Z, Ling G, Ding N, Xun Z, Zhu C, Hua H , Chen X",Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing,PeerJ,2018,"Core microbiome, Dental caries, High-throughput sequencing, Oral microflora, Primary Sjögren’s syndrome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Sjogren syndrome,EFO:0000699,Controls,PSS,Patients with Sjogren syndrome,23,22,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,decreased,decreased,unchanged,NA,decreased,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota",2|1239|909932|1843489|31977|29465;2|1239|909932|909929;2|1239|909932|1843489|31977;2|1224|1236;2|1224,Complete,Shaimaa Elsafoury
bsdb:35/1/2,Study 35,case-control,30280027,10.7717/peerj.5649,NA,"Zhou Z, Ling G, Ding N, Xun Z, Zhu C, Hua H , Chen X",Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing,PeerJ,2018,"Core microbiome, Dental caries, High-throughput sequencing, Oral microflora, Primary Sjögren’s syndrome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Sjogren syndrome,EFO:0000699,Controls,PSS,Patients with Sjogren syndrome,23,22,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,decreased,decreased,unchanged,NA,decreased,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Actinomycetota",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|201174|1760|85006|1268|32207;2|976|200643|171549|171551|836;2|1239|186801|3082720|186804|1257;2|1224|28216;2|201174|1760|2037|2049;2|1224|1236|135625|712;2|1224|28216|206351|481;2|1224|28216|206351;2|201174|1760|85006|1268;2|976|200643|171549|171551;2|201174|1760|2037;2|32066|203490;2|32066;2|32066|203490|203491;2|1239|186801;2|1239|186801|186802;2|1224|1236|135625;2|201174,Complete,Shaimaa Elsafoury
bsdb:36/1/1,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,obese adolescent,Adolescents who are obese,25,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adult control group.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|201174|1760|2037|2049|1654;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106|74426;2|201174|1760|85009|31957|1912216|1747;2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:36/1/2,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,obese adolescent,Adolescents who are obese,25,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adult control group.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,2|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:36/2/1,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adult,Adults who are obese,20,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adults compared to the Adolescents control group.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|31979;2|201174|1760|85009|31957|1912216|1747;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:36/2/2,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adult,Adults who are obese,20,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adults compared to the Adolescents control group.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|976|200643|171549|815|816|47678;2|976|200643|171549|2005519;2|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:36/3/1,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,control adolescent,NA,12,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",2|1239|186801|186802|216572|119852;2|976|200643|171549|815|816|47678;2|976|200643|171549|2005519,Complete,Shaimaa Elsafoury
bsdb:36/3/2,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,control adolescent,NA,12,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:36/4/1,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,obese adult,obese adolescent,Adolescents who are obese,20,25,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Obese adult group.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|201174|1760|2037|2049|1654;2|201174;2|201174|84998|1643822|1643826|447020;2|1239;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:36/5/1,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 5,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,Adolescents who are obese,12,25,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adolescents control group.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",2|201174|1760|2037|2049|1654;2|201174;2|201174|84998|1643822|1643826|447020;2|1239;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106|74426;2|201174|1760|85009|31957|1912216|1747;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465|29466,Complete,Shaimaa Elsafoury
bsdb:36/5/2,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 5,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,Adolescents who are obese,12,25,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adolescents control group.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|976|200643|171549|815|816|47678;2|976;2|976|200643|171549|2005519;2|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:36/6/1,Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 6,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,obese adult,Adults who are obese,12,20,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adults compared to the Adults control group.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|201174|1760|85009|31957|1912216|1747;2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:37/1/1,Study 37,case-control,23733170,10.1007/s00248-013-0245-9,NA,"Wu N, Yang X, Zhang R, Li J, Xiao X, Hu Y, Chen Y, Yang F, Lu N, Wang Z, Luan C, Liu Y, Wang B, Xiang C, Wang Y, Zhao F, Gao GF, Wang S, Li L, Zhang H , Zhu B",Dysbiosis signature of fecal microbiota in colorectal cancer patients,Microbial ecology,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC patients,NA,20,19,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Cladogram of Colorectal cancer and healthy microbiota,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia",2|1239|1737404|1737405|1570339|165779;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|236752;2|32066|203490|203491|203492;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|526524|526525|128827|61170;2|1224|28216|206351|481|32257;2|32066|203490|203491|1129771|32067;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1239|526524|526525|128827|123375;2|1239|91061|1385|90964;2|1239|1737404,Complete,Fatima
bsdb:37/1/2,Study 37,case-control,23733170,10.1007/s00248-013-0245-9,NA,"Wu N, Yang X, Zhang R, Li J, Xiao X, Hu Y, Chen Y, Yang F, Lu N, Wang Z, Luan C, Liu Y, Wang B, Xiang C, Wang Y, Zhao F, Gao GF, Wang S, Li L, Zhang H , Zhu B",Dysbiosis signature of fecal microbiota in colorectal cancer patients,Microbial ecology,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC patients,NA,20,19,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Cladogram of Colorectal cancer and healthy microbiota,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826|33958|1243;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:38/1/1,Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,head of child,head of teenager,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,Davvve,ChiomaBlessing",Significant microbial genera and species associated with teen head VS child head,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2|201174|1760|85009|31957|1912216;2|201174|1760|85009|31957|1912216|1747,Complete,Shaimaa Elsafoury
bsdb:38/1/2,Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,head of child,head of teenager,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,Davvve,ChiomaBlessing",Significant microbial genera and species associated with teen head VS child head,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis",2759|4751|5204|1538075|162474|742845|55193;2759|4751|5204|1538075|162474|742845|55193|76773;2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
bsdb:38/2/1,Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 2,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child neck,teen neck,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen neck VS child neck,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",2|201174|1760|85009|31957|1912216;2|201174|1760|85009|31957|1912216|1747;2759|4751|5204|1538075|162474|742845|55193;2759|4751|5204|1538075|162474|742845|55193|76773,Complete,Shaimaa Elsafoury
bsdb:38/2/2,Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 2,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child neck,teen neck,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen neck VS child neck,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis",2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
bsdb:38/3/1,Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 3,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child underarm,teen underarm,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen underarm VS child underarm,increased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2759|4751|5204|1538075|162474|742845|55193|76773;2|1239|91061|1385|90964|1279|1282,Complete,Shaimaa Elsafoury
bsdb:38/3/2,Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 3,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child underarm,teen underarm,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen underarm VS child underarm,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,2|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
bsdb:39/1/1,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,youth underarm before,youth underarm after exercise,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,2|1239|91061|1385|90964|1279|1282,Complete,Shaimaa Elsafoury
bsdb:39/1/2,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,youth underarm before,youth underarm after exercise,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,2|1224|28211|204455|31989|265,Complete,Shaimaa Elsafoury
bsdb:39/2/1,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 2,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,youth Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri",2|1224|1236|2887326|468|469;2|201174|1760|85009|31957|1912216|33011;2|1224|1236|2887326|468|469|108981,Complete,Shaimaa Elsafoury
bsdb:39/3/1,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 3,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,Children underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,2|1224|28211|204455|31989|265,Complete,Shaimaa Elsafoury
bsdb:39/4/1,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 4,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,Children Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:39/4/2,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 4,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,Children Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,2|201174|1760|85009|31957|1912216,Complete,Shaimaa Elsafoury
bsdb:39/5/1,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 5,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,teen underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,2|1224|28211|204455|31989|265,Complete,Shaimaa Elsafoury
bsdb:39/6/1,Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 6,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,teen Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,2|1224|1236|2887326|468|469,Complete,Shaimaa Elsafoury
bsdb:40/1/1,Study 40,case-control,28863139,10.1371/journal.pone.0183509,NA,"Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT , Arias Vasquez A",Gut microbiome in ADHD and its relation to neural reward anticipation,PloS one,2017,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,Controls,ADHD,cases were diagnosed based on DSM-IV symptoms using the Schedule for Affective Disorders and Schizophrenia for School-Age Children,77,19,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of microbial taxa for ADHD cases versus healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",2|201174;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|84111;2|201174|1760|85004|31953|1678|28026;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|1853231|283168;2|976|200643|171549|171551;2|976|200643|171549|171550;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759;2|976|200643|171549|815|909656|821;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|820;2|28221;2|200940|3031449|213115,Complete,Shaimaa Elsafoury
bsdb:40/1/2,Study 40,case-control,28863139,10.1371/journal.pone.0183509,NA,"Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT , Arias Vasquez A",Gut microbiome in ADHD and its relation to neural reward anticipation,PloS one,2017,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,Controls,ADHD,cases were diagnosed based on DSM-IV symptoms using the Schedule for Affective Disorders and Schizophrenia for School-Age Children,77,19,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of microbial taxa for ADHD cases versus healthy controls,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|3085636|186803|33042|33043;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|35829;2|1239|186801|3085636|186803|33042,Complete,Shaimaa Elsafoury
bsdb:41/1/1,Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis,NA,16,28,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between first episode psychosis patients and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Saccharophagus,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Deferribacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae|g__Halothiobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Deferribacter|s__Deferribacter desulfuricans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cenocepacia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfosporosinus|s__Desulfosporosinus acidiphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae|g__Halothiobacillus|s__Halothiobacillus neapolitanus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Saccharophagus|s__Saccharophagus degradans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella|s__Francisella hispaniensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma|s__Tropheryma whipplei,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella canis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum|s__Halorubrum lacusprofundi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Nitrosococcus|s__Nitrosococcus halophilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella clarridgeiae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",2|1224|28211|356|118882;2|1239|91061|186826|33958;2|1224|1236|135613|255526;2|201174|1760|85006|2805591|2038;2|1224|28211|356|118882|528;2|1224|1236|1706369|1706371|316625;2157|28890|183963|2235|1644056|56688;2|1239|91061|186826|33958|1578;2|200930|68337|191393|191394|53572;2|1224|1236|135613|255526|109262;2|1239|91061|186826|33958|1578|1579;2|200930|68337|191393|191394|53572|197162;2|1224|28216|80840|119060|32008|95486;2|1239|186801|186802|2937909|79206|885581;2|1224|1236|135613|255526|109262|927;2|1224|1236|1706369|1706371|316625|86304;2|1224|1236|72273|34064|262|622488;2|201174|1760|85006|2805591|2038|2039;2|1224|28211|356|118882|234|36855;2|1239|91061|186826|33958|1578|33959;2157|28890|183963|2235|1644056|56688|2247;2|1239|91061|186826|33958|2742598|1598;2|1224|1236|135613|1046|1227|133539;2|1224|28211|356|772|773|56426;2|1224|28211|356|118882|234|529;2|1239|91061|1385;2|1224|28211|356;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|1578|1596;2|201174|1760|85004|31953|1678|1689,Complete,Shaimaa Elsafoury
bsdb:41/1/2,Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis,NA,16,28,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",Taxonomic differences of fecal microbiota between first episode psychosis patients and healthy controls,decreased,"k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Anabaena,k__Bacteria|p__Chlorobiota|c__Chlorobiia|o__Chlorobiales|f__Chlorobiaceae|g__Chlorobium|s__Chlorobium chlorochromatii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae|g__Gallionella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae|g__Gallionella|s__Gallionella capsiferriformans,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas|s__Nitrosomonas sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira|s__Nitrosospira multiformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Archaea|p__Euryarchaeota|c__Thermococci|o__Thermococcales|f__Thermococcaceae|g__Thermococcus|s__Thermococcus gammatolerans,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Trichormus|s__Trichormus variabilis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus|s__Xenorhabdus nematophila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc gasicomitatum",2|1117|3028117|1161|1162|1163;2|1090|191410|191411|191412|1091|337090;2|1224|28216|32003|90627|96;2|1224|28216|32003|90627|96|370405;2|1239|909932;2|1224|28216|32003|206379|914|42353;2|1224|28216|32003|206379|35798;2|1224|28216|32003|206379|35798|1231;2|1239|909932|909929;2157|28890|183968|2258|2259|2263|187878;2|1117|3028117|1161|1162|264688|264691;2|1239|909932|1843489|31977;2|1224|1236|91347|1903414|626|628;2|1239|91061|186826|33958|1243|115778,Complete,Shaimaa Elsafoury
bsdb:41/2/1,Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis (physically active),NA,16,15,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1+results (text),10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between physically active psychosis patients and healthy controls,increased,"k__Archaea|p__Thermoproteota|c__Thermoprotei|o__Thermoproteales|f__Thermoproteaceae,k__Archaea|p__Thermoproteota|c__Thermoprotei|o__Thermoproteales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2157|28889|183924|2266|2267;2157|28889|183924|2266;2|1239|91061|186826|33958,Complete,NA
bsdb:41/2/2,Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis (physically active),NA,16,15,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 1+results (text),10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between physically active psychosis patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489|31977,Complete,NA
bsdb:42/1/1,Study 42,case-control,30483228,10.3389/fmicb.2018.02682,NA,"Guo C, Li Y, Wang P, Li Y, Qiu C, Li M, Wang D, Zhao R, Li D, Wang Y, Li S, Dai W , Zhang L",Alterations of Gut Microbiota in Cholestatic Infants and Their Correlation With Hepatic Function,Frontiers in microbiology,2018,"16S rRNA, bacterial biomarkers, co-abundance network, hepatic function, infantile cholestasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Extrahepatic cholestasis,EFO:1000933,healthy infants,cholestasis infants,NA,37,43,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2+ text,10 January 2021,Christina Brown,WikiWorks,Differentially abundundant gut microbiota in cholestatic infants vs healthy infants,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1239|91061|186826|1300|1301;2|1239|91061|186826|81852|1350;2|1239|91061|1385|90964|1279;2|1239|909932|1843489|31977|906;2|1224|28211|356|69277|28100;2|1239|909932|909929|1843491|158846,Complete,Shaimaa Elsafoury
bsdb:42/1/2,Study 42,case-control,30483228,10.3389/fmicb.2018.02682,NA,"Guo C, Li Y, Wang P, Li Y, Qiu C, Li M, Wang D, Zhao R, Li D, Wang Y, Li S, Dai W , Zhang L",Alterations of Gut Microbiota in Cholestatic Infants and Their Correlation With Hepatic Function,Frontiers in microbiology,2018,"16S rRNA, bacterial biomarkers, co-abundance network, hepatic function, infantile cholestasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Extrahepatic cholestasis,EFO:1000933,healthy infants,cholestasis infants,NA,37,43,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2 + text,10 January 2021,Christina Brown,WikiWorks,Differentially abundundant gut microbiota in cholestatic infants vs healthy infants,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|207244;2|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
bsdb:43/1/1,Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 1,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,controls,behcet's disease,Patients with Behcet's disease,15,31,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table 4,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differential abundant taxa in patients with Behcet's disease VS controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|976|200643|171549|171552|1283313;2|1224|1236|135625|712|724|729,Complete,Shaimaa Elsafoury
bsdb:43/1/2,Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 1,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,controls,behcet's disease,Patients with Behcet's disease,15,31,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Table 4,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differential abundant taxa in patients with Behcet's disease VS controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|1283313|671218;2|976;2|29547|3031852|213849|72294|194|199;2|1239|186801|186802;2|976|200643|171549|171552|2974257|76123;2|1239|186801|3085636|186803|1164882|979627;2|1239|186801|3085636|186803;2|201174|84998|84999|1643824|2767353|1382;2|32066|203490|203491|1129771|32067|104608;2|976|200643|171549|171552|838|60133;2|1239|909932|909929|1843491|970|2053611;2|1239|526524|526525|128827|123375|102148;2|1239|909932|1843489|31977|29465|1926307,Complete,Shaimaa Elsafoury
bsdb:43/2/1,Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 2,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,non-immunosuppressent users among behcet's patients,immunosuppressant users,NA,19,12,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text,10 January 2021,Shaimaa Elsafoury,WikiWorks,the association between the use of immunosuppressants in BD patients with gut microbiota,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae",2|976|117743|200644|2762318|59735;2|976|200643|171549|171552|838;2|976|200643|171549|171551|836|41976,Complete,Shaimaa Elsafoury
bsdb:43/2/2,Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 2,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,non-immunosuppressent users among behcet's patients,immunosuppressant users,NA,19,12,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text,10 January 2021,Shaimaa Elsafoury,WikiWorks,the association between the use of immunosuppressants in BD patients with gut microbiota,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.",2|976|200643|171549|171552|2974251|305719;2|1239|186801|3085636|186803|265975|1969407,Complete,Shaimaa Elsafoury
bsdb:44/1/1,Study 44,case-control,27450202,10.1111/1462-2920.13463,NA,"Riva A, Borgo F, Lassandro C, Verduci E, Morace G, Borghi E , Berry D",Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations,Environmental microbiology,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,36,42,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,Table 1 & Supplementary Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundance in pediatric obesity  versus normal weight  controls,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:44/1/2,Study 44,case-control,27450202,10.1111/1462-2920.13463,NA,"Riva A, Borgo F, Lassandro C, Verduci E, Morace G, Borghi E , Berry D",Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations,Environmental microbiology,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,36,42,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,Table 1 & Supplementary Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundance in pediatric obesity  versus normal weight  controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris",2|976;2|976|200643;2|976|200643|171549;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|815|909656|821;2|976|200643|171549|815|816|46506,Complete,Shaimaa Elsafoury
bsdb:45/1/1,Study 45,laboratory experiment,30466372,10.1080/1028415X.2018.1537169,NA,"Reichelt AC, Loughman A, Bernard A, Raipuria M, Abbott KN, Dachtler J, Van TTH , Moore RJ","An intermittent hypercaloric diet alters gut microbiota, prefrontal cortical gene expression and social behaviours in rats",Nutritional neuroscience,2018,"Adolescence, Diet, Memory, Microbiota, Obesity, Social interaction",Experiment 1,Australia,Rattus norvegicus,Feces,UBERON:0001988,Obesity,EFO:0001073,control rats,Rats fed  HFHS,NA,8,8,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3a & 3b,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance of rats fed high fat and high surgar diet (HFHS) VS. Controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",2|1239|186801|3085636|186803|572511;2|201174|1760|85004|31953|1678;2|1239|909932|1843488|909930|33024;2|1239|526524|526525|128827|174708,Complete,Shaimaa Elsafoury
bsdb:46/1/1,Study 46,case-control,27007700,10.1089/chi.2015.0194,NA,"Borgo F, Verduci E, Riva A, Lassandro C, Riva E, Morace G , Borghi E",Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study,Childhood obesity (Print),2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,33,28,previous month,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, figure 2",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Relative abundance of bacterial and fungal gut microbes in obese children vs. controls,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces sp.,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|s__[Candida] sp. (uncertain placement)",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|838;2759|4751|4890|4891|4892|4893|4930|4935;2759|4751|4890|4891|4892|1853550,Complete,Fatima
bsdb:46/1/2,Study 46,case-control,27007700,10.1089/chi.2015.0194,NA,"Borgo F, Verduci E, Riva A, Lassandro C, Riva E, Morace G , Borghi E",Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study,Childhood obesity (Print),2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,33,28,previous month,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 2",17 October 2023,Uchechukwu,"Uchechukwu,Davvve,MyleeeA",Difference in relative proportions of gut microbial communities in obese versus normal-weight children,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces sp.,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas|s__uncultured Candidatus Saccharimonas sp.,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|s__[Candida] sp. (uncertain placement)",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|838;2759|4751|4890|4891|4892|4893|4930|4935;2|95818|2093818|2093825|2171986|1331051|1983405;2759|4751|4890|4891|4892|1853550,Complete,NA
bsdb:46/2/1,Study 46,case-control,27007700,10.1089/chi.2015.0194,NA,"Borgo F, Verduci E, Riva A, Lassandro C, Riva E, Morace G , Borghi E",Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study,Childhood obesity (Print),2017,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,Obese children,33,28,previous month,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Text, Figure 2",17 October 2023,Uchechukwu,"Uchechukwu,Davvve",Differences in relative proportions of gut microbial communities in obese versus normal-weight,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae",2|1239|186801|3085636|186803|1766253|39491;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|4891|4892|4893|4930|4932,Complete,NA
bsdb:47/1/1,Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,high dietary fiber,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Text and figure 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|2005519;2|1224|28211;2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:47/1/2,Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,high dietary fiber,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Text and figure 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,decreased,k__Bacteria|p__Mycoplasmatota,2|544448,Complete,Shaimaa Elsafoury
bsdb:47/2/1,Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,hight moderate to vigrous physical activity,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text and figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1224|1236|91347|543;2|1224|1236|91347,Complete,Shaimaa Elsafoury
bsdb:47/2/2,Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,hight moderate to vigrous physical activity,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text and figure 4,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks,Lwaldron,Iram jamshed,Folakunmi",Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|976|200643|171549|171552|577309,Complete,Shaimaa Elsafoury
bsdb:48/1/1,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 and Table 3,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552;2|1224|28216|80840|995019;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:48/1/2,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2 and Table 3,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815;2|976|200643|171549|171550;2|1239|186801|186802|541000;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
bsdb:48/2/1,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI zscores,high BMI zscore,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:48/2/2,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI zscores,high BMI zscore,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:48/3/1,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low triglycerides,high triglycerides,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:48/3/2,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low triglycerides,high triglycerides,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:48/4/1,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low total cholesterol,high total cholesterol,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:48/5/1,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low HDL-C,high HDL-C,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:48/6/1,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low sensetive C reactive protein,high senstive C reactive protein,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:48/6/2,Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low sensetive C reactive protein,high senstive C reactive protein,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815|816;2|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
bsdb:49/1/1,Study 49,case-control,29576948,10.7717/peerj.4458,NA,"Wu Y, Chi X, Zhang Q, Chen F , Deng X",Characterization of the salivary microbiome in people with obesity,PeerJ,2018,"Body-Mass Index, High-throughput nucleotide sequencing, Microbiome, Obesity, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Obesity,EFO:0001073,controls,Obesity group,obesity group (BMI ≥30),29,33,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Differentially abundant taxa between people with obesity and normal weight control,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|976|200643|171549;2|976|200643;2|1224|1236|135615|868;2|1239|91061|186826|186828;2|1239|186801|3085636|186803|43996;2|1224|28216|80840|80864;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|91061|186826|186828|117563;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|186807;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|526524|526525|128827|123375;2|1224|28211|356|335928;2|1239|186801|3082720|186804,Complete,Shaimaa Elsafoury
bsdb:49/1/2,Study 49,case-control,29576948,10.7717/peerj.4458,NA,"Wu Y, Chi X, Zhang Q, Chen F , Deng X",Characterization of the salivary microbiome in people with obesity,PeerJ,2018,"Body-Mass Index, High-throughput nucleotide sequencing, Microbiome, Obesity, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Obesity,EFO:0001073,controls,Obesity group,obesity group (BMI ≥30),29,33,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Differentially abundant taxa between people with obesity and normal weight control,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|1236;2|976|117743;2|1224|1236|135625;2|1224|28216|80840;2|976|117743|200644;2|201174|1760|85007;2|1224|1236|135615;2|1224|1236|135614;2|1224|1236|135625|712;2|1224|28216|80840|119060;2|976|117743|200644|49546;2|201174|1760|85007|1653;2|1224|1236|135625|712|724;2|1224|1236|135615|868|2717;2|1239|91061|1385|90964;2|976|117743|200644|49546|1016;2|1224|28216|80840|119060|47670;2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279;2|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
bsdb:50/1/1,Study 50,case-control,21850056,10.1038/ismej.2011.109,NA,"Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, Jia W, Cai S , Zhao L",Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers,The ISME journal,2012,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colrectal cancer patients,All patients were categorized according to histopathological features by TNM classification of malignant tumors after surgery,56,46,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of genera that were significantly different between Healthy controls and Colorectal cancer patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|976|200643|171549|171551|836;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1301;2|1239|186801|3082720|186804|1257,Complete,Shaimaa Elsafoury
bsdb:50/1/2,Study 50,case-control,21850056,10.1038/ismej.2011.109,NA,"Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, Jia W, Cai S , Zhao L",Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers,The ISME journal,2012,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colrectal cancer patients,All patients were categorized according to histopathological features by TNM classification of malignant tumors after surgery,56,46,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of genera that were significantly different between Healthy controls and Colorectal cancer patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|186806|1730;2|1224|28216|80840|995019|577310,Complete,Shaimaa Elsafoury
bsdb:51/1/1,Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,postoperation patients,Carcinoma patients,The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,47,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplemental Figure 5 and Table S2,10 January 2021,Rimsha Azhar,WikiWorks,The relative abundance of genus in carcinoma and postoperative patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|150022;2|1224|28216|80840|119060|48736;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|404402;2|976|200643|171549|171552|1283313;2|201174|1760|85007|1653|1716;2|1239|526524|526525|2810280|135858;2|1239|526524|526525|128827|1573535;2|1239|1737404|1737405|1570339|543311;2|1224|1236|72274|135621|286;2|1239|91061|1385|539738|1378;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1239|91061|186826|33958|46255;2|1239|91061|186826|186828|117563;2|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
bsdb:51/1/2,Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,postoperation patients,Carcinoma patients,The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,47,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplemental Figure 5 and Table S2,10 January 2021,Rimsha Azhar,WikiWorks,The relative abundance of genus in carcinoma and postoperative patients,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|32066|203490|203491|1129771|32067;2|201174|1760|85004|31953|196082;2|201174|1760|85004|31953|1678;2|201174|1760|85006|85023|33882;2|201174|1760|85007|2805586|1847725;2|1239|526524|526525|128827|1573534;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|1506577;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|2316020|33038,Complete,Shaimaa Elsafoury
bsdb:51/2/1,Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CIT(cleain intestine),NDA(new dev. adenoma),The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,26,21,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2.5,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4 and Table B,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identified differene in abundace between NDA and CIT,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",2|1239|91061|186826|186827|46123;2|201174|84998|84999|1643824|1380;2|1224|1236|91347|1903414|581;2|976|200643|171549|171552|838;2|1239|526524|526525|128827|123375,Complete,Shaimaa Elsafoury
bsdb:51/2/2,Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CIT(cleain intestine),NDA(new dev. adenoma),The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,26,21,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2.5,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4 and Table B,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identified differene in abundace between NDA and CIT,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|976|200643|171549|1853231|574697;2|1239|186801|186802|216572|1263;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|1737404|1737405|1570339|150022;2|1239|186801|186802|186806|1730|290054;2|1239|186801|3085636|186803|437755;2|1239|186801|186802|216572|459786;2|200940|3031449|213115|194924|872;2|1239|186801|186802|216572|244127,Complete,Shaimaa Elsafoury
bsdb:52/1/1,Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,Healthy controls,Substance use disorder patients,NA,45,48,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 1,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance in community compositions between SUD and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera",2|976|200643|171549|171552;2|1224|28211|204455|31989;2|1224|28216|206389|75787;2|1224|28211;2|976|200643|171549|171552|838;2|1224|28211|204455|31989|265;2|1239|186801|186802|31979|1485;2|1224|28216|206389|2008794|33057,Complete,Shaimaa Elsafoury
bsdb:52/1/2,Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,Healthy controls,Substance use disorder patients,NA,45,48,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 2,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance in community compositions between SUD and healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|976|200643|171549|815;2|976|200643|171549|171550;2|1224|1236|91347|543;2|1239|526524|526525|128827;2|200940|3031449|213115|194924;2|1239|91061;2|1239|526524;2|28221;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|189330;2|976|200643|171549|2005525|375288;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|207244;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|1407607;2|976|200643|171549|171550|239759;2|1239|186801|186802|204475;2|976|200643|171549|815|816;2|1239|526524|526525;2|1239|91061|186826;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
bsdb:52/2/1,Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,adjusted Healthy controls,Substance use disorder patients,NA,28,29,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 5B,10 January 2021,Fatima Zohra,WikiWorks,Significantly different microbial composition between SUD and age matched healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206389|2008794|33057;2|1224|28211|204455|31989|265;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:52/2/2,Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,adjusted Healthy controls,Substance use disorder patients,NA,28,29,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 5B,10 January 2021,Fatima Zohra,WikiWorks,Significantly different microbial composition between SUD and age matched healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",2|1239|186801|3085636|186803|207244;2|976|200643|171549|2005525|375288;2|1239|186801|186802|204475;2|200940|3031449|213115|194924|35832;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|1407607,Complete,Shaimaa Elsafoury
bsdb:53/1/1,Study 53,case-control,26683192,10.1371/journal.pone.0145453,NA,"Shukla SK, Cook D, Meyer J, Vernon SD, Le T, Clevidence D, Robertson CE, Schrodi SJ, Yale S , Frank DN",Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS),PloS one,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,healthy controls,chronic fatigue syndrome patients,patients met the ME/CFS case definition criteria established by Fukuda et al in 1994,10,10,current use,16S,NA,Roche454,Kolmogorov-Smirnov Test,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative Abundance of Bacterial Phyla in Blood and Stool Samples from ME/CFS Patients and Health Controls.,decreased,k__Bacteria|p__Acidobacteriota,2|57723,Complete,Shaimaa Elsafoury
bsdb:54/1/1,Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 1,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,meconium,meconium samples,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,decreased,NA,NA,unchanged,Signature 1,Figure 4B,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant bacteria in meconium sample compared to placenta sample from LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|91061|1385|186817;2|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
bsdb:54/1/2,Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 1,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,meconium,meconium samples,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,decreased,NA,NA,unchanged,Signature 2,Figure 4B,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant bacteria in meconium sample compared to placenta sample from LEfSe analysis,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:54/2/1,Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 2,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,colostrum,maternal colostrum samples,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Figure 4D,10 January 2021,Rimsha Azhar,"Merit,WikiWorks,ChiomaBlessing",Differentially abundant bacteria in colostrum samples compared to placenta samples from LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|91061|1385|186817;2|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
bsdb:54/2/2,Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 2,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,colostrum,maternal colostrum samples,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Figure 4D,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant bacteria in colostrum samples compared to placenta samples from LEfSe analysis,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:55/1/1,Study 55,laboratory experiment,23056268,10.1371/journal.pone.0046231,NA,"Bangsgaard Bendtsen KM, Krych L, Sørensen DB, Pang W, Nielsen DS, Josefsen K, Hansen LH, Sørensen SJ , Hansen AK",Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse,PloS one,2012,NA,Experiment 1,Denmark,Mus musculus,Caecum,UBERON:0001153,Stimulus or stress design,EFO:0001762,control,grid floor induced stress,cases were exposed to a stress factor which is a grid floor exposure for two weeks. this implies that the use of grid floor is a sufficient stressor for inducing a depression-like behavioral state in the TST.,14,14,NA,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,WikiWorks,Significantly different taxa between control mice and grid floor housed mice,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|1853231|283168;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:56/1/1,Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Type II diabetes mellitus,MONDO:0005148,adult stool,Healthy baby meconium,NA,9,13,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial Composition of the Meconium and Comparison to the healthy Adult and healthy Infant Microbiome,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1224;2|1224|28216|80840|80864;2|1224|1236|91347|543;2|1224|28216|80840|80864|283;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|1224|1236|91347|1903414|583;2|1224|1236|91347|543|620,Complete,Shaimaa Elsafoury
bsdb:56/1/2,Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Type II diabetes mellitus,MONDO:0005148,adult stool,Healthy baby meconium,NA,9,13,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial Composition of the Meconium and Comparison to the healthy Adult and healthy Infant Microbiome,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976;2|1239;2|74201;2|976|200643|171549|815;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:56/2/1,Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 2,United States of America,Homo sapiens,Meconium,UBERON:0007109,Gestational diabetes,EFO:0004593,Healthy baby meconium,Baby meconium with GDM mothers,NA,13,5,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Significant difference between neonates from mothers with different diabetes states,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|28216;2|1224|28211|356|118882;2|1224|28216|80840|506;2|1224|28216|80840|80864;2|1224|28211|356|335928;2|1224|28216|80840|506|507;2|1224|28216|80840|119060|106589;2|1224|28216|80840|80864|283;2|1224|28216|80840|80864|80865;2|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
bsdb:56/3/1,Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 3,United States of America,Homo sapiens,Meconium,UBERON:0007109,Type II diabetes mellitus,MONDO:0005148,Healthy baby meconium,Baby meconium with DM mothers,NA,13,5,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 4,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Significant difference between neonates from mothers with different diabetes states,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Arsenicicoccus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|28211|204441|433;2|1239|909932|1843488|909930|904;2|201174|1760|85006|85021|267408;2|201174|84998|84999|1643824|1380;2|976|200643|171549|815;2|976;2|976|200643;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|201174|1760|85006|85020;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|976|200643|171549|2005520|156973;2|1239|526524|526525|128827;2|1239|526524;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|91061|1385|539738|1378;2|201174|1760|85007|85026|2053;2|1239|526524|526525|128827|61170;2|201174|1760|85006|1268|57493;2|1239|186801|3085636|186803;2|201174|1760|85006|85023|33882;2|201174|1760|1643682|85030|88138;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1224|28211|356|69277;2|1239|91061|1385|186818|162291;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1224|28211|204441|433|125216;2|1239|186801|186802|216572|1263;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977,Complete,Fatima
bsdb:57/1/1,Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,9,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfosporosinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|976|200643|171549|171552|838;2|1239|186801|186802|31979|1485;2|1239|186801|186802|2937909|79206;2|1239|186801|3082720|186804|1257;2|1224|28216|80840|506|507;2|1224|28216|80840|119060|32008;2|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
bsdb:57/1/2,Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,9,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1743;2|1239|91061|186826|1300|1301;2|1224|28211|204457|41297|13687;2|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
bsdb:57/2/1,Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,overweight irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,11,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|201174|1760|85004|31953|1678;2|201174|84998|84999|1643824|1380;2|201174|84998|84999|1643824|133925;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186818|162291;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186806|113286;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|177971;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|970;2|1224|28216|80840|92793;2|1224|28216|80840|80864|80865;2|29547|3031852|213849|72294|194;2|1224|1236|72274|135621|286;2|203691|203692|136|2845253|157;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:57/2/2,Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,overweight irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,11,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Aestuariimicrobium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Haloanella,k__Bacteria|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae|g__Dehalogenimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85009|31957|396388;2|976|117743|200644|2762318|59732;2|976|117743|200644|49546|109244;2|200795|301297|1202465|1202464|670486;2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1301;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:58/1/1,Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,High fat diet,EFO:0002757,nebowrns of maternal control,newborns of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",13,13,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Neonaatal meconium identified by  LEfSe betwen maternal high-fat or maternal control diet during pregnancy,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|91061|186826|1300|1357;2|1239|91061|186826|186828|117563;2|1239|91061|186826|81852|1350,Complete,Shaimaa Elsafoury
bsdb:58/1/2,Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,High fat diet,EFO:0002757,nebowrns of maternal control,newborns of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",13,13,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Neonaatal meconium identified by  LEfSe betwen maternal high-fat or maternal control diet during pregnancy,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",2|1224|28216|80840|995019|40544;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|1224|28216|80840|80864|283,Complete,Shaimaa Elsafoury
bsdb:58/2/1,Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,High fat diet,EFO:0002757,6 months babies control,6 months babies of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",75,75,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5 + Supplemental Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The impact of maternal gestational diet persists to 6 weeks of age,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|561,Complete,Shaimaa Elsafoury
bsdb:58/2/2,Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,High fat diet,EFO:0002757,6 months babies control,6 months babies of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",75,75,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5 + Supplemental Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The impact of maternal gestational diet persists to 6 weeks of age,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:59/1/1,Study 59,time series / longitudinal observational,30656437,10.1186/s11671-018-2834-5,NA,"Mao Z, Li Y, Dong T, Zhang L, Zhang Y, Li S, Hu H, Sun C , Xia Y",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota and Increased Blood Glucose of Rat,Nanoscale research letters,2019,"Gut microbiota, Increased fasting blood glucose, Pregnancy exposure, TiO2 NPs",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Titanium dioxide nanoparticle,CHEBI:51050,control pregnant rats at gestational day 10,pregnant rats exposed to titanium dioxide nanoparticles,The female rats were daily gavage administrated with 5 mg/kg bw/day of TiO2 NPs from the 5th to 18th day after pregnancy.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,10 January 2021,Yaseen Javaid,WikiWorks,Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota of preganat rats,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Shaimaa Elsafoury
bsdb:59/1/2,Study 59,time series / longitudinal observational,30656437,10.1186/s11671-018-2834-5,NA,"Mao Z, Li Y, Dong T, Zhang L, Zhang Y, Li S, Hu H, Sun C , Xia Y",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota and Increased Blood Glucose of Rat,Nanoscale research letters,2019,"Gut microbiota, Increased fasting blood glucose, Pregnancy exposure, TiO2 NPs",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Titanium dioxide nanoparticle,CHEBI:51050,control pregnant rats at gestational day 10,pregnant rats exposed to titanium dioxide nanoparticles,The female rats were daily gavage administrated with 5 mg/kg bw/day of TiO2 NPs from the 5th to 18th day after pregnancy.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota of preganat rats,decreased,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae|s__bacterium Ellin6075,2|57723|204432|204433|204434|234266,Complete,Fatima
bsdb:60/1/1,Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,controls,Type-2 DM cases,NA,100,50,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 5,10 January 2021,Yaseen Javaid,WikiWorks,Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study. (all the bacteria either have zero mean or not detectable in both groups except Aquabacterium),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Actinotalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter",2|201174|1760|85006|85016|458839;2|1224|1236|135622|72275|111142;2|976|1853228|1853229|563835|504481;2|201174|1760|85006|85023|255204,Complete,Shaimaa Elsafoury
bsdb:60/1/2,Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,controls,Type-2 DM cases,NA,100,50,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 5,10 January 2021,Yaseen Javaid,WikiWorks,Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study. (all the bacteria either have zero mean or not detectable in both groups except Aquabacterium),decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia",2|1224|28216|80840|92793;2|1224|1236|135614|32033|338;2|201174|1760|85010|2070|1847,Complete,Shaimaa Elsafoury
bsdb:60/2/1,Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,carier of pathogens controls,Type-2 DM cariers of pathogens,The non-carrier meant that the individual did not have sequence read for the specific pathogen.,NA,NA,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,Table 6,10 January 2021,Shaimaa Elsafoury,WikiWorks,Associations between blood microbiome and the subsequent risk of Type-2 diabetes mellitus,increased,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,2|976|1853228|1853229|563835|504481,Complete,Shaimaa Elsafoury
bsdb:60/2/2,Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,carier of pathogens controls,Type-2 DM cariers of pathogens,The non-carrier meant that the individual did not have sequence read for the specific pathogen.,NA,NA,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,NA,NA,NA,NA,NA,Signature 2,Table 6,10 January 2021,Shaimaa Elsafoury,WikiWorks,Associations between blood microbiome and the subsequent risk of Type-2 diabetes mellitus,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:61/1/1,Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal weight mother at age 1 month,infants of overweight mothers,mothers whose prepregnancy body mass index (BMI; in kg/m2) was >25,26,16,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Tale 4,10 January 2021,Rimsha Azhar,WikiWorks,Mirobial groups in feacal samples at 1 and 6 months of age according to maternal weight gain during pregnancy and BMI,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:61/2/1,Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal weight mother at age 6 month,infants of overweight mothers,mothers whose prepregnancy body mass index (BMI; in kg/m2) was >25,26,16,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Tale 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Mirobial groups in feacal samples at 1 and 6 months of age according to maternal weight gain during pregnancy and BMI,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya|s__Hathewaya histolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",2|1239|186801|186802|31979|1769729|1498;2|201174|1760|85004|31953|1678|1686,Complete,Shaimaa Elsafoury
bsdb:61/3/1,Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal maternal weight gain mothers at age 1 month,infants of excessive maternal weight gain mothers,Weight gain >16.0 kg in women with BMI (in kg/m2) <25 and >11.5 kg in women with BMI >25 was considered excessive,20,22,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial counts in infant fecal samples at 1 and 6 months of age according to maternal weight gain during pregnancy,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:61/4/1,Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal maternal weight gain mothers at age 6 months,infants of excessive maternal weight gain mothers,Weight gain >16.0 kg in women with BMI (in kg/m2) <25 and >11.5 kg in women with BMI >25 was considered excessive,20,22,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial counts in infant fecal samples at 1 and 6 months of age according to maternal weight gain during pregnancy,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya|s__Hathewaya histolytica,2|1239|186801|186802|31979|1769729|1498,Complete,Shaimaa Elsafoury
bsdb:62/1/1,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,N/A,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,16 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium Marseille-P2399",2|1239|186801|186802|216572|244127;2|201174|1760|85004|31953|1678;2|1239|186801|186802|1671661;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|186801|186802|186806|1730|290054;2157|28890;2|1239|186801|186802|216572|216851|1946507;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1649459|2613924;2|1239|186801|186802|216572|596767;2|1224|1236|91347|543|570|573;2157|28890|183925|2158|2159|2172;2|976|200643|171549|815|909656|357276;2|1239|909932|909929|1806836,Complete,Shaimaa Elsafoury
bsdb:62/1/2,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,N/A,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,20 June 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",2|1239;2|1239|186801|186802|3085642;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1235800;2|1239|186801|186802|216572;2|976|200643|171549|171552|838;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|3068309,Complete,NA
bsdb:62/2/1,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Unimpaired-PD (PD-NC),Mild Cognitive Impairment-PD,Parkinson’s disease (PD) patients with mild cognitive impairment (MCI).,60,58,N/A,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d and table 3c,20 June 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:62/2/2,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Unimpaired-PD (PD-NC),Mild Cognitive Impairment-PD,Parkinson’s disease (PD) patients with mild cognitive impairment (MCI).,60,58,N/A,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d and table 3c,20 June 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma",2|74201|203494|48461|1647988|239934|239935;2|544448|31969|186332|186333|2152,Complete,NA
bsdb:62/3/1,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 3,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment -PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (MCI).,90,58,N/A,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,20 June 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium Marseille-P2399",2|201174|1760|85004|31953|1678;2|1239|186801|186802|1671661;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|186801|186802|186806|1730|290054;2157|28890;2|1239|186801|186802|216572|216851|1946507;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1649459|2613924;2|1239|186801|186802|216572|596767;2|1224|1236|91347|543|570|573;2157|28890|183925|2158|2159|2172;2|976|200643|171549|815|909656|357276;2|1239|909932|909929|1806836,Complete,NA
bsdb:62/3/2,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 3,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment -PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (MCI).,90,58,N/A,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,16 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",2|1239|186801|186802|3085642;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1235800;2|976|200643|171549|171552|838;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|3068309,Complete,NA
bsdb:62/4/1,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 4,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,N/A,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,2|1239|186801|186802|1671661,Complete,NA
bsdb:62/4/2,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 4,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,N/A,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,17 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|3068309;2|1239|186801|3085636|186803|1235800,Complete,NA
bsdb:62/5/1,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 5,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (NC).,90,58,N/A,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|3085642;2|1239|186801|3085636|186803,Complete,NA
bsdb:62/6/1,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 6,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,N/A,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium Marseille-P2399,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|1239|186801|186802|216572|596767;2|1239|186801|186802|216572|216851|1946507;2|1239|909932|909929|1806836;2|1239|186801|186802|1671661;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|244127,Complete,NA
bsdb:62/6/2,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 6,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,N/A,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,17 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1",2|1239|186801|3085636|186803|1766253;2|1239;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|3068309;2|1239|186801|3085636|186803|1235800,Complete,NA
bsdb:62/7/1,Study 62,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P , Wilmes P",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 7,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (NC).,90,58,N/A,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,Aleru Divine,Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|3085642;2|1239|186801|3085636|186803,Complete,NA
bsdb:63/1/1,Study 63,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K , Yamashiro Y",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,"C-section, Lactobacillus, RT-qPCR, dysbiosis, gut bacteria, intestinal microbiota, meconium",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery after 7 days of delivery,C-section delivery,NA,134,17,No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling),16S,NA,RT-qPCR,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,2|1239|91061|186826|33958|1578|1596,Complete,Shaimaa Elsafoury
bsdb:63/2/1,Study 63,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K , Yamashiro Y",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,"C-section, Lactobacillus, RT-qPCR, dysbiosis, gut bacteria, intestinal microbiota, meconium",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery after 3 months of delivery,C-section delivery,NA,134,17,No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling),16S,NA,RT-qPCR,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:63/3/1,Study 63,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K , Yamashiro Y",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,"C-section, Lactobacillus, RT-qPCR, dysbiosis, gut bacteria, intestinal microbiota, meconium",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery after 6 months of delivery,C-section delivery,NA,134,17,No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling),16S,NA,RT-qPCR,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,2|1239|91061|186826|33958|2742598|1598,Complete,Shaimaa Elsafoury
bsdb:64/1/1,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within negative diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,6,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Yaseen Javaid,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-negative group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii",2|976|200643|171549|171552;2|1239|909932|909929|1843491|970|69823;2|1239|91061|186826|1300|1301|1302,Complete,Shaimaa Elsafoury
bsdb:64/1/2,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within negative diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,6,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-negative group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia",2|1224|1236|135625|712|416916;2|976|117743|200644|49546|1016|1019;2|1224|1236|135615|868|2717|2718;2|1224|1236|135615|868|2717|194702;2|201174|1760|85007|1653|1716|43768;2|976|200643|171549|171552|2974257|840;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1224|28216|206351|481|482|484;2|976|200643|171549|171551|836|1924944;2|201174|1760|85009|31957;2|1239|909932|909929|1843491|970|135083,Complete,Fatima
bsdb:64/2/1,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic within negative periodontitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,8,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Yaseen Javaid,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-negative samples,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia",2|201174|1760|2037;2|1224|28216|80840;2|1224|28216|206351;2|976|200643|171549|2005525|195950|28112,Complete,Shaimaa Elsafoury
bsdb:64/2/2,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic within negative periodontitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,8,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Yaseen Javaid,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-negative samples,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens",2|976|117743|200644|49546|1016|1018;2|1224|1236|135615|868|2717|194702;2|201174|1760|85007|1653|1716|43768;2|976|200643|171549|171552|2974257|840;2|1224|28216|206351|481|482|484,Complete,Shaimaa Elsafoury
bsdb:64/3/1,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 3,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic within positive periodontitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",6,12,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-positive samples,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",2|976|117743|200644|49546|1016|1019;2|201174|1760|85009|31957,Complete,Shaimaa Elsafoury
bsdb:64/4/1,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within positive diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",8,12,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-positive background,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",2|976|200643|171549;2|1239|186801|3082720|3118655|44259|143361;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|837;2|508458|649775|649776|649777;2|976|200643|171549|2005525|195950|28112;2|203691|203692|136|2845253|157|58231,Complete,Shaimaa Elsafoury
bsdb:64/4/2,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within positive diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",8,12,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-positive background,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|495;2|201174|1760|85006|1268|32207|2047;2|1239|909932|1843489|31977|29465,Complete,Shaimaa Elsafoury
bsdb:64/5/1,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within both positive and negative diabetic background,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",13,18,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within both the diabetes-positive and diabetes-negative background,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola",2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552;2|203691|203692|136|2845253|157|158,Complete,Shaimaa Elsafoury
bsdb:64/5/2,Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within both positive and negative diabetic background,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",13,18,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within both the diabetes-positive and diabetes-negative background,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis",2|201174|1760|2037|2049|1654|1655;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|68892,Complete,Shaimaa Elsafoury
bsdb:65/1/1,Study 65,case-control,22762355,10.1111/j.1600-0765.2012.01498.x,NA,"Casarin RC, Barbagallo A, Meulman T, Santos VR, Sallum EA, Nociti FH, Duarte PM, Casati MZ , Gonçalves RB",Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis,Journal of periodontal research,2013,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic,Diabetic,"chronic periodontitis, according to the criteria of the 1999 International Classification; the presence of at least 15 teeth; >= 30% of the sites and at least nine teeth pre-senting a probing pocket depth of >= 5 mm with bleeding on probing (with two or more of these teeth having a probing pocket depth of >= 7 mm); uncontrolled type-2 DM, determined by a glycated hemoglobin (HbA1c) concentration of > 8%",11,12,3 months,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Table 3 & text,10 January 2021,Yaseen Javaid,WikiWorks,Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Deferribacterota,k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|201174;2|200930;2|1239;2|32066;2|1224;2|1239|91061|186826|1300|1301|28037;2|32066|203490|203491|203492|848|851;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|39778;2|1224|28216|206351|481|538|539;2|1224|1236|135625|712|416916;2|1224|28216|206351|481|482;2|1239|91061|1385|539738|1378;2|1224|28216|206351|481|538;2|201174|1760|2037|2049|1654;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1239|909932|909929|1843491|970,Complete,Shaimaa Elsafoury
bsdb:65/1/2,Study 65,case-control,22762355,10.1111/j.1600-0765.2012.01498.x,NA,"Casarin RC, Barbagallo A, Meulman T, Santos VR, Sallum EA, Nociti FH, Duarte PM, Casati MZ , Gonçalves RB",Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis,Journal of periodontal research,2013,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic,Diabetic,"chronic periodontitis, according to the criteria of the 1999 International Classification; the presence of at least 15 teeth; >= 30% of the sites and at least nine teeth pre-senting a probing pocket depth of >= 5 mm with bleeding on probing (with two or more of these teeth having a probing pocket depth of >= 7 mm); uncontrolled type-2 DM, determined by a glycated hemoglobin (HbA1c) concentration of > 8%",11,12,3 months,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 & Table 3 & text,10 January 2021,Yaseen Javaid,WikiWorks,Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis.,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976;2|203691;2|508458;2|1239|186801|3082720|3118655|44259|143361;2|976|200643|171549|171551|836|837;2|1239|186801|186802|186806|1730;2|1239|186801|3082720|3118655|44259;2|976|200643|171549|171551|836;2|1239|186801|3082720|186804;2|976|200643|171549|2005525|195950|28112;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Shaimaa Elsafoury
bsdb:66/1/1,Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,cesarean infants with jaundice,cesarean infants with jaundice,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,gestational age,gestational diabetes,maternal age,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in cesarean infants with jaundice,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,2|1224|28216|80840|119060|106589,Complete,Shaimaa Elsafoury
bsdb:66/1/2,Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,cesarean infants with jaundice,cesarean infants with jaundice,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,gestational age,gestational diabetes,maternal age,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in cesarean infants with jaundice,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum|s__Bifidobacterium pseudolongum subsp. globosum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|1239|186801|186802|31979;2|1224|1236|135625|712;2|201174|1760|85004|31953|1678|1694|1690;2|1224|1236|135625,Complete,Shaimaa Elsafoury
bsdb:66/2/1,Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 2,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,infants with jaundice,infants with jaundice,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,feeding practices,gestational age,gestational diabetes,maternal age,mode of birth,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in all infants,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,2|1239|186801|186802|31979|1485|1502,Complete,Shaimaa Elsafoury
bsdb:66/2/2,Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 2,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,infants with jaundice,infants with jaundice,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,feeding practices,gestational age,gestational diabetes,maternal age,mode of birth,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in all infants,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:67/1/1,Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,Welch's T-Test,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Mean relative abundance in autistic (AD) and neurotypical (NT) subjects,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:67/2/1,Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,LEfSe,0.01,FALSE,2,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|1239|91061|186826|33958|1578;2|201174|84998|84999|84107|102106;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|1239|186801|3085636|186803|189330;2|976|200643,Complete,Shaimaa Elsafoury
bsdb:67/2/2,Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,LEfSe,0.01,FALSE,2,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|171550|239759;2|1239|909932|1843489|31977;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977|39948;2|976|200643|171549|2005525|375288;2|1239|909932|1843489|31977|29465;2|200940|3031449|213115|194924|35832;2|976|200643|171549,Complete,Shaimaa Elsafoury
bsdb:67/3/1,Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non constipated autistic,constipated autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",29,5,3 months,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differences in the bacterial taxa between constipated and non-constipated autistic (AD) patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
bsdb:67/4/1,Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non constipated neurotypical,constipated neurotypical,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",29,11,3 months,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differences in the bacterial taxa between constipated and non-constipated neurotypical (NT) subjects,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,2|1239|186801|186802|204475,Complete,Shaimaa Elsafoury
bsdb:68/1/1,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,142,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,decreased,Signature 1,Supplemental Table 4,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174|1760|2037|2049;2|201174|1760|2037;2|1239|526524|526525|128827|2749846|31971;2|1239|91061;2|976|200643|171549|815|816|28116;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|186802;2|1224|1236;2|1239|186801|3085636|186803|140625;2|1239|186801|3085636|186803;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|186801|186802|541000;2|1224;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:68/1/2,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,142,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,decreased,Signature 2,Supplemental Table 4,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186807|51514;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|1239|186801|186802;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171550,Complete,Shaimaa Elsafoury
bsdb:68/2/1,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,overweight,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,246,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|976|200643|171549|815|816;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|140625;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263;2|200940|3031449|213115|194924|35832,Complete,Shaimaa Elsafoury
bsdb:68/2/2,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,overweight,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,246,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Table 4,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|1239|186801|186802|186807|51514;2|1239|526524|526525|128827;2|1239|186801|186802;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:68/3/1,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,obese men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",80,70,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|976|200643|171549|2005525|375288|823;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|541000;2|1239|909932|1843489|31977;2|1224;2|1224|1236,Complete,Shaimaa Elsafoury
bsdb:68/3/2,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,obese men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",80,70,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",2|1239|186801|186802|31979;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186807|51514;2|1239|186801|186802|216572|1263;2|1239|1737404|1737405|1737406,Complete,Shaimaa Elsafoury
bsdb:68/4/1,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,overweight men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m3",80,171,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium",2|976|200643|171549|815|816;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|140625,Complete,Shaimaa Elsafoury
bsdb:68/4/2,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,overweight men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m3",80,171,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1239|186801|3082768|990719;2|1224|28216|80840;2|1239|186801|186802|31979;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186807|51514;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|1737404|1737405|1570339|150022;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|1263;2|508458|649775;2|1239|1737404|1737405|1737406;2|1239|186801|3085636|186803|2316020|33038,Complete,Shaimaa Elsafoury
bsdb:68/5/1,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,obese women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m5",131,72,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|140625;2|1224;2|1224|28216|80840;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|1737404|1737405|1737406;2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:68/5/2,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,obese women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m5",131,72,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|1239|186801|186802|186807|51514;2|1239|186801;2|1239|186801|186802|1898207,Complete,Shaimaa Elsafoury
bsdb:68/6/1,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,overweight women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m7",131,75,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|140625;2|1224;2|1224|28216|80840;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:68/6/2,Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,overweight women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m7",131,75,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia",2|1239|186801|186802|31979;2|1239|186801,Complete,Shaimaa Elsafoury
bsdb:69/1/1,Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Sex design,EFO:0001752,male,female,NA,259,292,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,age,NA,increased,NA,unchanged,unchanged,increased,Signature 1,supplementry figure S2,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index  and gut microbiota by Gender,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:69/2/1,Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,female normal weight,female obese,NA,168,20,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,unchanged,increased,Signature 1,Text + fig 2B,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index and gut microbiota by Gender,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,Shaimaa Elsafoury
bsdb:69/3/1,Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male normal weight,male obese,NA,93,38,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,Text + fig 2B,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index and gut microbiota by Gender,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|976|200643|171549|1853231|574697;2|32066|203490|203491|203492|848,Complete,Shaimaa Elsafoury
bsdb:69/4/1,Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,NA,261,58,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,Text + fig 2B,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index and gut microbiota by Gender,increased,"k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|32066;2|32066|203490|203491|203492|848,Complete,Shaimaa Elsafoury
bsdb:70/1/1,Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,pediatric normal weight,pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",67,71,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table S6,10 January 2021,Marianthi Thomatos,WikiWorks,Composition of gut microbiota in obese and normal-weight mexican school-age children,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|85831;2|976|200643|171549|815|816|28116;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179;2|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:70/1/2,Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,pediatric normal weight,pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",67,71,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table S6,10 January 2021,Marianthi Thomatos,WikiWorks,Composition of gut microbiota in obese and normal-weight mexican school-age children,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|3082768|990719;2|976|200643|171549|815|909656|310297;2|1224|1236|91347|543;2|976|200643|171549|171550;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803;2|976|200643|171549|171552|2974265|363265;2|976|200643|171549|171552|2974251|165179;2|1224|28216|80840|995019|40544;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:70/2/1,Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,female pediatric normal weight,female pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",29,29,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,2|976|200643|171549|815|816|28111,Complete,Shaimaa Elsafoury
bsdb:70/2/2,Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,female pediatric normal weight,female pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",29,29,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,2|976|200643|171549|1853231|283168,Complete,Shaimaa Elsafoury
bsdb:70/3/1,Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 3,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male pediatric normal weight,male pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",38,42,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,2|976|200643|171549|815|816|28111,Complete,Shaimaa Elsafoury
bsdb:70/3/2,Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 3,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male pediatric normal weight,male pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",38,42,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,2|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
bsdb:71/1/1,Study 71,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW , Neu J",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,NA,Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,19,33,NA,16S,4,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,feeding practices,sex",NA,increased,increased,NA,NA,NA,Signature 1,Table S6 in File S1,10 January 2021,Rimsha Azhar,WikiWorks,Meconium microbiome related to mode of delivery in premature infants,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",2|1239|91061|186826|33958|1243;2|1239|909932|1843489|31977|909928;2|1239|91061|186826|81852|2737;2|1239|186801|3085636|186803|830,Complete,Shaimaa Elsafoury
bsdb:71/2/1,Study 71,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW , Neu J",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,NA,Experiment 2,United States of America,Homo sapiens,Meconium,UBERON:0007109,Premature birth,EFO:0003917,>/=33 weeks,infants <33 weeks gestational age,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,17,35,NA,16S,4,Ion Torrent,Spearman Correlation,0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,feeding practices,sex",NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 1,10 January 2021,Rimsha Azhar,WikiWorks,"Phyla, family, and genera taxonomy significantly correlated with gestational age",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Actinomycetota",2|1239;2|1239|91061|1385|186817;2|1239|91061|1385|90964;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1239|91061|186826|81850;2|1239|186801|186802|31979;2|1239|186801|3082720|186804;2|1239|909932|1843489|31977;2|1239|526524|526525|128827;2|201174|1760|85004|31953;2|1224|1236|91347|543;2|1239|91061|1385|186817|1386;2|1239|91061|1385|90964|1279;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|2737;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1243;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|909928;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|547;2|1224|1236|91347|543|544;2|1224|1236|91347|1903409|551;2|1224|1236|91347|543|570;2|1224|1236|91347|543|160674;2|1224|1236|91347|1903409|53335;2|1224|1236|91347|1903414|29487;2|976|200643|171549|2005525|195950;2|201174,Complete,Shaimaa Elsafoury
bsdb:71/2/2,Study 71,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW , Neu J",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,NA,Experiment 2,United States of America,Homo sapiens,Meconium,UBERON:0007109,Premature birth,EFO:0003917,>/=33 weeks,infants <33 weeks gestational age,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,17,35,NA,16S,4,Ion Torrent,Spearman Correlation,0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,feeding practices,sex",NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 1,10 January 2021,Rimsha Azhar,WikiWorks,"Phyla, family, and genera taxonomy significantly correlated with gestational age",decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalicibacterium,2|1224|28216|80840|75682|223927,Complete,Shaimaa Elsafoury
bsdb:72/1/1,Study 72,case-control,30228282,10.1038/s41598-018-32219-2,NA,"Zhang M, Ma W, Zhang J, He Y , Wang J",Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,typically developing controls,autism,diagnosed with autistic spectrum disorder according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders-5th Edition),6,35,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,WikiWorks,The bacterial abundance at the level of phylum and genus in autistic and typically developing children with significant difference,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:72/1/2,Study 72,case-control,30228282,10.1038/s41598-018-32219-2,NA,"Zhang M, Ma W, Zhang J, He Y , Wang J",Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,typically developing controls,autism,diagnosed with autistic spectrum disorder according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders-5th Edition),6,35,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,WikiWorks,The bacterial abundance at the level of phylum and genus in autistic and typically developing children with significant difference,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1239;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1224|1236|91347|543|561;2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|543311;2|1239|526524|526525|128827|118747;2|1239|1737404|1737405|1570339|162289,Complete,Shaimaa Elsafoury
bsdb:73/1/1,Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,17,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|33042,Complete,Shaimaa Elsafoury
bsdb:73/1/2,Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,17,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|815|816;2|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
bsdb:73/2/1,Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese + metabolic syndrome,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,25,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|33042,Complete,Shaimaa Elsafoury
bsdb:73/2/2,Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese + metabolic syndrome,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,25,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|815|816;2|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
bsdb:74/1/1,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-obese,obese,obesity: BMI 30.5-60.3 kg/m2,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between obese and non-obese individuals,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802|216572|100175|100176;2|1239|186801|3085636|186803|1506553|1512,Complete,Shaimaa Elsafoury
bsdb:74/1/2,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-obese,obese,obesity: BMI 30.5-60.3 kg/m2,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between obese and non-obese individuals,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|820;2|976|200643|171549|171552|2974257|28134;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|310297;2|976|200643|171549|2005525|195950;2|976|200643|171549|171552|558436|839,Complete,Shaimaa Elsafoury
bsdb:74/2/1,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Nonobese microbiota cluster,obese,obesity: BMI 30.5-60.3 kg/m3,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Association of intestinal microbiota with local and systemic inflammation in obesity,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|1506577|36835;2|1239|186801|3085636|186803|2569097|39488,Complete,Shaimaa Elsafoury
bsdb:74/2/2,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Nonobese microbiota cluster,obese,obesity: BMI 30.5-60.3 kg/m3,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Association of intestinal microbiota with local and systemic inflammation in obesity,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|119852|119853,Complete,Shaimaa Elsafoury
bsdb:74/3/1,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI,high BMI,obesity: BMI 30.5-60.3 kg/m4,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high-BMI and low-BMI individuals,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum",2|1239|91061|1385|186822|55079;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802|186806|1730|1736;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|570|573;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|100175|100176;2|1239|186801|3085636|186803|841|166486;2|1224|1236|135623|641|662;2|1224|1236|91347|1903411|629;2|1239|186801|3085636|186803|1506577|36835,Complete,Shaimaa Elsafoury
bsdb:74/3/2,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI,high BMI,obesity: BMI 30.5-60.3 kg/m4,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high-BMI and low-BMI individuals,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes faecalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola",2|1224|28216|80840|506|507|511;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|820;2|1239|526524|526525|2810280|100883|100884;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|2974257|28134;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|195950;2|976|200643|171549|171552|558436|839,Complete,Shaimaa Elsafoury
bsdb:74/4/1,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low C-Reactive Protein,high C-Reactive Protein,obesity: BMI 30.5-60.3 kg/m5,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high C-reactive protein group and low C-reactive protein group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile",2|1239|91061|1385|186822|55079;2|1239|186801|3085636|186803|2719231|29370;2|1239|186801|186802|216572|100175|100176;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|292632|214851,Complete,Shaimaa Elsafoury
bsdb:74/4/2,Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low C-Reactive Protein,high C-Reactive Protein,obesity: BMI 30.5-60.3 kg/m5,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high C-reactive protein group and low C-reactive protein group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|329854;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|195950,Complete,Shaimaa Elsafoury
bsdb:75/1/1,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 1,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,right oropharynx of nonsmokers,right oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S3,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|976|117743|200644|49546|1016;2|1239|186801|3082720|186804|1257;2|32066|203490|203491|203492|848;2|1224|28216|80840|80864|12916;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
bsdb:75/1/2,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 1,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,right oropharynx of nonsmokers,right oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|52228;2|1239|91061|186826|1300|1301;2|1239|186801|186802|541000,Complete,Shaimaa Elsafoury
bsdb:75/2/1,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 2,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,left oropharynx of nonsmokers,left oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S5,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1224|1236|135625|712|416916,Complete,Shaimaa Elsafoury
bsdb:75/2/2,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 2,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,left oropharynx of nonsmokers,left oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S6,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|34104,Complete,Shaimaa Elsafoury
bsdb:75/3/1,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,right nasopharynx of nonsmokers,right nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S7,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Aquitalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea",2|201174|1760|2037|2049|1654;2|1239|91061|186826|33958|1243;2|1224|1236|2887326|468|469;2|1224|28216|206351|1499392|407217;2|1224|1236|91347|543|620;2|1224|28216|206389|2008794|349,Complete,Shaimaa Elsafoury
bsdb:75/3/2,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,right nasopharynx of nonsmokers,right nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S8,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum",2|201174|84998|1643822|1643826|84111;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|1239|91061|186826|186827|46123;2|1239|526524|526525|128827|174708;2|1239|186801|3082720|3030910|109326;2|1239|186801|3085636|186803|33042;2|1239|526524|526525|128827;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|84036;2|1239|186801|186802|216572|52784,Complete,Shaimaa Elsafoury
bsdb:75/4/1,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 4,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,left nasopharynx of nonsmokers,left nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S9,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|117743|200644|49546|237;2|1239|526524|526525|128827|1647;2|1239|91061|1385|539738|1378;2|1224|1236|91347|543|620;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:75/4/2,Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 4,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,left nasopharynx of nonsmokers,left nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S10,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|201174|84998|1643822|1643826|84111;2|976|200643|171549|171551|836;2|1239|91061|186826|186827|46123;2|1239|186801|186802|216572|52784;2|1239|186801|3082720|3030910|109326;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|84036;2|29547|3031852|213849|72294|194;2|1224|1236|135625|712|724;2|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
bsdb:76/1/1,Study 76,case-control,27231166,10.4103/0366-6999.182841,NA,"Qi CJ, Zhang Q, Yu M, Xu JP, Zheng J, Wang T , Xiao XH",Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,Chinese medical journal,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,type I diabetes mellitus children,type 1 diabetes mellitus,15,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Table 3 +  Figure 3,10 January 2021,Yaseen Javaid,WikiWorks,Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|1239|186801|3085636|186803|572511;2|1239|909932|1843488|909930|904,Complete,Rimsha Azhar
bsdb:76/1/2,Study 76,case-control,27231166,10.4103/0366-6999.182841,NA,"Qi CJ, Zhang Q, Yu M, Xu JP, Zheng J, Wang T , Xiao XH",Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,Chinese medical journal,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,type I diabetes mellitus children,type 1 diabetes mellitus,15,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Table 3 +  Figure 3,10 January 2021,Yaseen Javaid,WikiWorks,Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",2|1239|909932|1843489|31977|39948;2|1224|1236|135625;2|1224|1236|135625|712;2|1239|186801|3085636|186803;2|1224|1236|135625|712|724;2|1239|186801|3085636|1185407;2|1239|186801|186802|543314;2|201174|1760|85006;2|1224|28211|204458;2|1239|186801|186802|1392389,Complete,Rimsha Azhar
bsdb:77/1/1,Study 77,"cross-sectional observational, not case-control",28035686,10.1002/phar.1890,NA,"Flowers SA, Evans SJ, Ward KM, McInnis MG , Ellingrod VL",Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort,Pharmacotherapy,2017,"atypical antipsychotics, metabolic disease, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,non users,atypical antipsychotic users,Medication group was defined by the use of an Atypical Antipsychotics at the time of fecal sample collection,68,49,NA,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,decreased,NA,Signature 1,Figure3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant members of gut microbiota in bipolar disorder (BD) patients treated with atypical antipsychotics (AAP),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:77/1/2,Study 77,"cross-sectional observational, not case-control",28035686,10.1002/phar.1890,NA,"Flowers SA, Evans SJ, Ward KM, McInnis MG , Ellingrod VL",Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort,Pharmacotherapy,2017,"atypical antipsychotics, metabolic disease, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,non users,atypical antipsychotic users,Medication group was defined by the use of an Atypical Antipsychotics at the time of fecal sample collection,68,49,NA,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,decreased,NA,Signature 2,Figure3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant members of gut microbiota in bipolar disorder (BD) patients treated with atypical antipsychotics (AAP),decreased,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,Shaimaa Elsafoury
bsdb:78/1/1,Study 78,laboratory experiment,27829577,10.5056/jnm16105,NA,"Moussaoui N, Jacobs JP, Larauche M, Biraud M, Million M, Mayer E , Taché Y","Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex",Journal of neurogastroenterology and motility,2017,"Corticosterone, Microbiota, Permeability, Stress, psychological, Weaning",Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Stimulus or stress design,EFO:0001762,controls,limited nesting stress,pups exposed to limited nesting stress,23,23,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig3C + text,10 January 2021,Fatima Zohra,WikiWorks,Genera with differentially abundance in the LNS ( limited nesting stress) group compared to control,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera",2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186807|2740;2|1239|91061|186826|186827|1375;2|1239|91061|1385|90964|227979;2|1239|91061|186826|186827|66831;2|1239|186801|186802|31979|1485;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924|872;2|1239|91061|186826|186828|117563;2|201174|1760|85006|1268|32207;2|1224|1236|91347|1903414|583;2|1239|186801|186802|31979;2|1239|526524|526525|2810280|100883;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300;2|1239|91061|186826|81852;2|1239|526524|526525|2810281|191303;2157|28890|183925|2158|2159|2316,Complete,Claregrieve1
bsdb:78/1/2,Study 78,laboratory experiment,27829577,10.5056/jnm16105,NA,"Moussaoui N, Jacobs JP, Larauche M, Biraud M, Million M, Mayer E , Taché Y","Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex",Journal of neurogastroenterology and motility,2017,"Corticosterone, Microbiota, Permeability, Stress, psychological, Weaning",Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Stimulus or stress design,EFO:0001762,controls,limited nesting stress,pups exposed to limited nesting stress,23,23,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig3C + text,10 January 2021,Fatima Zohra,WikiWorks,Genera with differentially abundance in the LNS ( limited nesting stress) group compared to control,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|33042;2|1239|526524|526525|128827|2749846|31971;2|74201|203494|48461|1647988|239934|239935;2|200930|68337|191393|2945020|248038|248039;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|541000;2|976|200643|171549|2005519;2|1239|91061|1385|90964|1279;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186807;2|1239|526524|526525|128827;2|1239|186801|186802;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|244127;2|1224|1236|135625|712|724;2|976|200643|171549|1853231|283168,Complete,Claregrieve1
bsdb:79/1/1,Study 79,time series / longitudinal observational,25710027,10.1155/2015/806248,NA,"Damms-Machado A, Mitra S, Schollenberger AE, Kramer KM, Meile T, Königsrainer A, Huson DH , Bischoff SC",Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption,BioMed research international,2015,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Laparoscopic sleeve gastrectomy after 3 months and 6 Months combined,Laparoscopic sleeve gastrectomy baseline,NA,3,3,3 months,WMS,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1A,10 January 2021,Marianthi Thomatos,WikiWorks,Effects of laparoscopic sleeve gastrectomy (LSG) and very low calorie diet (VLCD) for obesity on gut microbiota composition,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_40A,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|1263;2|976|200643|171549|815|816|469593;2|1239|186801|186802|31979|1485|411489;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|189330|88431,Complete,Shaimaa Elsafoury
bsdb:79/2/1,Study 79,time series / longitudinal observational,25710027,10.1155/2015/806248,NA,"Damms-Machado A, Mitra S, Schollenberger AE, Kramer KM, Meile T, Königsrainer A, Huson DH , Bischoff SC",Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption,BioMed research international,2015,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,very low calorie diet after 3 months and 6 months,Very low calorie diet baseline,NA,3,3,3 months,WMS,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1B,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Effects of laparoscopic sleeve gastrectomy (LSG) and very low calorie diet (VLCD) for obesity on gut microbiota composition,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. D5,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. M62/1,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis",2|1239|91061;2|1239|186801|3085636|186803|572511|53443;2|1239|186801|186802|31979|1485|556261;2|1239|186801|186802|31979|1485|411486;2|1239|526524|526525|2810280|100883;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|1352;2|1239|186801|186802|186806|1730|1736;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|2719231|84030;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|541000;2|1239|186801|3082720|186804;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|1506553|1512;2|1239|526524|526525|2810280|100883|100884,Complete,Fatima
bsdb:80/1/1,Study 80,"cross-sectional observational, not case-control",24448554,10.1038/srep03814,NA,"Mejía-León ME, Petrosino JF, Ajami NJ, Domínguez-Bello MG , de la Barca AM",Fecal microbiota imbalance in Mexican children with type 1 diabetes,Scientific reports,2014,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,Type I diabetic children at onset,"T1D diagnose as established according to the American Diabetes Association criteria1, a positive anti-GAD and/or anti-IA-2 auto- antibodies result, HbA1C levels , 8%",8,8,3 months,16S,4,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,text,10 January 2021,Yaseen Javaid,WikiWorks,Fecal microbiota imbalance in Mexican children with type 1 diabetes,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:80/1/2,Study 80,"cross-sectional observational, not case-control",24448554,10.1038/srep03814,NA,"Mejía-León ME, Petrosino JF, Ajami NJ, Domínguez-Bello MG , de la Barca AM",Fecal microbiota imbalance in Mexican children with type 1 diabetes,Scientific reports,2014,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,Type I diabetic children at onset,"T1D diagnose as established according to the American Diabetes Association criteria1, a positive anti-GAD and/or anti-IA-2 auto- antibodies result, HbA1C levels , 8%",8,8,3 months,16S,4,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,text,10 January 2021,Yaseen Javaid,WikiWorks,Fecal microbiota imbalance in Mexican children with type 1 diabetes,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|904;2|1239|909932|909929|1843491|158846,Complete,Shaimaa Elsafoury
bsdb:81/1/1,Study 81,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, Bojsen-Møller KN, Dirksen C, Burgdorf KS, Holst JJ, Madsbad S, Wang J, Pedersen O, Hansen T , Arumugam M",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline,3 Months after Roux-en-Y gastric bypass surgery,NA,13,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 3 & Table S3,10 January 2021,Marianthi Thomatos,WikiWorks,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|573;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|39778;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|113107;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|31979|1485|1502;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1328;2|1239|186801|3085636|186803|2316020|46228;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|1853231|283168|28118;2|201174|1760|85004|31953|1678|1689;2|1239|91061|186826|81852|1350|1351;2|1239|909932|1843489|31977|906|187326;2|1239|186801|186802|216572|244127|169435;2|32066;2|1224,Complete,Shaimaa Elsafoury
bsdb:81/1/2,Study 81,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, Bojsen-Møller KN, Dirksen C, Burgdorf KS, Holst JJ, Madsbad S, Wang J, Pedersen O, Hansen T , Arumugam M",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline,3 Months after Roux-en-Y gastric bypass surgery,NA,13,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 3 & Table S3,10 January 2021,Marianthi Thomatos,WikiWorks,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:81/2/1,Study 81,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, Bojsen-Møller KN, Dirksen C, Burgdorf KS, Holst JJ, Madsbad S, Wang J, Pedersen O, Hansen T , Arumugam M",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline,one year after Roux-en-Y gastric bypass surgery,NA,13,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 3 & Table S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Fusobacteriota",2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|561|562;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|39778;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|68892;2|976|200643|171549|171550|239759|328814;2|1239|91061|186826|186828|117563|46124;2|201174|1760|2037|2049|2529408|1660;2|1224;2|32066,Complete,Shaimaa Elsafoury
bsdb:82/1/1,Study 82,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:82/1/2,Study 82,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",2|1239|526524|526525|2810280|3025755|29348;2|203691|203692|1643686|143786|29521|159;2|32066|203490|203491|203492|848|860,Complete,Shaimaa Elsafoury
bsdb:83/1/1,Study 83,time series / longitudinal observational,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,after surgery,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,6,3 weeks,WMS,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 &Table 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter succinogenes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Leptospirales|f__Leptospiraceae|g__Leptospira|s__Leptospira interrogans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium kansasii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella|s__Nakamurella multipartita,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mendocina,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Thermomicrobiota|c__Thermomicrobia|o__Thermomicrobiales|f__Thermomicrobiaceae|g__Thermomicrobium|s__Thermomicrobium roseum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema pallidum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Eukaryota|p__Evosea|c__Eumycetozoa|o__Dictyosteliales|f__Dictyosteliaceae|g__Dictyostelium,k__Eukaryota|p__Ciliophora|c__Litostomatea|o__Entodiniomorphida|f__Ophryoscolecidae|g__Epidinium",2|1224|1236|2887326|468|469|40214;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|207244|105841;2|203691|203692|1643686|143786|29521|159;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|65842|204430|218872|204431|832|833;2|32066|203490|203491|203492|848|860;2|29547|3031852|213849|72293|209;2|1239|91061|186826|33958|1578|1579;2|203691|203692|1643688|170|171|173;2|1239|91061|186826|33958|2742598|1598;2|201174|1760|85007|1762|1763|1768;2|201174|1760|1643684|85031|53460|53461;2|1224|1236|72274|135621|286|300;2|1239|91061|1385|90964|1279|1282;2|3027942|189775|189776|189777|499|500;2|203691|203692|136|2845253|157|160;2|1239|526524|526525|2810280|3025755|29348;2759|2605435|142796|2058949|2058185|5782;2759|5878|5988|40634|47890|40637,Complete,Fatima
bsdb:83/1/2,Study 83,time series / longitudinal observational,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,after surgery,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,6,3 weeks,WMS,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 &Table 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora",2|1224|1236|91347|543|544;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|69218;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|28901;2|1224|1236|91347|543|620|621;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2759|4751|4890|147550|5139|5148|5140,Complete,Fatima
bsdb:84/1/1,Study 84,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,after surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii",2|1224|1236|91347|543|547|69218;2|1239|909932|1843489|31977|29465|29466;2|1224|1236|91347|543|620|621,Complete,Shaimaa Elsafoury
bsdb:84/1/2,Study 84,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,after surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Thermomicrobiota|c__Thermomicrobia|o__Thermomicrobiales|f__Thermomicrobiaceae|g__Thermomicrobium|s__Thermomicrobium roseum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter succinogenes",2|1239|526524|526525|2810280|3025755|29348;2|203691|203692|1643686|143786|29521|159;2|1239|91061|186826|33958|2742598|1598;2|1239|186801|3085636|186803|207244|105841;2|32066|203490|203491|203492|848|860;2|3027942|189775|189776|189777|499|500;2|1239|91061|1385|90964|1279|1282;2|65842|204430|218872|204431|832|833,Complete,Shaimaa Elsafoury
bsdb:85/1/1,Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,NA,Experiment 1,Gabon,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,two-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1266,Complete,Shaimaa Elsafoury
bsdb:85/2/1,Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,NA,Experiment 2,Congo,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,two-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:85/3/1,Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,NA,Experiment 3,Gabon,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,seven-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1266,Complete,Shaimaa Elsafoury
bsdb:85/4/1,Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,NA,Experiment 4,Congo,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,seven-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|976|200643|171549|815|816;2|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
bsdb:86/1/1,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 3,c-section,meconium samples were collected at day 1 after delivery,6,3,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 1,Figure 7 and Fig. S4,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:86/2/1,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 5,c-section,meconium samples were collected at day 1 after delivery,7,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,k__Bacteria|p__Bacillota,2|1239,Complete,Shaimaa Elsafoury
bsdb:86/2/2,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 5,c-section,meconium samples were collected at day 1 after delivery,7,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:86/3/1,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 3,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 28,c-section,meconium samples were collected at day 1 after delivery,7,6,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,unchanged,Signature 1,Figure 6S and Fig. S4,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:86/4/1,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 4,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 150,c-section,meconium samples were collected at day 1 after delivery,6,4,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:86/5/1,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 5,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 365,c-section,meconium samples were collected at day 1 after delivery,5,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:86/6/1,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 6,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,full-term delivery >39 weeks at day 3,late preterm 34-36 weeks,meconium samples were collected at day 1 after delivery,4,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Kruskall-Wallis,0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text pg11 and figure 7s,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:86/7/1,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 7,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,overall time point infants samples of c-section,meconium samples were collected at day 1 after delivery,8,7,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplemantry file 9,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|74201|203494|48461|1647988|239934;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|946234;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|1578;2|201174|1760|85009|31957|1743;2|201174|1760|85006|1268|32207;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803,Complete,Fatima
bsdb:86/7/2,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 7,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,overall time point infants samples of c-section,meconium samples were collected at day 1 after delivery,8,7,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supplemantry file 9,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:86/8/NA,Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 8,Luxembourg,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,NA,4,6,"11 mothers (6 controls and 5 cases) used antibiotics 12 hours before and after delivery, 3 VD mothers were positive group B Streptococcus screening.",16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:87/1/1,Study 87,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I, Sánchez-Alcoholado L, Martín-Tejedor B, Castellano-Castillo D, Moreno-Indias I, Urda-Cardona A, Tinahones FJ, Fernández-García JC , Queipo-Ortuño MI",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,maturity-onset diabetes of the young 2 (MODY2) and healthy Controls,Type I Diabetics,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",28,15,3 months,16S,23,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Yaseen Javaid,WikiWorks,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976;2|976|200643|171549|815;2|976|200643|171549|171550;2|1224|1236|91347|543;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|541000;2|1239|909932|1843489|31977;2|1239|91061|186826|1300;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|547;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:87/1/2,Study 87,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I, Sánchez-Alcoholado L, Martín-Tejedor B, Castellano-Castillo D, Moreno-Indias I, Urda-Cardona A, Tinahones FJ, Fernández-García JC , Queipo-Ortuño MI",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,maturity-onset diabetes of the young 2 (MODY2) and healthy Controls,Type I Diabetics,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",28,15,3 months,16S,23,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Yaseen Javaid,WikiWorks,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota",2|1239;2|201174,Complete,Shaimaa Elsafoury
bsdb:87/2/1,Study 87,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I, Sánchez-Alcoholado L, Martín-Tejedor B, Castellano-Castillo D, Moreno-Indias I, Urda-Cardona A, Tinahones FJ, Fernández-García JC , Queipo-Ortuño MI",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,healthy Controls,Type I Diabetics and maturity-onset diabetes of the young 2 (MODY2),"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",13,30,3 months,16S,23,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,breastfeeding duration,delivery procedure,race,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:88/1/1,Study 88,"cross-sectional observational, not case-control",30268819,10.1016/j.schres.2018.09.014,NA,"Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R , Jeste DV",Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects,Schizophrenia research,2019,"Bacteria, Gut-brain axis, Microbes, Phylum, Probiotics, Psychosis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,non-psychiatric controls,schizophrenia,outpatients with schizophrenia or schizoaffective disorder,25,25,NA,16S,4,Illumina,Kruskall-Wallis,0.01,TRUE,NA,demographics,"age,antimicrobial agent,body mass index,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant genera in schizophrenia and non-psychiatric controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|906;2|1239|186801|186802;2|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:88/1/2,Study 88,"cross-sectional observational, not case-control",30268819,10.1016/j.schres.2018.09.014,NA,"Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R , Jeste DV",Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects,Schizophrenia research,2019,"Bacteria, Gut-brain axis, Microbes, Phylum, Probiotics, Psychosis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,non-psychiatric controls,schizophrenia,outpatients with schizophrenia or schizoaffective disorder,25,25,NA,16S,4,Illumina,Kruskall-Wallis,0.01,TRUE,NA,demographics,"age,antimicrobial agent,body mass index,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant genera in schizophrenia and non-psychiatric controls,decreased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|1224;2|1224|1236|135625|712|724;2|1224|28216|80840|995019|40544;2|1239|186801|186802|31979|1485;2|1224|1236|135625|712|724|729,Complete,Atrayees
bsdb:89/1/1,Study 89,case-control,26789999,https://doi.org/10.1159/000441768,https://pubmed.ncbi.nlm.nih.gov/26789999/,"Takahashi K, Nishida A, Fujimoto T, Fujii M, Shioya M, Imaeda H, Inatomi O, Bamba S, Sugimoto M , Andoh A",Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease,Digestion,2016,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,CD patients,Patients with Crohn's disease,46,68,NA,16S,34,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2",9 June 2023,Atrayees,Atrayees,Relative abundance of bacteria between control and CD,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:89/1/2,Study 89,case-control,26789999,https://doi.org/10.1159/000441768,https://pubmed.ncbi.nlm.nih.gov/26789999/,"Takahashi K, Nishida A, Fujimoto T, Fujii M, Shioya M, Imaeda H, Inatomi O, Bamba S, Sugimoto M , Andoh A",Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease,Digestion,2016,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,CD patients,Patients with Crohn's disease,46,68,NA,16S,34,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, Table 2",9 June 2023,Atrayees,Atrayees,Relative abundance of bacteria between control and CD,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis",2|1239|186801|3085636|3018741|698776;2|1239|186801|186802|186806|1730;2|1239|526524|526525|128827|61170;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|572511|871665;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|2719313|460384,Complete,NA
bsdb:90/1/1,Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 1,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in vaginal delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,10,10,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,increased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|29547|3031852|213849|72293|209,Complete,Shaimaa Elsafoury
bsdb:90/1/2,Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 1,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in vaginal delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,10,10,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia",2|1224|1236|2887326|468|469;2|1224|2008785|119069|206349|70774;2|1239|91061|186826|1300|1301;2|1224|28211|204457|41297|13687;2|201174|1760|85007|1653|1716;2|201174|84995|84996|84997|42255;2|1224|28211|204457|41297|165695;2|1239|91061|1385|186817|129337;2|1224|28216|206351|481|482;2|1239|1737404|1737405|1570339|165779;2|1224|28211|356|119045|407;2|1239|909932|1843489|31977|29465;2|201174|1760|85006|1268|1269;2|1239|91061|186826|1300|1357;2|1224|28211|356|82115|357;2|1224|28211|356|212791;2|1224|28216|80840|75682|29580;2|1224|28216|80840|80864|80865,Complete,Shaimaa Elsafoury
bsdb:90/2/1,Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 2,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in C-section delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,40,40,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|81852|1350,Complete,Shaimaa Elsafoury
bsdb:90/2/2,Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 2,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in C-section delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,40,40,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium",2|1224|1236|72274|135621|286;2|1239|91061|1385|186817|400634;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|1224|28216|80840|119060|106589;2|32066|203490|203491|1129771|32067;2|201174|1760|2037|2049|1654;2|32066|203490|203491|203492|848;2|1224|28211|204457|41297|13687;2|201174|84995|84996|84997|42255;2|1224|1236|135619|28256|2745;2|203691|203692|136|2845253|157;2|1224|1236|135625|712|724;2|1224|28211|204458|76892|41275;2|1224|1236|135615|868|2717;2|1224|28211|204457|41297|165695,Complete,Shaimaa Elsafoury
bsdb:91/1/1,Study 91,"cross-sectional observational, not case-control",29459704,10.1038/s41598-018-21657-7,NA,"Shi YC, Guo H, Chen J, Sun G, Ren RR, Guo MZ, Peng LH , Yang YS",Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,the first-pass meconium stools from within 24 h of delivery,8,10,None of VD mothers received antibiotics during delivery. CSD mothers recieved prophylactic antibiotics after delivery.,WMS,NA,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Comparison of the microbiome of vaginally delivered and C-section-delivered newborns,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas veronii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus amyloliquefaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales,k__Bacteria|p__Deinococcota|c__Deinococci,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Deinococcota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1224|1236|135624|84642|642|654;2|1224|28211;2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817|1386|1390;2|1239|91061|1385|186817|1386|1402;2|1297|188787|118964|183710;2|1297|188787|118964;2|1297|188787;2|1297|188787|118964|183710|1298;2|1297;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239;2|976|200643|171549|815|909656|821;2|1224|1236|135614|32033|40323;2|1224|1236|135614|32033;2|1224|1236|135614;2|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:91/1/2,Study 91,"cross-sectional observational, not case-control",29459704,10.1038/s41598-018-21657-7,NA,"Shi YC, Guo H, Chen J, Sun G, Ren RR, Guo MZ, Peng LH , Yang YS",Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,the first-pass meconium stools from within 24 h of delivery,8,10,None of VD mothers received antibiotics during delivery. CSD mothers recieved prophylactic antibiotics after delivery.,WMS,NA,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,ComparisonofthemicrobiomesofvaginallydeliveredandC-section-deliverednewborns,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|201174|1760;2|201174;2|201174|1760|2037;2|201174|1760|85009|31957;2|1224|1236;2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85009|31957|1743;2|1224|1236|72274;2|201174|1760|85010|2070;2|1224|28216|80840;2|1224|28216;2|1224|28216|80840|80864|283;2|1224|28216|80840|80864;2|1224|28216|80840|80864|283|285;2|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
bsdb:92/1/1,Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,obese without non-alcoholic fatty liver disease,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,11,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota",2|1224|1236;2|201174,Complete,Shaimaa Elsafoury
bsdb:92/1/2,Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,obese without non-alcoholic fatty liver disease,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,11,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease,decreased,k__Bacteria|p__Bacillota|c__Clostridia,2|1239|186801,Complete,Shaimaa Elsafoury
bsdb:92/2/1,Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|201174|1760;2|976|200643|171549|171552|838;2|32066|203490;2|29547;2|1224|1236,Complete,Shaimaa Elsafoury
bsdb:92/2/2,Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria",2|1239|526524;2|1224|28211,Complete,Shaimaa Elsafoury
bsdb:92/3/1,Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,obese without non-alcoholic fatty liver disease,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,11,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Campylobacterota",2|201174|1760;2|976|200643|171549|171552|838;2|32066|203490;2|29547,Complete,Shaimaa Elsafoury
bsdb:92/3/2,Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,obese without non-alcoholic fatty liver disease,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,11,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|1239|526524;2|1224|28211;2|1224|1236,Complete,Shaimaa Elsafoury
bsdb:93/1/1,Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 1,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,Delivery via cesarean section,172,40,None,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of delivery mode on the microbiome in the CS group compared to the vaginal delivery group,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:93/2/1,Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 2,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Antimicrobials use during delivery (no),Antimicrobials use during delivery (yes),"Mothers who used antimicrobials during delivery (Cefuroxime (n= 31), penicillin (n= 28), piperacillin-tazobactam (n=2))",151,61,None.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of antimicrobial use on the microbiome of the first stool in the group who received antimicrobials (YES) compared to those did not (NO),increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:93/3/1,Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 3,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Maternal consumption of probiotics (NO),Maternal consumption of probiotics (YES),Mothers who consumed probiotics (lactobacilli) during pregnancy,151,61,None.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of probiotics on the microbiome in the group who consumed lactobacilli (YES) compared to the group who did not (NO),increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:93/4/1,Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 4,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Furry pets at home (NO),Furry pets at home (YES),Mothers who have furry pets at home during pregnancy,108,104,None.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"antimicrobial agent during labor,delivery procedure,probiotics during pregnancy",NA,increased,NA,NA,NA,increased,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of furry pets at home on the microbiome in the group who have furry pets at home (YES) compared to the group who don't have (NO),increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:93/4/2,Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 4,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Furry pets at home (NO),Furry pets at home (YES),Mothers who have furry pets at home during pregnancy,108,104,None.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"antimicrobial agent during labor,delivery procedure,probiotics during pregnancy",NA,increased,NA,NA,NA,increased,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of furry pets at home on the microbiome in the group who have furry pets at home (YES) compared to the group who don't have (NO),decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239;2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:94/1/1,Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline participants,3 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community of obese patients following weight-loss intervention,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum|s__Anaerobiospirillum succiniciproducens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47",2|1224|1236|135624|83763|13334|13335;2|201174|84998|84999|84107|102106|74426;2|1224|28216|80840|995019|577310|487175;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|292632|214851;2|1224|28216|80840|469610,Complete,Fatima
bsdb:94/1/2,Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline participants,3 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema brennaborense,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter heparinus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gadei,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfitobacterium|s__Desulfitobacterium hafniense,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulforamulus|s__Desulforamulus ruminis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus mucilaginosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sp. M18,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces coelicolor,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia heliotrinireducens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Thermanaerovibrio|s__Thermanaerovibrio acidaminovorans,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum",2|203691|203692|136|2845253|157|81028;2|976|117747|200666|84566|84567|984;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|2005520|156973|156974;2|1239|186801|186802|2937909|36853|49338;2|1239|186801|186802|186807|2916693|1564;2|1239|909932|909929|1843491|970|69823;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|216572|253238|253239;2|1239|186801|186802|216572|459786|351091;2|1239|186801|186802|216572|1017280|106588;2|1239|526524|526525|128827|61170|61171;2|1239|91061|1385|186817|2837504|1398;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|81852|1350|1352;2|1239|91061|1385|186822|44249|61624;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3085636|186803|2719313|333367;2|1239|186801|3085636|186803|248744|168384;2|200940|3031651|3031668|213422|28231|443143;2|1224|1236|91347|543|561|562;2|1224|1236|72274|135621|2901164|316;2|201174|1760|85011|2062|1883|1902;2|201174|84998|1643822|1643826|84108|84110;2|201174|84998|1643822|1643826|84111|84112;2|74201|203494|48461|1647988|239934|239935;2|508458|649775|649776|649777|81461|81462;2|508458|649775|649776|3029087|1434006|651822,Complete,Shaimaa Elsafoury
bsdb:94/2/1,Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,3 months participants,6 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gadei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Thermanaerovibrio|s__Thermanaerovibrio acidaminovorans",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|2005520|156973|156974;2|1239|186801|3085636|186803|2719313|333367;2|1239|186801|3085636|186803|2719231|84030;2|200940|3031449|213115|194924|872|876;2|1224|1236|91347|543|561|562;2|201174|84998|1643822|1643826|84111|84112;2|201174|84998|1643822|1643826|644652|471189;2|508458|649775|649776|649777|81461|81462,Complete,Shaimaa Elsafoury
bsdb:94/2/2,Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,3 months participants,6 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum|s__Anaerobiospirillum succiniciproducens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae|g__Micavibrio|s__Micavibrio aeruginosavorus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47",2|1224|1236|135624|83763|13334|13335;2|1239|91061|186826|1300|1357|1358;2|3018035|3031418|213481|213483|213485|349221;2|1224|28216|80840|995019|577310|487175;2|1239|186801|3085636|186803|841|360807;2|1239|91061|186826|1300|1301|1308;2|1239|909932|1843489|31977|29465|29466;2|1224|28216|80840|469610,Complete,Fatima
bsdb:94/3/1,Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,6 months participants,24 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,increased,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter heparinus,2|976|117747|200666|84566|84567|984,Complete,Shaimaa Elsafoury
bsdb:94/3/2,Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,6 months participants,24 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",2|74201|203494|48461|1647988|239934|239935;2|1224|1236|91347|543|561|562;2|201174|84998|84999|84107|102106|74426,Complete,Shaimaa Elsafoury
bsdb:95/1/1,Study 95,"cross-sectional observational, not case-control",30568265,10.1038/s41366-018-0290-z,https://pubmed.ncbi.nlm.nih.gov/30568265/,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control babies at the age of 3,overweight/obese babies,NA,356,146,7 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,education level",NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3 & 4,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in overweight 3 year old children,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|841,Complete,Shaimaa Elsafoury
bsdb:95/1/2,Study 95,"cross-sectional observational, not case-control",30568265,10.1038/s41366-018-0290-z,https://pubmed.ncbi.nlm.nih.gov/30568265/,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control babies at the age of 3,overweight/obese babies,NA,356,146,7 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,education level",NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3 & 4,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in overweight 3 year old children,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:96/1/1,Study 96,case-control,27499582,10.3164/jcbn.15-152,NA,"Andoh A, Nishida A, Takahashi K, Inatomi O, Imaeda H, Bamba S, Kito K, Sugimoto M , Kobayashi T",Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population,Journal of clinical biochemistry and nutrition,2016,"16S sequence, Bacteroides, Firmicutes, SCFA, datamining",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,10,10,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, 3, 4",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community comparison between obese and lean Japanese population,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",2|1239|909932|1843488|909930|904|187327;2|976|200643|171549|171550|239759;2|1239|1737404|1737405|1570339|165779;2|1239|186801|3085636|186803|33042;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378|1379;2|1239|91061|186826|186828|117563|46124;2|1224|1236|91347|543|570|573;2|201174|84998|84999|1643824|2767353|1382;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|841|301302;2|201174|1760|85006|1268|32207|43675;2|201174|1760|2037|2049|2529408|52773;2|1239|186801|3085636|186803|207244|649756,Complete,Fatima
bsdb:96/1/2,Study 96,case-control,27499582,10.3164/jcbn.15-152,NA,"Andoh A, Nishida A, Takahashi K, Inatomi O, Imaeda H, Bamba S, Kito K, Sugimoto M , Kobayashi T",Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population,Journal of clinical biochemistry and nutrition,2016,"16S sequence, Bacteroides, Firmicutes, SCFA, datamining",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,10,10,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Table 2, 3, 4",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community comparison between obese and lean Japanese population,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena",2|976|200643|171549|815|816;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|2719313|358743;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|1737404|1737405|1570339|150022;2|1239|526524|526525|128827|61170|61171;2|1239|186801|3085636|186803|1164882;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|186802|3085642|2048137|39484;2|1239|186801|3085636|186803|2005359|290055,Complete,Fatima
bsdb:97/1/1,Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,obese patients prior to Sleeve gastrectomy SG0,obese patients had a body mass index (BMI) of >28 kg/m2.,20,19,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Marianthi Thomatos,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving sleeve gastrectomy,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|541000;2|32066|203490|203491|203492|848|850;2|1239|186801|3082720|186804,Complete,Shaimaa Elsafoury
bsdb:97/2/1,Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,Roux-en-Y gastric bypass (RYGB),obese patients had a body mass index (BMI) of >28 kg/m2.,20,7,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3082720|186804;2|1239|909932|1843489|31977|906,Complete,Shaimaa Elsafoury
bsdb:97/3/1,Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,obese patients prior to Sleeve gastrectomy SG0,obese patients three months after Sleeve gastrectomy SG3,obese patients had a body mass index (BMI) of >28 kg/m2.,19,8,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving sleeve gastrectomy,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1308;2|976|200643|171549|171551;2|976|200643|171549|171550|239759|214856,Complete,Shaimaa Elsafoury
bsdb:97/4/1,Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,patients prior to Roux-en-Y gastric bypass RYGB0,obese patients 3 moths after Roux-en-Y gastric bypass RYGB3,obese patients had a body mass index (BMI) of >28 kg/m2.,7,3,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,increased,"k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|909932;2|1239|909932|909929;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:97/4/2,Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,patients prior to Roux-en-Y gastric bypass RYGB0,obese patients 3 moths after Roux-en-Y gastric bypass RYGB3,obese patients had a body mass index (BMI) of >28 kg/m2.,7,3,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1308,Complete,Shaimaa Elsafoury
bsdb:98/1/1,Study 98,"cross-sectional observational, not case-control",30962186,10.2215/CJN.12161018,NA,"Shah NB, Allegretti AS, Nigwekar SU, Kalim S, Zhao S, Lelouvier B, Servant F, Serena G, Thadhani RI, Raj DS , Fasano A",Blood Microbiome Profile in CKD : A Pilot Study,Clinical journal of the American Society of Nephrology : CJASN,2019,"Blood microbiome, Cross-Sectional Studies, DNA, Bacterial, Ribosomal, Dysbiosis, Endotoxemia, Enterobacteriaceae, Metagenomics, Microbiota, Permeability, Pilot Projects, Polymerase Chain Reaction, Proteobacteria, Pseudomonadaceae, Renal Insufficiency, Chronic, Sequence Analysis, chronic kidney disease, glomerular filtration rate",Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,Chronic kidney disease,EFO:0003884,controls,CKD,NA,20,20,current use,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,"age,body mass index,hyperlipidemia,hypertension,immunosuppressant use measurement,leukocyte",NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3 and Table 2,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flectobacillaceae|g__Pseudarcicella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia intermedia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",2|1224|28211|204441|433;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|351;2|1239|91061|1385|186817|1386;2|976|1853228|1853229|563835;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|1224|28211|356|45401;2|1224|28211|356|45401|81;2|1224|1236|118969|444|445;2|1224|1236|118969|444;2|1224|1236|118969;2|1224|1236|135614|32033|68;2|1239|186801|3082720|186804;2|1224;2|976|768503|768507|3141701|1664383;2|1224|1236|72274|135621|286;2|976|1853228|1853229|563835|504481;2|1224|1236|91347|1903411|613;2|1224|1236|91347|1903411|629;2|1224|1236|91347|1903411|629|631;2|1224|28211|204441,Complete,Shaimaa Elsafoury
bsdb:98/1/2,Study 98,"cross-sectional observational, not case-control",30962186,10.2215/CJN.12161018,NA,"Shah NB, Allegretti AS, Nigwekar SU, Kalim S, Zhao S, Lelouvier B, Servant F, Serena G, Thadhani RI, Raj DS , Fasano A",Blood Microbiome Profile in CKD : A Pilot Study,Clinical journal of the American Society of Nephrology : CJASN,2019,"Blood microbiome, Cross-Sectional Studies, DNA, Bacterial, Ribosomal, Dysbiosis, Endotoxemia, Enterobacteriaceae, Metagenomics, Microbiota, Permeability, Pilot Projects, Polymerase Chain Reaction, Proteobacteria, Pseudomonadaceae, Renal Insufficiency, Chronic, Sequence Analysis, chronic kidney disease, glomerular filtration rate",Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,Chronic kidney disease,EFO:0003884,controls,CKD,NA,20,20,current use,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,"age,body mass index,hyperlipidemia,hypertension,immunosuppressant use measurement,leukocyte",NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3 and Table 2,10 January 2021,Rimsha Azhar,"Fatima,Lwaldron,WikiWorks",Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.,decreased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Acidimicrobiaceae,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Acidobacteriota|c__Terriglobia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Aurantimicrobium,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Bryobacteraceae|g__Bryobacter,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Grylloblattodea|f__Grylloblattidae|g__Galloisiana|s__Galloisiana yuasai,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Microscillaceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Ohtaekwangia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2|201174|84992|84993|84994;2|201174|84992|84993;2|57723|204432;2|201174|1760|85006|85023|1705353;2|57723|204432|332160|1962910|911113;2|57723|204432|332160;2|201174|1760|85007|1653|1716;2|200940|3031451|3024411|213121;2759|33208|6656|50557|58557|244939|73579|378494;2|1239|186801|3085636|186803;2|976|768503|768507|1937962;2|976|768503|768507|2762286|1210119;2|1224|28211|204455|31989|265;2|1224|28211|204457|41297|13687;2|1224|1236|135614|32033|40323;2|1239|186801|3085636|186803|1506577,Complete,Shaimaa Elsafoury
bsdb:99/1/1,Study 99,case-control,28628112,10.1038/nm.4358,NA,"Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, Shi J, Zhao S, Liu W, Wang X, Xia H, Liu Z, Cui B, Liang P, Xi L, Jin J, Ying X, Wang X, Zhao X, Li W, Jia H, Lan Z, Li F, Wang R, Sun Y, Yang M, Shen Y, Jie Z, Li J, Chen X, Zhong H, Xie H, Zhang Y, Gu W, Deng X, Shen B, Xu X, Yang H, Xu G, Bi Y, Lai S, Wang J, Qi L, Madsen L, Wang J, Ning G, Kristiansen K , Wang W",Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention,Nature medicine,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,79,72,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbiome alterations in obesity among cohort of lean vs obese Chinese,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",2|1239|186801|3085636|186803|572511|40520;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|32066|203490|203491|203492|848|861;2|32066|203490|203491|203492|848|856;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906|907;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|2569097|39488,Complete,Fatima
bsdb:99/1/2,Study 99,case-control,28628112,10.1038/nm.4358,NA,"Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, Shi J, Zhao S, Liu W, Wang X, Xia H, Liu Z, Cui B, Liang P, Xi L, Jin J, Ying X, Wang X, Zhao X, Li W, Jia H, Lan Z, Li F, Wang R, Sun Y, Yang M, Shen Y, Jie Z, Li J, Chen X, Zhong H, Xie H, Zhang Y, Gu W, Deng X, Shen B, Xu X, Yang H, Xu G, Bi Y, Lai S, Wang J, Qi L, Madsen L, Wang J, Ning G, Kristiansen K , Wang W",Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention,Nature medicine,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,79,72,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiome alterations in obesity among cohort of lean vs obese Chinese,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|371601;2|976|200643|171549|815|816|820;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|329854;2|976|200643|171549|171550|239759|328814;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|815|816|28111;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|571;2|1224|1236|135625|712|724|729;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,ChiomaBlessing
bsdb:100/1/1,Study 100,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova DA, Tkacheva ON, Doudinskaya EN, Strazhesko ID, Kotovskaya YV, Popenko AS, Tyakht AV , Alexeev DG",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,"cardiovascular risk factors, diet, glucose metabolism, gut microbiota, metabolic status",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI,High BMI,NA,69,23,3 months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in patients with obesity,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|91347|1903411|613;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:100/2/1,Study 100,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova DA, Tkacheva ON, Doudinskaya EN, Strazhesko ID, Kotovskaya YV, Popenko AS, Tyakht AV , Alexeev DG",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,"cardiovascular risk factors, diet, glucose metabolism, gut microbiota, metabolic status",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-abdominal obesity,Abdominal obesity,NA,39,53,3 months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in patients with obesity,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|91347|1903411|613;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:100/2/2,Study 100,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova DA, Tkacheva ON, Doudinskaya EN, Strazhesko ID, Kotovskaya YV, Popenko AS, Tyakht AV , Alexeev DG",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,"cardiovascular risk factors, diet, glucose metabolism, gut microbiota, metabolic status",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-abdominal obesity,Abdominal obesity,NA,39,53,3 months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in patients with obesity,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,2|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:101/1/1,Study 101,case-control,21829158,10.1038/ijo.2011.153,NA,"Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, Valero R, Raccah D, Vialettes B , Raoult D",Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii,International journal of obesity (2005),2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,obese,"Obese patients, as defined by a BMI>=30 kg/m2",47,68,less than one month before stool collection,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,"Text & Tables 2, 3, 4 & 5",10 January 2021,Marianthi Thomatos,WikiWorks,Gut alterations of Lactobacillus or bifidobacterium species between obese and controls,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:101/1/2,Study 101,case-control,21829158,10.1038/ijo.2011.153,NA,"Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, Valero R, Raccah D, Vialettes B , Raoult D",Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii,International journal of obesity (2005),2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,obese,"Obese patients, as defined by a BMI>=30 kg/m2",47,68,less than one month before stool collection,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,"Text & Tables 2, 3, 4 & 5",10 January 2021,Marianthi Thomatos,WikiWorks,Gut alterations of Lactobacillus or bifidobacterium species between obese and controls,decreased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",2157|28890|183925|2158|2159|2172|2173;2|201174|1760|85004|31953|1678|28025;2|1239|91061|186826|33958|2759736|1597;2|1239|91061|186826|33958|2767842|1590,Complete,Shaimaa Elsafoury
bsdb:102/1/1,Study 102,"cross-sectional observational, not case-control",26279179,10.1038/srep13212,NA,"Fugmann M, Breier M, Rottenkolber M, Banning F, Ferrari U, Sacco V, Grallert H, Parhofer KG, Seissler J, Clavel T , Lechner A","The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes",Scientific reports,2015,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,normoglycemic controls,Women with gestational DM,Gestational Diabetes Mellitus  was diagnosed by a standardized oral glucose tolerance test (OGTT) after the 23rd week of the preceding pregnecy,35,42,14 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text and Figure 2,10 January 2021,Yaseen Javaid,WikiWorks,Comparison of relative sequence abundances at the different bacterial taxonomic ranks between pGDM and controls.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|909932|1843489|31977;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:102/1/2,Study 102,"cross-sectional observational, not case-control",26279179,10.1038/srep13212,NA,"Fugmann M, Breier M, Rottenkolber M, Banning F, Ferrari U, Sacco V, Grallert H, Parhofer KG, Seissler J, Clavel T , Lechner A","The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes",Scientific reports,2015,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,normoglycemic controls,Women with gestational DM,Gestational Diabetes Mellitus  was diagnosed by a standardized oral glucose tolerance test (OGTT) after the 23rd week of the preceding pregnecy,35,42,14 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Text and Figure 2,10 January 2021,Yaseen Javaid,WikiWorks,Comparison of relative sequence abundances at the different bacterial taxonomic ranks between pGDM and controls.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239;2|1239|186801;2|1239|186801|186802;2|976|200643|171549|171550;2|1239|186801|3085636|186803|572511;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:103/1/1,Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed female,NA,24,24,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 January 2021,Fatima Zohra,WikiWorks,Sex differences in gut microbiota in female patients with major depressive disorder,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|186801|3085636|186803|572511;2|201174;2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|553372;2|201174|84998|84999|1643824|1380;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|644652;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|216851;2|200940|3031449|213115|194924|872;2|201174|84998|84999;2|1239|186801|3085636|186803;2|201174|1760|85004|31953;2|201174|1760|85004;2|1224|1236|135625;2|1224|1236|135625|712;2|1239|186801|186802|186806;2|201174|84998|84999|84107,Complete,Shaimaa Elsafoury
bsdb:103/1/2,Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed female,NA,24,24,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,10 January 2021,Fatima Zohra,WikiWorks,Sex differences in gut microbiota in female patients with major depressive disorder,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter",2|1239|186801|186802|404402;2|1224|28216|80840|995019|40544;2|508458|649775|649776|3029088|638847,Complete,Shaimaa Elsafoury
bsdb:103/2/1,Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed male,NA,20,20,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Fatima Zohra,"Fatima,WikiWorks",Sex differences in gut microbiota in male patients with major depressive disorder,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|201174|84998|84999|1643824|1380;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827,Complete,Fatima
bsdb:103/2/2,Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed male,NA,20,20,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,10 January 2021,Fatima Zohra,WikiWorks,Sex differences in gut microbiota in male patients with major depressive disorder,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter",2|201174|84998|84999|84107;2|1239|186801;2|201174|84998|1643822|1643826|644652;2|1239|186801|3082720|3030910|109326;2|508458|649775|649776|3029088|638847,Complete,Shaimaa Elsafoury
bsdb:104/1/1,Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 1),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,10 January 2021,Fatima Zohra,WikiWorks,Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239;2|976|200643|171549|171552|838;2|1224|1236|91347|543|570;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:104/1/2,Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 1),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,10 January 2021,Fatima Zohra,WikiWorks,Major bacterial organism in subjects of MDD and control groups,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:104/2/1,Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 2),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:104/2/2,Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 2),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Major bacterial organism in subjects of MDD and control groups,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:104/3/1,Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 3),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239;2|1239|186801|3082720|186804,Complete,Fatima
bsdb:104/3/2,Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 3),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Major bacterial organism in subjects of MDD and control groups,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Shaimaa Elsafoury
bsdb:105/1/1,Study 105,case-control,27988330,10.1016/j.jpsychires.2016.12.007,NA,"Evans SJ, Bassis CM, Hein R, Assari S, Flowers SA, Kelly MB, Young VB, Ellingrod VE , McInnis MG",The gut microbiome composition associates with bipolar disorder and illness severity,Journal of psychiatric research,2017,"Bipolar disorder, Faecalibacterium, Generalized Anxiety Disorder scale, Microbiome, Patient Health Questionnaire, Pittsburg Sleep Quality Index",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Healthy controls,Bipolar,Individuals with bipolar disorder,64,115,NIL,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2b,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Table 2b gives the mean and (SD) values for OTU fractional representations (percent of total) for all OTUs greater than 1% total in either group. P-values derive from logistical regressions with diagnosis (1,0) as the outcome measure and OTU as the predictor, adjusting for age, gender and BMI. Values in bold remained significant following FDR correction at the p<0.05 level.t",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:106/1/1,Study 106,"cross-sectional observational, not case-control",30261302,10.1016/j.bbi.2018.09.026,NA,"Coello K, Hansen TH, Sørensen N, Munkholm K, Kessing LV, Pedersen O , Vinberg M",Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives,"Brain, behavior, and immunity",2019,"Bipolar disorder, Gut microbiota, Microbiota, Newly diagnosed, Unaffected relatives",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthy controls,bipolar disorder patients,NA,77,113,NA,16S,34,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,physical activity,sex,smoking behavior,waist circumference",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"table 2, figure3",10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",gut microbiota composition in patients with newly diagnosed bipolar and healthy controls,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,2|1239|186801|186802|216572|946234,Complete,Folakunmi
bsdb:106/2/1,Study 106,"cross-sectional observational, not case-control",30261302,10.1016/j.bbi.2018.09.026,NA,"Coello K, Hansen TH, Sørensen N, Munkholm K, Kessing LV, Pedersen O , Vinberg M",Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives,"Brain, behavior, and immunity",2019,"Bipolar disorder, Gut microbiota, Microbiota, Newly diagnosed, Unaffected relatives",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,unaffected relatives,bipolar disorder patients,Healthy first degree relatives of bipolar disorder patients,39,113,NA,16S,34,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,physical activity,sex,smoking behavior,waist circumference",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"table 2, figure3",21 February 2024,Folakunmi,Folakunmi,Gut microbiota composition in patients with newly diagnosed bipolar and their unaffected first degree relatives,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,2|1239|186801|186802|216572|946234,Complete,Folakunmi
bsdb:107/1/1,Study 107,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, Bulik CM , Carroll IM","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T1,Patients with anorexia at hospital admission (T1),12,16,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differences in microbial taxa among anorexia patients at hospital admission (T1) VS healthy comparison group (HCG),increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",2|1239|91061;2|201174|84998|84999,Complete,ChiomaBlessing
bsdb:107/1/2,Study 107,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, Bulik CM , Carroll IM","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T1,Patients with anorexia at hospital admission (T1),12,16,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differences in microbial taxa among anorexia patients at hospital admission (T1) VS healthy comparison group (HCG),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803|207244;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:107/2/1,Study 107,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, Bulik CM , Carroll IM","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T2,Patients with anorexia at hospital discharge (T2),12,10,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differences in microbial taxa among anorexia patients at hospital discharge (T2) VS healthy comparison group (HCG),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|201174|84998|84999;2|976|200643|171549|2005525|375288,Complete,ChiomaBlessing
bsdb:107/2/2,Study 107,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, Bulik CM , Carroll IM","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T2,Patients with anorexia at hospital discharge (T2),12,10,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 3,10 February 2024,ChiomaBlessing,ChiomaBlessing,Differences in microbial taxa among anorexia patients at hospital discharge (T2) VS healthy comparison group (HCG),decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,ChiomaBlessing
bsdb:108/1/1,Study 108,case-control,26682545,10.1371/journal.pone.0145274,NA,"Morita C, Tsuji H, Hata T, Gondo M, Takakura S, Kawai K, Yoshihara K, Ogata K, Nomoto K, Miyazaki K , Sudo N",Gut Dysbiosis in Patients with Anorexia Nervosa,PloS one,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,healthy controls,anorexia nervosa patients,female patients with anorexia nervosa,21,25,3 months,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.002,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"table 3, table 5",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",gut microbiome dysbiosis in patients with anorexia nervosa versus healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",2|976|200643|171549|815|816|817;2|1239|91061|186826|33958|2767842|1590;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|572511|1532;2|1239|186801|186802|216572|1535,Complete,Claregrieve1
bsdb:109/1/1,Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,normal weight participants,anorexia patients before weight gain,NA,55,55,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,figure 3,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",gut microbiota of anorexia patients before and after weight gain compared to healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|201174;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|244127;2|201174|1760|85004|31953|1678;2|74201;2|1239|186801|186802|31979|1485,Complete,Lwaldron
bsdb:109/1/2,Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,normal weight participants,anorexia patients before weight gain,NA,55,55,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 2,figure 3,10 January 2021,Fatima Zohra,WikiWorks,gut microbiota of anorexia patients before and after weight gain compared to healthy controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|841,Complete,Lwaldron
bsdb:109/2/1,Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,HC,anorexia patients after weight gain,NA,55,44,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,increased,unchanged,NA,NA,NA,Signature 1,figure 3,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",gut microbiota of anorexia patients before and after weight gain compared to healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|201174;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239|186801|186802|31979|1485,Complete,Lwaldron
bsdb:109/2/2,Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,HC,anorexia patients after weight gain,NA,55,44,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,increased,unchanged,NA,NA,NA,Signature 2,figure 3,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",gut microbiota of anorexia patients before and after weight gain compared to healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|815|816;2|976;2|1239|186801|186802|31979|1485,Complete,Lwaldron
bsdb:110/1/1,Study 110,time series / longitudinal observational,29859859,10.1016/j.schres.2018.05.017,NA,"Yuan X, Zhang P, Wang Y, Liu Y, Li X, Kumar BU, Hei G, Lv L, Huang XF, Fan X , Song X","Changes in metabolism and microbiota after 24-week risperidone treatment in drug naïve, normal weight patients with first episode schizophrenia",Schizophrenia research,2018,"Metabolism, Microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,Drug-naive first-episode schizophrenia patients,41,41,1 month,16S,NA,RT-qPCR,T-Test,0.05,FALSE,NA,NA,"age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,table 2,10 January 2021,Fatima Zohra,WikiWorks,comparison of fecal bacteria between schizophrenic patients and controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|561|562;2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:110/1/2,Study 110,time series / longitudinal observational,29859859,10.1016/j.schres.2018.05.017,NA,"Yuan X, Zhang P, Wang Y, Liu Y, Li X, Kumar BU, Hei G, Lv L, Huang XF, Fan X , Song X","Changes in metabolism and microbiota after 24-week risperidone treatment in drug naïve, normal weight patients with first episode schizophrenia",Schizophrenia research,2018,"Metabolism, Microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,Drug-naive first-episode schizophrenia patients,41,41,1 month,16S,NA,RT-qPCR,T-Test,0.05,FALSE,NA,NA,"age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,table 2,27 June 2023,Atrayees,Atrayees,comparison of fecal bacteria between schizophrenic patients and controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,2|1239|186801|3085636|186803|572511|1532,Complete,Atrayees
bsdb:111/1/1,Study 111,"cross-sectional observational, not case-control",29580894,10.1016/j.bbr.2018.03.036,NA,"Jiang HY, Zhou YY, Zhou GL, Li YC, Yuan J, Li XH , Ruan B",Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder,Behavioural brain research,2018,"Gut-brain axis, Hyperactivity, Inattention, Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,healthy control,ADHD,Treatment-Naive Children diagnosed with ADHD,32,51,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1d , Figure S8",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","(d) LEfSe identified the most differentially abundant taxons between HC and ADHD groups at genus level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative
abundance > 0.5%). HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an
LDA significant threshold > 2 are shown 

LEfSe identified the most differentially abundant taxons between HC and ADHD groups at family level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative abundance >0.5%). (Red) ADHD taxa; (Green) taxa enriched in HCs. HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an LDA significant threshold >2 are shown.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1224|1236|2887326|468|469;2|1239|186801|3082768|990719|990721;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|128827|1573534;2|1239|186801|186802|186807;2|1239|186801|3082720|186804;2|201174|84998|84999|84107|1473205;2|1224|1236|135614|32033|40323;2|1239|186801|3082720|186804|1505652;2|1224|1236|2887326|468;2|1224|1236|135614|32033,Complete,Peace Sandy
bsdb:111/1/2,Study 111,"cross-sectional observational, not case-control",29580894,10.1016/j.bbr.2018.03.036,NA,"Jiang HY, Zhou YY, Zhou GL, Li YC, Yuan J, Li XH , Ruan B",Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder,Behavioural brain research,2018,"Gut-brain axis, Hyperactivity, Inattention, Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,healthy control,ADHD,Treatment-Naive Children diagnosed with ADHD,32,51,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure1, Figure S8",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","d) LEfSe identified the most differentially abundant taxons between HC and ADHD groups at genus level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative abundance > 0.5%). HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an LDA significant threshold > 2 are shown

LEfSe identified the most differentially abundant taxons between HC and ADHD groups at family level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative abundance >0.5%). (Red) ADHD taxa; (Green) taxa enriched in HCs. HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an LDA significant threshold >2 are shown.",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2|1224|28216|80840|506;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|1506553;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050|39485;2|1224|28216|80840|995019|40544;2|1239|909932|1843488|909930|904;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|1506577,Complete,Peace Sandy
bsdb:112/1/1,Study 112,case-control,30001426,10.1371/journal.pone.0200728,NA,"Prehn-Kristensen A, Zimmermann A, Tittmann L, Lieb W, Schreiber S, Baving L , Fischer A",Reduced microbiome alpha diversity in young patients with ADHD,PloS one,2018,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,controls,ADHD males,NA,17,14,NA,16S,12,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of taxa in male ADHD and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|976|200643|171549|815|816,Complete,NA
bsdb:112/1/2,Study 112,case-control,30001426,10.1371/journal.pone.0200728,NA,"Prehn-Kristensen A, Zimmermann A, Tittmann L, Lieb W, Schreiber S, Baving L , Fischer A",Reduced microbiome alpha diversity in young patients with ADHD,PloS one,2018,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,controls,ADHD males,NA,17,14,NA,16S,12,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of taxa in male ADHD and healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|171552;2|1239|186801|3082768|424536;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:113/1/1,Study 113,"cross-sectional observational, not case-control",27288567,10.1016/j.jad.2016.05.038,NA,"Aizawa E, Tsuji H, Asahara T, Takahashi T, Teraishi T, Yoshida S, Ota M, Koga N, Hattori K , Kunugi H",Possible association of Bifidobacterium and Lactobacillus in the gut microbiota of patients with major depressive disorder,Journal of affective disorders,2016,"Bifidobacterium, Distress, Gut microbiota, Irritable bowel syndrome, Lactobacillus, Major depressive disorder",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,57,43,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of gut microbiota of patients with major depressive disorder,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Amylolactobacillus|s__Amylolactobacillus amylophilus",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|2767876|1603,Complete,NA
bsdb:114/1/1,Study 114,case-control,30584306,10.2147/NDT.S188340,NA,"Huang Y, Shi X, Li Z, Shen Y, Shi X, Wang L, Li G, Yuan Y, Wang J, Zhang Y, Zhao L, Zhang M, Kang Y , Liang Y",Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"Firmicutes, brain–gut axis, depression, gut microbiota, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,27,27,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Fig 1, fig 3b, figure 4",10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of firmicutes in patients with major depressive disorder,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1224|28216|80840|75682|846;2|1239|1737404|1737405|1570339|543311;2|1239|526524|526525|128827|118747;2|1224|1236|72274|135621|286;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|539738|1378,Complete,Atrayees
bsdb:114/1/2,Study 114,case-control,30584306,10.2147/NDT.S188340,NA,"Huang Y, Shi X, Li Z, Shen Y, Shi X, Wang L, Li G, Yuan Y, Wang J, Zhang Y, Zhao L, Zhang M, Kang Y , Liang Y",Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"Firmicutes, brain–gut axis, depression, gut microbiota, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,27,27,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Fig 1, fig 3b, figure 4",10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of firmicutes in patients with major depressive disorder,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1239;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|216851;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:115/1/1,Study 115,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H, Xie XH, Zhao J, Lai WT, Wang MB, Xu D, Liu YH, Guo YY, Xu SX, Deng WF, Yang QF, Xiao L, Zhang YL, He FS, Wang S , Liu TB","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,"Bipolar disorder, Diversity, G(m) coefficient, Gut microbiota, Major depressive disorder, Shotgun metagenomics sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,30,31,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 1,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks,Comparison of bacterial abundance of major depressive disorder and healthy controls,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",2|1239;2|201174;2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|459786;2|1239|91061|186826|1300|1301;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|906;2|1239|909932|1843488|909930|904;2|1224|1236|91347|543;2|976|200643|171549|171552|838;2|1224|1236|91347|543|561|562;2|1239|909932|1843489|31977|906|907;2|1239|186801|186802|216572|459786|351091;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|171552|838|28132;2|201174|1760|85004|31953|1678|1689,Complete,NA
bsdb:115/1/2,Study 115,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H, Xie XH, Zhao J, Lai WT, Wang MB, Xu D, Liu YH, Guo YY, Xu SX, Deng WF, Yang QF, Xiao L, Zhang YL, He FS, Wang S , Liu TB","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,"Bipolar disorder, Diversity, G(m) coefficient, Gut microbiota, Major depressive disorder, Shotgun metagenomics sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,30,31,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 2,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks,Comparison of bacterial abundance of major depressive disorder and healthy controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|976;2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|195950;2|1224|1236|135625|712|724|729,Complete,NA
bsdb:115/2/1,Study 115,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H, Xie XH, Zhao J, Lai WT, Wang MB, Xu D, Liu YH, Guo YY, Xu SX, Deng WF, Yang QF, Xiao L, Zhang YL, He FS, Wang S , Liu TB","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,"Bipolar disorder, Diversity, G(m) coefficient, Gut microbiota, Major depressive disorder, Shotgun metagenomics sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthy controls,bipolar,NA,30,30,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks,Comparison of bacterial abundance of bipolar disorder with major depressive disorder and healthy controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes",2|976;2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|195950;2|976|200643|171549|815|816|290053,Complete,NA
bsdb:116/1/1,Study 116,case-control,23433344,10.1186/1741-7015-11-46,NA,"Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F , Queipo-Ortuño MI",Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study,BMC medicine,2013,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,healthy controls,children with type 1 diabetes,"Type 1 diabetes was diagnosed following the criteria of the American Diabetes Association and the appearance of at least two persistent, confirmed anti-islet autoantibodies (insulin autoantibodies, glutamic acid decarboxylase autoantibodies or tyrosine phosphatase autoantibodies)",16,16,3 months,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5 &6,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976;2|1239|186801|186802|31979|1485;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465,Complete,Shaimaa Elsafoury
bsdb:116/1/2,Study 116,case-control,23433344,10.1186/1741-7015-11-46,NA,"Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F , Queipo-Ortuño MI",Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study,BMC medicine,2013,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,healthy controls,children with type 1 diabetes,"Type 1 diabetes was diagnosed following the criteria of the American Diabetes Association and the appearance of at least two persistent, confirmed anti-islet autoantibodies (insulin autoantibodies, glutamic acid decarboxylase autoantibodies or tyrosine phosphatase autoantibodies)",16,16,3 months,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 5 &6,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174;2|1239;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|572511|1532;2|1239|186801|3085636|186803|1766253|39491;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:117/1/1,Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 1,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,elderly controls,elderly pneumonia patients,patients >= 60 years of age with pneumonia,91,100,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,increased,NA,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between elderly controls and elderly pneumonia patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae",2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301|257758,Complete,Claregrieve1
bsdb:117/1/2,Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 1,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,elderly controls,elderly pneumonia patients,patients >= 60 years of age with pneumonia,91,100,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,increased,NA,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,Merit,WikiWorks",Differential microbial abundance between elderly controls and elderly pneumonia patients,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|32066|203490|203491|1129771|32067;2|201174|1760|85004|31953|196082;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:117/2/1,Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 2,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,adult controls,adult pneumonia patients,patients <60 years of age with pneumonia,187,27,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy adult controls and pneumonia patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae",2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301|257758,Complete,Claregrieve1
bsdb:117/2/2,Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 2,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,adult controls,adult pneumonia patients,patients <60 years of age with pneumonia,187,27,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy adult controls and pneumonia patients,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|91061;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:118/1/1,Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal born children,cesarean born,cesarean delivery,60,34,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1C and Text,10 January 2021,Yaseen Javaid,"Merit,WikiWorks",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Amylolactobacillus|s__Amylolactobacillus amylophilus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales",2|1239|91061|186826|33958|2767876|1603;2|1239;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|1898207;2|1239|186801|186802;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489,Complete,Rimsha Azhar
bsdb:118/1/2,Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal born children,cesarean born,cesarean delivery,60,34,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1C and Text,10 January 2021,Yaseen Javaid,WikiWorks,The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,Rimsha Azhar
bsdb:118/2/1,Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,cesarean born and breastfed,cesarean born and mixed-fed,cesarean delivery and mixed-fed,24,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3d and Text,10 January 2021,Rimsha Azhar,WikiWorks,Enriched taxa of different level from cesarean born breastfed infants and from cesarean born mixed-fed infants,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|909932;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350,Complete,Rimsha Azhar
bsdb:118/2/2,Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,cesarean born and breastfed,cesarean born and mixed-fed,cesarean delivery and mixed-fed,24,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3d and Text,10 January 2021,Rimsha Azhar,WikiWorks,Enriched taxa of different level from cesarean born breastfed infants and from cesarean born mixed-fed infants,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|186801|3085636|186803|1506577;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552,Complete,Rimsha Azhar
bsdb:119/1/1,Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid negative,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,21,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Yaseen Javaid,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:119/1/2,Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid negative,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,21,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Yaseen Javaid,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,2|976|200643|171549|815|816|47678,Complete,Shaimaa Elsafoury
bsdb:119/2/1,Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid positive,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",35,9,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:119/2/2,Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid positive,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",35,9,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:119/3/1,Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,opoid negative among Metaformin negative,Opoid positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,35,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:119/3/2,Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,opoid negative among Metaformin negative,Opoid positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,35,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:120/1/1,Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 1,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Activity Based Anorexia group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1224;2|976|200643|171549|171552|838;2157|28890;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:120/1/2,Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 1,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Activity Based Anorexia group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|201174;2|976|200643|171549|815|816;2|976;2|201174|1760|85004|31953|1678;2|1239;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:120/2/1,Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 2,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Ad libitum group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|1239;2|1239|91061|186826|81852|1350;2|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
bsdb:120/2/2,Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 2,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Ad libitum group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|201174;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:121/1/1,Study 121,case-control,28808698,10.3290/j.cjdr.a38769,NA,"Deng K, Ouyang XY, Chu Y , Zhang Q",Subgingival Microbiome of Gingivitis in Chinese Undergraduates,The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA),2017,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,healthy controls,gingivitis,Patients with gingivitis,12,54,3 months,16S,34,Illumina,ANOSIM,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,figure 3 and text,10 January 2021,Marianthi Thomatos,"Lwaldron,WikiWorks,ChiomaBlessing",Subgingival Microbiome of Gingivitis in Chinese undergraduates VS healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales genomosp. P1,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|241556;2|976;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|28131;2|203691;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Shaimaa Elsafoury
bsdb:121/1/2,Study 121,case-control,28808698,10.3290/j.cjdr.a38769,NA,"Deng K, Ouyang XY, Chu Y , Zhang Q",Subgingival Microbiome of Gingivitis in Chinese Undergraduates,The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA),2017,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,healthy controls,gingivitis,Patients with gingivitis,12,54,3 months,16S,34,Illumina,ANOSIM,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,figure 3 and text,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Subgingival Microbiome of Gingivitis in Chinese undergraduates VS healthy controls,decreased,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,2|976|117743|200644|49546|1016,Complete,Shaimaa Elsafoury
bsdb:122/1/1,Study 122,case-control,24421902,10.1371/journal.pone.0083744,NA,"Xuan C, Shamonki JM, Chung A, Dinome ML, Chung M, Sieling PA , Lee DJ",Microbial dysbiosis is associated with human breast cancer,PloS one,2014,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,normal tissue,tumor tissue,NA,20,20,NA,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 1,Table S2 and Figure 1d,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",OTUs enriched in paired normal or tumor tissue,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium radiotolerans,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae",2|1224|28211|356|119045|407|31998;2|976|117743|200644|49546|237;2|1224|28211|356|119045|407;2|1224|28211|356|119045,Complete,Atrayees
bsdb:122/1/2,Study 122,case-control,24421902,10.1371/journal.pone.0083744,NA,"Xuan C, Shamonki JM, Chung A, Dinome ML, Chung M, Sieling PA , Lee DJ",Microbial dysbiosis is associated with human breast cancer,PloS one,2014,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,normal tissue,tumor tissue,NA,20,20,NA,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 2,Table S2 and Figure 1d,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",OTUs enriched in paired normal or tumor tissue,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium aromaticivorans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",2|1224|28211|204457|41297|165695|13690;2|1224|28211|204457|41297|13687;2|1224|28216|32003|206379|914;2|1224|28211|204457|41297|165696|48935;2|1224|28211|356|41294|374;2|1239|91061|186826|1300|1301|257758;2|1224|28211|204457|41297,Complete,Atrayees
bsdb:123/1/1,Study 123,laboratory experiment,31141574,10.1371/journal.pone.0217553,NA,"Deshpande NG, Saxena J, Pesaresi TG, Carrell CD, Ashby GB, Liao MK , Freeman LR",High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats,PloS one,2019,NA,Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Diet,EFO:0002755,low fat diet,high fat diet,"High fat diet rats were fed (20% protein, 35% carbohydrate, 45% fat by calories).  Controls or low fat diet were fed (20% protein, 70% carbohydrate, 10% fat by calories) for eight weeks.",6,6,NA,16S,NA,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Lora Kasselman,WikiWorks,Mean relative abundances for gut genera and p-value for differences between high-fat and control animals are listed. Class and phylum are indicated as well,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|1239|91061|186826|1300|1357;2|1239|91061|186826|186828|117563;2|1239|186801|186802|216572|1486725;2|1239|186801|3082720|3030910|109326;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|100175;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|44748;2|1239|186801|3085636|186803|1506577;2|1239|526524|526525|2810280|1505663;2|1239|526524|526525|128827|61170;2|201174|1760|85006|1268|32207;2|201174|84998|1643822|1643826|447020;2|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
bsdb:123/1/2,Study 123,laboratory experiment,31141574,10.1371/journal.pone.0217553,NA,"Deshpande NG, Saxena J, Pesaresi TG, Carrell CD, Ashby GB, Liao MK , Freeman LR",High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats,PloS one,2019,NA,Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Diet,EFO:0002755,low fat diet,high fat diet,"High fat diet rats were fed (20% protein, 35% carbohydrate, 45% fat by calories).  Controls or low fat diet were fed (20% protein, 70% carbohydrate, 10% fat by calories) for eight weeks.",6,6,NA,16S,NA,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Lora Kasselman,WikiWorks,Mean relative abundances for gut genera and p-value for differences between high-fat and control animals are listed. Class and phylum are indicated as well,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella",2|1224|1236|91347|543|544;2|976|200643|171549|2005519|397864;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|588605,Complete,Shaimaa Elsafoury
bsdb:124/1/1,Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,distance runners (high carb),body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae",2|1239|186801|3085636|186803|572511|418240;2|1224|1236|91347|543|547|550,Complete,Shaimaa Elsafoury
bsdb:124/1/2,Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,distance runners (high carb),body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|216572|1263|40519;2|976|200643|171549|815|816|47678;2|1224|1236|91347|543|561|562;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|561;2|1239|91061|186826|1300|1357,Complete,Shaimaa Elsafoury
bsdb:124/2/1,Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella",2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|216851;2|1239|186801|186802|31979|1485;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1432051,Complete,Shaimaa Elsafoury
bsdb:124/2/2,Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|2569097|39488;2|976|200643|171549|815|816|46506;2|1239|186801|186802|216572|1263|40519;2|201174|1760|85004|31953|1678|216816|1679;2|1224|1236|91347|543|561|562;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|2767885|1599;2|1224|28216|80840|995019|577310;2|1239|91061|186826|33958|1243,Complete,Shaimaa Elsafoury
bsdb:124/3/1,Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,distance runners (high carb),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:124/3/2,Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,distance runners (high carb),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",2|1224|1236|91347|543|547|550;2|1239|91061|186826|33958|46255|1583;2|1239|526524|526525|128827|1522;2|976|200643|171549|815|816|47678;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|547;2|1239|91061|186826|33958|46255;2|1239|91061|186826|33958|1243,Complete,Shaimaa Elsafoury
bsdb:125/1/1,Study 125,case-control,31109865,10.1016/j.job.2019.03.003,NA,"Takahashi Y, Park J, Hosomi K, Yamada T, Kobayashi A, Yamaguchi Y, Iketani S, Kunisawa J, Mizuguchi K, Maeda N , Ohshima T",Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing,Journal of oral biosciences,2019,"Bacteria, Epidemiology, Metagenomics, Microbiota, Mouth neoplasms",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,noncancer individuals,Oral Squamous Cell Cancer patients,All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.,80,60,28 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,"Fig 1,3 and Text",10 January 2021,Utsav Patel,WikiWorks,Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|1239|186801|3082720|186804|1257;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|1283313;2|976|117743|200644|49546|1016,Complete,Shaimaa Elsafoury
bsdb:125/1/2,Study 125,case-control,31109865,10.1016/j.job.2019.03.003,NA,"Takahashi Y, Park J, Hosomi K, Yamada T, Kobayashi A, Yamaguchi Y, Iketani S, Kunisawa J, Mizuguchi K, Maeda N , Ohshima T",Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing,Journal of oral biosciences,2019,"Bacteria, Epidemiology, Metagenomics, Microbiota, Mouth neoplasms",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,noncancer individuals,Oral Squamous Cell Cancer patients,All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.,80,60,28 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,"Fig 1,3 and Text",10 January 2021,Utsav Patel,WikiWorks,Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|724,Complete,Shaimaa Elsafoury
bsdb:126/1/1,Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,healthy controls,Oral leukoplakia,Oral leukoplakia patients,19,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. healthy control: a case-control study,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|1224|1236|135625|712|724;2|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
bsdb:126/1/2,Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,healthy controls,Oral leukoplakia,Oral leukoplakia patients,19,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. healthy control: a case-control study,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|91061|186826|1300|1301;2|1239|91061|186826|186827|46123,Complete,Shaimaa Elsafoury
bsdb:126/2/1,Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,healthy controls,Oral Squamous Cell Cancer patients,Oral Squamous Cell Cancer patients,19,16,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in OSCC vs. healthy control: a case-control study,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|1224|1236|135625|712|724;2|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
bsdb:126/2/2,Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,healthy controls,Oral Squamous Cell Cancer patients,Oral Squamous Cell Cancer patients,19,16,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in OSCC vs. healthy control: a case-control study,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|91061|186826|1300|1301;2|1239|91061|186826|186827|46123,Complete,Shaimaa Elsafoury
bsdb:126/3/1,Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,Oral Squamous Cell Cancer patients,Oral leukoplakia,Oral leukoplakia patients,16,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. OSCC: a case-control study,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:126/3/2,Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,Oral Squamous Cell Cancer patients,Oral leukoplakia,Oral leukoplakia patients,16,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. OSCC: a case-control study,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,2|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
bsdb:127/1/1,Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,subjects with ongoing or recent history of alcohol overconsumption of more than 20 or 40 g of alcohol per day,18,24,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, 3",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of microbiota between patients with alcohol overconsumption and controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801|186802|31979|1485;2|1239|526524|526525|128827|61170;2|1224;2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:127/1/2,Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,subjects with ongoing or recent history of alcohol overconsumption of more than 20 or 40 g of alcohol per day,18,24,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, 3",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of microbiota between patients with alcohol overconsumption and controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:127/2/1,Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between alcohol overconsumers and controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",2|1239|909932|1843488|909930|904;2|201174|1760|2037;2|1224|28216|80840|506;2|1239|526524|526525|128827|118747;2|1239|186801|186802|31979|1485;2|200940|3031449|213115;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|3085636|186803|2383;2|1224|1236|91347|543|561;2|1239|526524|526525|128827|61170;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|201174|1760|85006|1268;2|1224|1236|91347|1903414|581;2|1224;2|201174|1760|85006|1268|32207;2|1224|28216|80840|995019|40544;2|1239|1737404|1737405|1737406,Complete,Claregrieve1
bsdb:127/2/2,Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between alcohol overconsumers and controls,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas",2|201174;2|201174|84998|1643822|1643826|447020;2|1239|186801;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|186801|186802|216572|216851;2|1239|909932|909929|1843491|52225;2|976|200643|171549|1853231|283168;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1224|1236|135624|83763|674963,Complete,Claregrieve1
bsdb:128/1/1,Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,intestinal metaplasia,gastric cancer,NA,37,17,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 1,10 January 2021,Rimsha Azhar,"Fatima,Merit,WikiWorks",The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|976|200643|171549|171552|1283313;2|1239|186801|3085636|186803|43996;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186806;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|437755;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|201174|84998|1643822|1643826|84108;2|1239|91061|186826|1300|1301;2|1239|91061|186826,Complete,Atrayees
bsdb:128/1/2,Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,intestinal metaplasia,gastric cancer,NA,37,17,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Bacteria|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Portiera",2|1224|1236|2887326|468|469;2|1224|28216|206351|1499392|57739;2|1224|28216|32003|2008793|378210;2|200940|3024408|213462|213465;2|1224|1236|135619|28256|235572,Complete,Atrayees
bsdb:128/2/1,Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,atrophic gastric,gastric cancer,NA,37,74,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",2|1239|91061|186826|1300|1301;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|539738|1378;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186806|1730;2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|39948;2|201174|84998|1643822|1643826|84108;2|1239|186801|186802|186806;2|1239|186801|186802|186807|2740;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|437755,Complete,Atrayees
bsdb:128/2/2,Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,atrophic gastric,gastric cancer,NA,37,74,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Portiera",2|1224|28216|206351|1499392|57739;2|1224|1236|135619|28256|235572,Complete,Atrayees
bsdb:128/3/1,Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,superficial gastric,gastric cancer,NA,37,77,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 1,10 January 2021,Rimsha Azhar,"Merit,WikiWorks",The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|1283313;2|1239|186801|3085636|186803|43996;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|437755;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|201174|84998|1643822|1643826|84108;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:128/3/2,Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,superficial gastric,gastric cancer,NA,37,77,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Bacteria|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Portiera",2|1224|28216|80840|80864;2|1224|28216|80840|80864|47420;2|1224|1236|2887326|468|469;2|1224|28216|206351|1499392|57739;2|1224|28216|32003|2008793|378210;2|200940|3024408|213462|213465;2|1224|1236|135619|28256|235572,Complete,Atrayees
bsdb:129/1/1,Study 129,case-control,27346372,10.1038/srep28484,NA,"Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA , Mangalam AK",Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls,Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy controls,Multiple sclerosis,Relapsing remitting MS (RRMS),36,31,Currently taking antibiotics,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 3, Table 2",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Microbial signatures of the gut microbiota of MS patients.
(A) Barplots comparing the abundances of differentially abundant taxa between MS and control. These “signature” taxa are selected by Wilcoxon rank-sum tests and a false discovery rate of 5%. Error bars represent standard errors. Phylum, family and genus-level taxa are plotted.

Differentially abundant taxa between MS and control samples at phylum, family and genus-level.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota",2|1224|1236|72274|135621|351;2|1239|186801|3085636|186803|572511;2|1224|28211|204458|76892;2|1239|186801|3085636|186803|189330;2|976|117743|200644|49546;2|976|117743|200644|49546|237;2|1239|186801|3085636|186803;2|1224|28211|356|82115|13159;2|976|117747|200666|84566|84567;2|1224|1236|72274|135621|286;2|976|117747|200666|84566;2|1224|1236|72274|135621;2|1224,Complete,Peace Sandy
bsdb:129/1/2,Study 129,case-control,27346372,10.1038/srep28484,NA,"Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA , Mangalam AK",Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls,Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy controls,Multiple sclerosis,Relapsing remitting MS (RRMS),36,31,Currently taking antibiotics,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 3, Table 2",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Microbial signatures of the gut microbiota of MS patients. (A) Barplots comparing the abundances of differentially abundant taxa between MS and control. These “signature” taxa are selected by Wilcoxon rank-sum tests and a false discovery rate of 5%. Error bars represent standard errors. Phylum, family and genus-level taxa are plotted.

Differentially abundant taxa between MS and control samples at phylum, family and genus-level.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174;2|201174|84998|1643822|1643826|447020;2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|1239|526524|526525|2810280|100883;2|201174|84998|84999|84107;2|1224|1236|91347|543;2|1239|526524|526525|128827;2|1224|1236|135625|712|724;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|544448|31969|2085|2092|2093;2|976|200643|171549|2005525|375288;2|1224|1236|135625|712;2|976|200643|171549|171551;2|1224;2|1239|909932|1843489|31977,Complete,Peace Sandy
bsdb:130/1/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low Southern European Atlantic Diet,high Southern European Atlantic Diet,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",3,7,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Lora Kasselman,WikiWorks,"Bacterial groups quantified in human fecal samples in subjects with low, intermediate, and high adherence to Southern European Atlantic Diet (SEAD)",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:130/2/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low Southern European Atlantic Diet,intermediate Southern European Atlantic Diet,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",3,21,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Lora Kasselman,WikiWorks,"Bacterial groups quantified in human fecal samples in subjects with low, intermediate, and high adherence to Southern European Atlantic Diet (SEAD)",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:130/3/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,<20 years participants,> 30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Lora Kasselman,WikiWorks,Gut microbiota composition in subjects of different age,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Shaimaa Elsafoury
bsdb:130/4/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,>20 years participants,20-30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,15,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Gut microbiota composition in subjects of different age,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Shaimaa Elsafoury
bsdb:130/5/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,20-30 years participants,> 30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",15,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Gut microbiota composition in subjects of different age,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:130/6/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI < 20,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota",2|201174;2|976,Complete,Shaimaa Elsafoury
bsdb:130/6/2,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI < 20,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:130/7/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI <20,BMI 20-25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,15,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:130/8/1,Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI 20-25,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",15,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Shaimaa Elsafoury
bsdb:131/1/1,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days controls,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S2",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1239|186801|186802|216572|119852;2|976|200643|171549|171551,Complete,Shaimaa Elsafoury
bsdb:131/2/1,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 2,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days Cara Cara,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S3",10 January 2021,Lora Kasselman,"Aiyshaaaa,WikiWorks,Merit","Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|1737404|1737405|1737406;2|1239|186801;2|1239|909932|1843489|31977;2|976|200643|171549|1853231;2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:131/2/2,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 2,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days Cara Cara,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Table 1, Table 2, Table S4",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,2|976|200643|171549|1853231|283168,Complete,Shaimaa Elsafoury
bsdb:131/3/1,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 3,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days Bahia,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S5",10 January 2021,Lora Kasselman,"WikiWorks,Merit","Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|1239|909932|1843489|31977;2|1239|186801;2|1239|186801|186802|31979;2|1239|1737404|1737405|1737406;2|976|200643|171549|1853231,Complete,Shaimaa Elsafoury
bsdb:131/4/1,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 4,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,controls at time 7,Cara Cara,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S7",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",2|976|200643|171549|2005525|375288;2|976|200643|171549|2005519;2|1239|526524|526525|128827|2749846|31971;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|541000;2|1239|186801|186802|216572|244127;2|1224|1236|91347|543;2|976|200643|171549|1853231|574697,Complete,Shaimaa Elsafoury
bsdb:131/4/2,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 4,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,controls at time 7,Cara Cara,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 1, Table 2, Table S8",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,2|1239|186801|3082768|990719,Complete,Shaimaa Elsafoury
bsdb:131/5/1,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 5,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,controls at time 7,Bahia,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S9",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|201174|84998|1643822|1643826|447020;2|1239|91061|186826|81852|1350;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|541000;2|1239|186801|186802|216572|244127,Complete,Shaimaa Elsafoury
bsdb:131/6/1,Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 6,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Bahia at time 7,Cara Cara,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S11",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,2|1239|526524|526525|128827|2749846|31971,Complete,Shaimaa Elsafoury
bsdb:132/1/1,Study 132,randomized controlled trial,30279332,10.3390/nu10101402,NA,"Hess J, Wang Q, Gould T , Slavin J",Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults,Nutrients,2018,"fiber, gut health, laxation, microbiota, mushrooms, prebiotic",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,mushroom,Meat,NA,16,16,3 months,16S,123,Illumina,Linear Regression,0.004,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 9 and text,10 January 2021,Lora Kasselman,WikiWorks,Percent abundance across 5 days of fecal collection for identified abundant bacterial taxa (mushroom diet vs meat diet),increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1239;2|1239|186801|3085636|186803|189330,Complete,Shaimaa Elsafoury
bsdb:132/1/2,Study 132,randomized controlled trial,30279332,10.3390/nu10101402,NA,"Hess J, Wang Q, Gould T , Slavin J",Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults,Nutrients,2018,"fiber, gut health, laxation, microbiota, mushrooms, prebiotic",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,mushroom,Meat,NA,16,16,3 months,16S,123,Illumina,Linear Regression,0.004,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 9 and text,10 January 2021,Lora Kasselman,WikiWorks,Percent abundance across 5 days of fecal collection for identified abundant bacterial taxa (mushroom diet vs meat diet),decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|207244;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:133/1/1,Study 133,"cross-sectional observational, not case-control",30188331,10.1097/GME.0000000000001202,NA,"Yoshikata R, Myint KZ, Ohta H , Ishigaki Y","Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial","Menopause (New York, N.Y.)",2019,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"Equol producer (""healhtier"" diet)","Equol NON producer (""unhealthier"" diet)",cross sectional,45,13,NA,16S,3,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, Table 3, and text",10 January 2021,Lora Kasselman,WikiWorks,TABLE 2. Comparisons of microbial results between equol producers and nonproducers,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,NA
bsdb:133/2/1,Study 133,"cross-sectional observational, not case-control",30188331,10.1097/GME.0000000000001202,NA,"Yoshikata R, Myint KZ, Ohta H , Ishigaki Y","Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial","Menopause (New York, N.Y.)",2019,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"Equol producer (""healhtier"" diet)","Equol NON producer (""unhealthier"" diet)",cross sectional,45,13,NA,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, Table 3, and text",10 January 2021,Lora Kasselman,WikiWorks,TABLE 2. Comparisons of microbial results between equol producers and nonproducers,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,NA
bsdb:134/1/1,Study 134,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager HM, Licht TR, Poulsen SK, Larsen TM , Bahl MI","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before Average Danish Diet,6 months after Average Danish Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",26,26,NA,16S,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,10 January 2021,Lora Kasselman,WikiWorks,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|1239|186801|3085636|186803|2569097|39488;2|201174;2|200940|3031449|213115|194924|872,Complete,Shaimaa Elsafoury
bsdb:134/2/1,Study 134,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager HM, Licht TR, Poulsen SK, Larsen TM , Bahl MI","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before  New Nordic Diet,6 months after  New Nordic Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",36,36,NA,16S,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|2569097|39488;2|1239|91061|186826|33958|1578|1579;2|201174;2|1224|1236|91347|543|561|562;2|200940|3031449|213115|194924|872,Complete,Shaimaa Elsafoury
bsdb:134/2/2,Study 134,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager HM, Licht TR, Poulsen SK, Larsen TM , Bahl MI","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before  New Nordic Diet,6 months after  New Nordic Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",36,36,NA,16S,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",2|976|200643|171549|171550|239759;2157|28890|183925|2158|2159|2172|2173,Complete,Shaimaa Elsafoury
bsdb:135/1/1,Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low animal protein,High animal protein,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
bsdb:135/1/2,Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low animal protein,High animal protein,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,NA
bsdb:135/2/1,Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,high fiber,Low fiber,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota",2|976;2|201174,Complete,NA
bsdb:135/2/2,Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,high fiber,Low fiber,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",decreased,k__Bacteria|p__Actinomycetota,2|201174,Complete,NA
bsdb:136/1/1,Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"high vegetable, fruit, grain","Low vegetable, fruit, grains,",low fiber,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Figure 2,10 January 2021,Lora Kasselman,WikiWorks,"Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary
recommendations. Red branches of the cladogram denote the taxa that were increased in abundance,
while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of
the effect size >2 in LEfSe method (n = 430 paired samples).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|976|200643|171549|815;2|976|200643|171549|171551;2|976|200643|171549|171552;2|976|200643|171549|171550;2|1239|186801|186802|216572;2|1239|909932|1843488|909930;2|1239|909932|1843489|31977;2|1224|28216|80840|995019;2|200940|3031449|213115|194924;2|1239|91061|186826|33958,Complete,NA
bsdb:136/1/2,Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"high vegetable, fruit, grain","Low vegetable, fruit, grains,",low fiber,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Figure 2,10 January 2021,Lora Kasselman,WikiWorks,"Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary
recommendations. Red branches of the cladogram denote the taxa that were increased in abundance,
while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of
the effect size >2 in LEfSe method (n = 430 paired samples).",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|186801|186802|31979|1485;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|459786;2157|28890|183925|2158|2159;2|201174|1760|85004|31953;2|201174|84998|84999|84107;2|1239|91061|1385|90964;2|1239|91061|186826|81852;2|1239|91061|186826|1300;2|1239|186801|3082768|424536;2|1239|186801|186802|31979;2|1239|526524|526525|128827;2|1239;2|1224|28211|204457|41297;2|1224|1236|91347|543;2|74201|203494|48461|203557,Complete,NA
bsdb:136/2/1,Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before dietary intervention,two weeks after a dietry intervention,NA,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|404402|404403;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|1300|1357|1358;2|201174|1760|85004|31953|1678|216816|1679;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1301;2|74201|203494|48461|203557;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300;2|1239|91061|186826|81852;2|74201|203494;2|74201|203494|48461;2|1239|186801|3085636|186803|189330|88431;2|74201;2|1224|28211;2|1239|186801|186802|186806|1730;2|1239|91061;2|201174|1760|85004|31953|1678|1680;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107|102106;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979;2|1239|186801|186802;2|1239|186801;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|1239|186801|3085636|186803|572511,Complete,Shaimaa Elsafoury
bsdb:136/2/2,Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before dietary intervention,two weeks after a dietry intervention,NA,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S8,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|28111;2|28221;2|200940|3031449|213115|194924|872;2|200940|3031449|213115;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050|39485;2|1239|91061|186826|33958;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|815|909656|310297;2|1239|186801|3085636|186803|841|301301;2|1239|186801|186802|216572|1263;2|201174|84998|1643822|1643826|84108;2|201174|84998|1643822|1643826|84108|572010;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|186802|216572|39492,Complete,Fatima
bsdb:137/1/1,Study 137,case-control,31358825,10.1038/s41598-019-45588-z,NA,"Yang TW, Lee WH, Tu SJ, Huang WC, Chen HM, Sun TH, Tsai MC, Wang CC, Chen HY, Huang CC, Shiu BH, Yang TL, Huang HT, Chou YP, Chou CH, Huang YR, Sun YR, Liang C, Lin FM, Ho SY, Chen WL, Yang SF, Ueng KC, Huang HD, Huang CN, Jong YJ , Lin CC",Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,CRC,CRC positive during colonoscopy,104,62,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Figure 4A, Text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and colorectal cancer patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1224|1236|135624|84642|642;2|32066|203490|203491|203492|848,Complete,Claregrieve1
bsdb:137/1/2,Study 137,case-control,31358825,10.1038/s41598-019-45588-z,NA,"Yang TW, Lee WH, Tu SJ, Huang WC, Chen HM, Sun TH, Tsai MC, Wang CC, Chen HY, Huang CC, Shiu BH, Yang TL, Huang HT, Chou YP, Chou CH, Huang YR, Sun YR, Liang C, Lin FM, Ho SY, Chen WL, Yang SF, Ueng KC, Huang HD, Huang CN, Jong YJ , Lin CC",Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,CRC,CRC positive during colonoscopy,104,62,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Figure 4A, Text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and colorectal cancer patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815|816;2|200940|3031449|213115|194924|35832;2|1224|1236|91347|543|544;2|1224|1236|91347|543|413496;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:138/1/1,Study 138,case-control,31065547,10.3389/fcimb.2019.00112,NA,"Zhuang H, Cheng L, Wang Y, Zhang YK, Zhao MF, Liang GD, Zhang MC, Li YG, Zhao JB, Gao YN, Zhou YJ , Liu SL",Dysbiosis of the Gut Microbiome in Lung Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA, biomarkers, gut microbiota, lung cancer, microbial diversity, next generation sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls,lung cancer,lung cancer patients,30,30,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Supplementary Figure S3",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between lung cancer patients and healthy controls by LefSe,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|526524|526525|2810280|1505663;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|1392389;2|1239|91061|1385|90964|69965;2|1224|1236|91347|543|160674;2|1239|91061|1385|90964,Complete,Claregrieve1
bsdb:138/1/2,Study 138,case-control,31065547,10.3389/fcimb.2019.00112,NA,"Zhuang H, Cheng L, Wang Y, Zhang YK, Zhao MF, Liang GD, Zhang MC, Li YG, Zhao JB, Gao YN, Zhou YJ , Liu SL",Dysbiosis of the Gut Microbiome in Lung Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA, biomarkers, gut microbiota, lung cancer, microbial diversity, next generation sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls,lung cancer,lung cancer patients,30,30,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Supplementary Figure S3",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between lung cancer patients and healthy controls by LefSe,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|201174|1760;2|201174|84998|1643822|1643826|447020;2|1224|1236|135622|72275;2|1224|1236|135622;2|1224|1236|135622|72275|226;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106;2|976|200643|171549|2005519|1348911;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|28050;2|1239|91061|1385|186817|175304;2|1239|186801|3085636|186803|437755;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|46205;2|1239|186801|186802|216572|1508657;2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:139/1/1,Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Head and neck squamous cell carcinoma,EFO:0000181,controls,HNSCC,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,129,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking behavior",NA,NA,NA,NA,unchanged,unchanged,Signature 1,Table 2,10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and HNSCC patients,increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Fatima Zohra
bsdb:139/1/2,Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Head and neck squamous cell carcinoma,EFO:0000181,controls,HNSCC,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,129,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking behavior",NA,NA,NA,NA,unchanged,unchanged,Signature 2,Table 2,10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and HNSCC patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena",2|1224|28216;2|976|117743|200644|49546|1016|327575;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|32257;2|976|200643|171549|171552|2974257|425941;2|1239|909932|909929|1843491|970|69823,Complete,Fatima Zohra
bsdb:139/2/1,Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Larynx cancer cases,histologically confirmed incident HNSCC involving the larynx,254,58,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and larynx cancer patients,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",2|1239|91061|186826|186827|46123;2|1224|28216;2|976|117743|200644|49546|1016;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|32257;2|1224|28216|206351|481|32257|502;2|1224|28216|206351|481|482;2|1224|28216|206351;2|1239|91061|186826|1300|1301|1305,Complete,Fatima Zohra
bsdb:139/3/1,Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Pharynx cancer cases,histologically confirmed incident HNSCC involving the pharynx,254,30,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and pharynx cancer patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi",2|201174|1760|2037|2049|1654|544580;2|1224|28216;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|32257;2|1224|28216|206351;2|1239|909932|1843489|31977|29465|419208,Complete,Fatima Zohra
bsdb:139/4/1,Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Oral cavity cancer cases,histologically confirmed incident HNSCC involving the oral cavity,254,41,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and oral cavity cancer patients,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,2|201174|1760|2037|2049|1654,Complete,Fatima Zohra
bsdb:139/4/2,Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Oral cavity cancer cases,histologically confirmed incident HNSCC involving the oral cavity,254,41,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and oral cavity cancer patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra",2|1224|28216|206351|481|482|490;2|1239|1737404|1737405|1570339|543311|33033,Complete,Fatima Zohra
bsdb:140/1/1,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sclerosis,multiple sclerosis patients,43,60,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,increased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Micromonospora,k__Archaea|p__Euryarchaeota",2157|28890|183925|2158|2159|2172;2|74201|203494|48461|1647988|239934;2|201174|1760|85008|28056|84593;2157|28890,Complete,Claregrieve1
bsdb:140/1/2,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sclerosis,multiple sclerosis patients,43,60,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,2|976|200643|171549|1853231|574697,Complete,Claregrieve1
bsdb:140/2/1,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,multiple sclerosis patients,patients with multiple sclerosis,43,60,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Micromonospora,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Archaea|p__Euryarchaeota",2|201174|1760|85008|28056|84593;2157|28890|183925|2158|2159|2172;2|74201|203494|48461|1647988|239934;2157|28890,Complete,Claregrieve1
bsdb:140/2/2,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,multiple sclerosis patients,patients with multiple sclerosis,43,60,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,2|976|200643|171549|1853231|574697,Complete,Claregrieve1
bsdb:140/3/1,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Illumina MiSeq,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|203557|2735,Complete,Claregrieve1
bsdb:140/3/2,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Illumina MiSeq,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|1853231|574697;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:140/4/1,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Roche 454,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Archaea|p__Euryarchaeota,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium",2|74201|203494|48461|1647988|239934;2157|28890;2157|28890|183925|2158|2159|2172;2|74201|203494|48461|203557|2735,Complete,Claregrieve1
bsdb:140/4/2,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Roche 454,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|1853231|574697;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:140/5/1,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:140/5/2,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,2|1239|186801|186802|31979|1266,Complete,Claregrieve1
bsdb:140/6/1,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis patients,28,32,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Roche 454,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:140/6/2,Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis patients,28,32,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Roche 454,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,2|1239|186801|186802|31979|1266,Complete,Claregrieve1
bsdb:141/1/1,Study 141,prospective cohort,30633889,10.1016/j.trsl.2018.12.005,NA,"Brown RG, Al-Memar M, Marchesi JR, Lee YS, Smith A, Chan D, Lewis H, Kindinger L, Terzidou V, Bourne T, Bennett PR , MacIntyre DA",Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes,Translational research : the journal of laboratory and clinical medicine,2019,NA,Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Preterm premature rupture of the membranes,MONDO:0012511,controls,PPROM,(PPROM) preterm premature rupture of the membranes,36,60,9 months,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"body mass index,ethnic group,gestational age,maternal age",NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The effect size for each of the differentially abundant species was estimated using LDA,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|1737404|1737405|1570339|165779;2|201174|1760|2037|2049;2|1239|909932|1843489|31977|39948|309120;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|165779|33036;2|1239|1737404|1737405|1570339;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|2974257|386414;2|1239|909932|1843489|31977;2|1239|909932;2|32066|203490|203491;2|32066;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803;2|976|200643|171549|171552;2|976|200643|171549;2|976;2|976|200643|171549|171552|838;2|976|200643;2|1239|91061|186826|1300|1301;2|1239|186801|186802;2|1239|186801;2|1239|91061|186826|1300,Complete,Atrayees
bsdb:141/1/2,Study 141,prospective cohort,30633889,10.1016/j.trsl.2018.12.005,NA,"Brown RG, Al-Memar M, Marchesi JR, Lee YS, Smith A, Chan D, Lewis H, Kindinger L, Terzidou V, Bourne T, Bennett PR , MacIntyre DA",Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes,Translational research : the journal of laboratory and clinical medicine,2019,NA,Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Preterm premature rupture of the membranes,MONDO:0012511,controls,PPROM,(PPROM) preterm premature rupture of the membranes,36,60,9 months,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"body mass index,ethnic group,gestational age,maternal age",NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The effect size for each of the differentially abundant species was estimated using LDA,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota",2|1239|91061|186826|33958|2742598|1633;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061;2|1239,Complete,Atrayees
bsdb:142/1/1,Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,HNSCC,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample,25,17,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 6, Sup Fig1",10 January 2021,Utsav Patel,"WikiWorks,Aiyshaaaa",Relative abundance of oral microbiome in HNSCC patients and controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|29465,Complete,Rimsha Azhar
bsdb:142/1/2,Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,HNSCC,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample,25,17,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 6, Sup Fig1",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in HNSCC patients and controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|1236|135625|712|416916;2|1224|28216|80840|119060|47670;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|32066|203490|203491|1129771|32067,Complete,Rimsha Azhar
bsdb:142/2/1,Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,HPV -,HPV +,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who are HPV+,4,7,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 6, Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in HNSCC HPV + and HPV -,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella",2|1239|91061|186826|33958|1578;2|976|117743|200644|2762318|1013,Complete,Rimsha Azhar
bsdb:142/2/2,Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,HPV -,HPV +,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who are HPV+,4,7,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 6, Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in HNSCC HPV + and HPV -,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|28216|206351|481|538;2|1224|28216|206351|481|482;2|32066|203490|203491|1129771|32067,Complete,Rimsha Azhar
bsdb:142/3/1,Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,surgery,chemotherapy-radiation and surgery,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who received chemo/radiation and surgery,5,13,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,Rimsha Azhar
bsdb:142/3/2,Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,surgery,chemotherapy-radiation and surgery,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who received chemo/radiation and surgery,5,13,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6, text",19 December 2022,Claregrieve1,Claregrieve1,Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|1236|135625|712|724;2|1224|1236|135625|712|416916;2|32066|203490|203491|1129771|32067,Complete,Claregrieve1
bsdb:143/1/1,Study 143,"cross-sectional observational, not case-control",30239655,10.1093/ecco-jcc/jjy136,NA,"Kiernan MG, Coffey JC, McDermott K, Cotter PD, Cabrera-Rubio R, Kiely PA , Dunne CP",The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis,Journal of Crohn's & colitis,2019,NA,Experiment 1,Ireland,Homo sapiens,Mesenteric lymph node,UBERON:0002509,Inflammatory bowel disease,EFO:0003767,Ulcerative colitis,Crohn's disease,histopathologivally diagnosed ulcerative colitis and crohn's disease,8,5,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,increased,NA,NA,increased,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,WikiWorks,Abundance of phyla in MLN of crohn's disease (CD) and ulcerative colitis (UC) patients,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Rimsha Azhar
bsdb:143/2/1,Study 143,"cross-sectional observational, not case-control",30239655,10.1093/ecco-jcc/jjy136,NA,"Kiernan MG, Coffey JC, McDermott K, Cotter PD, Cabrera-Rubio R, Kiely PA , Dunne CP",The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis,Journal of Crohn's & colitis,2019,NA,Experiment 2,Ireland,Homo sapiens,Mesenteric lymph node,UBERON:0002509,Inflammatory bowel disease,EFO:0003767,Ulcerative colitis,Crohn's disease,histopathologivally diagnosed ulcerative colitis and crohn's disease,8,5,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,NA,NA,increased,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,WikiWorks,Abundance of phyla in MLN of crohn's disease (CD) and ulcerative colitis (UC) patients,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Rimsha Azhar
bsdb:144/1/1,Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),moderately polluted region (B),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,40,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239;2|201174;2|1239|186801;2|201174|1760;2|1239|186801|186802;2|201174|1760|2037;2|1239|186801|3085636|186803;2|201174|1760|85006|1268;2|201174|1760|2037|2049;2|1239|186801|186802|541000;2|201174|1760|85006|1268|32207;2|1239|186801|3085636|186803|265975;2|1224|28216|206351|481|482;2|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
bsdb:144/1/2,Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),moderately polluted region (B),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,40,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,"Merit,WikiWorks","Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549;2|976|200643;2|976;2|976|117743|200644;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1224|1236|72274;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:144/2/1,Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239;2|1224;2|201174;2|1239|186801;2|1239|186801|186802|541000;2|1224|1236;2|1224|28211;2|1239|186801|186802;2|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:144/2/2,Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,"Merit,WikiWorks","Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549;2|976|200643;2|976;2|29547|3031852|213849|72294|194;2|29547|3031852|213849;2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1224|28216|206351;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:144/3/1,Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,moderately poluuted region (B),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",40,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|1224;2|1224|1236;2|1224|28211;2|1224|1236|72274,Complete,Shaimaa Elsafoury
bsdb:144/3/2,Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,moderately poluuted region (B),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",40,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|32066;2|201174|1760;2|32066|203490;2|201174|1760|2037;2|32066|203490|203491;2|1224|28216|206351;2|29547|3031852|213849;2|201174|1760|85006|1268;2|32066|203490|203491|203492;2|1224|28216|206351|481;2|32066|203490|203491|1129771;2|201174|1760|2037|2049;2|201174|1760|85006|1268|32207;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|265975;2|201174|1760|2037|2049|1654;2|29547|3031852|213849|72294|194;2|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
bsdb:145/1/1,Study 145,case-control,15987522,10.1186/1479-5876-3-27,NA,"Mager DL, Haffajee AD, Devlin PM, Norris CM, Posner MR , Goodson JM","The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects",Journal of translational medicine,2005,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"disgnosed oral squamous cell carcinoma via biopsy, age 18 years or older and immunocompetent",229,45,3 months,NA,NA,DNA-DNA Hybridization,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,"age,sex,smoking behavior",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1 , Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in oral squamous cell carcinoma patients and controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea",2|976|200643|171549|171552|838|28132;2|976|117743|200644|49546|1016|1017;2|1239|91061|186826|1300|1301|28037;2|976|117743|200644|49546|1016|1018,Complete,Rimsha Azhar
bsdb:145/1/2,Study 145,case-control,15987522,10.1186/1479-5876-3-27,NA,"Mager DL, Haffajee AD, Devlin PM, Norris CM, Posner MR , Goodson JM","The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects",Journal of translational medicine,2005,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"disgnosed oral squamous cell carcinoma via biopsy, age 18 years or older and immunocompetent",229,45,3 months,NA,NA,DNA-DNA Hybridization,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,"age,sex,smoking behavior",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1 , Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in oral squamous cell carcinoma patients and controls,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum",2|32066|203490|203491|1129771|32067|40542;2|1239|186801|3085636|186803|1164882|467210,Complete,Rimsha Azhar
bsdb:146/1/1,Study 146,case-control,28924229,10.1038/s41598-017-11779-9,NA,"Zhao H, Chu M, Huang Z, Yang X, Ran S, Hu B, Zhang C , Liang J",Variations in oral microbiota associated with oral cancer,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases",40,40,2 weeks,16S,45,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 1c, Figure 3b, 3c, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota associated with oral cancer,increased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Spirochaetota",2|544448|31969|2085|2092|2093;2|203691|203692|136|2845253|157;2|29547|3031852|213849|72294|194;2|1224|28216|206351|481|538;2|1239|909932|909929|1843491|82202;2|976|200643|171549|171552|1283313;2|32066|203490|203491|203492|848;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|39948;2|1239|186801|3082720|186804|1257;2|1239|186801|3082720|3118655|44259;2|1239|186801|186802|186807|2740;2|1239|186801|3085636|186803|43996;2|1239|1737404|1737405|1570339|543311;2|976|117743|200644|49546|1016;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803;2|976;2|32066;2|203691,Complete,Rimsha Azhar
bsdb:146/1/2,Study 146,case-control,28924229,10.1038/s41598-017-11779-9,NA,"Zhao H, Chu M, Huang Z, Yang X, Ran S, Hu B, Zhang C , Liang J",Variations in oral microbiota associated with oral cancer,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases",40,40,2 weeks,16S,45,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 1c, Figure 3b, 3c, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota associated with oral cancer,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota",2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|186828|117563;2|1224|28216|80840|119060|47670;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|201174|1760|85004|31953|196081;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|1654;2|201174;2|1239,Complete,Rimsha Azhar
bsdb:147/1/1,Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Squamous cell carcinoma,EFO:0000707,controls,laryngeal squamous cell carcinoma (LSCC),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|43996;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1224|28216|80840|119060|32008;2|1239|186801|3082720|186804,Complete,Rimsha Azhar
bsdb:147/1/2,Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Squamous cell carcinoma,EFO:0000707,controls,laryngeal squamous cell carcinoma (LSCC),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207,Complete,Rimsha Azhar
bsdb:147/2/1,Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Site 2 (site below the epiglottis in the throat),Site 1 (upper portion of throat near the epiglottis),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Candidatus Saccharibacteria",2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|32067;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|91061|186826|186828|117563;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|265975;2|201174|84998|84999|1643824|1380;2|1239|186801|3085636|186803|437755;2|95818,Complete,Rimsha Azhar
bsdb:147/2/2,Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Site 2 (site below the epiglottis in the throat),Site 1 (upper portion of throat near the epiglottis),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|544448|31969|2085|2092|2093;2|1239|186801|3082720|3118655|44259;2|1239|186801|3085636|186803|43996;2|1224|28216|206351|481|538;2|203691|203692|136|2845253|157;2|1224|1236|135625|712|416916;2|1239|186801|3082720|186804,Complete,Rimsha Azhar
bsdb:148/1/1,Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,NIR-PCOS - NIR(Non-Insulin Resistance),NIR-PCOS - PCOS without insulin resistance,8,8,Administration of antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:148/1/2,Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,NIR-PCOS - NIR(Non-Insulin Resistance),NIR-PCOS - PCOS without insulin resistance,8,8,Administration of antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Peace Sandy
bsdb:148/2/1,Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,IR-PCOS IR-(Insulin Resistance),PCOS with Insulin resistance,8,9,Administration of antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|28050,Complete,Peace Sandy
bsdb:148/2/2,Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,IR-PCOS IR-(Insulin Resistance),PCOS with Insulin resistance,8,9,Administration of antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Peace Sandy
bsdb:148/3/1,Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,NIR-PCOS - NIR(Non-Insulin Resistance),IR-PCOS IR-(Insulin Resistance),PCOS with Insulin Resistance,8,9,Administration of antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643,Complete,Peace Sandy
bsdb:148/3/2,Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,NIR-PCOS - NIR(Non-Insulin Resistance),IR-PCOS IR-(Insulin Resistance),PCOS with Insulin Resistance,8,9,Administration of antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239,Complete,Peace Sandy
bsdb:149/1/1,Study 149,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O, Murugesan S, Nirmalkar K, Alcaraz LD, Hoyo-Vadillo C, Pizano-Zárate ML , García-Mena J",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,"Cholesterol, Gut microbiome, High-throughput sequencing, Mexican children, Obesity, Triglycerides",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight children,Obese children,Obese children aged between 9 and 11 years-old,10,10,None.,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4A,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing","Differentially abundant bacterial genera, families, or species in obese children compared to normal weight children.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:149/1/2,Study 149,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O, Murugesan S, Nirmalkar K, Alcaraz LD, Hoyo-Vadillo C, Pizano-Zárate ML , García-Mena J",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,"Cholesterol, Gut microbiome, High-throughput sequencing, Mexican children, Obesity, Triglycerides",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight children,Obese children,Obese children aged between 9 and 11 years-old,10,10,None.,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4A,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing","Differentially abundant bacterial genera, families, or species in obese children compared to normal weight children.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Archaea|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA",2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815;2|976|200643|171549|815|816|674529;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|291644;2|976|200643|171549|815|816|371601;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|33042|410072;2|28221;2|200940|3024418|213118;2157|28889|183924|114380|2272;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|2719313|358743;2|1239|526524|526525|128827|61170;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1239|91061|186826|1300|1301|1308;2|1239|909932|1843489|31977|29465|29466;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|186801|3085636|186803|658087;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1263|457412,Complete,ChiomaBlessing
bsdb:150/1/1,Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Healthy controls,Throat cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",29,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota composition associated with a risk of Throat Cancer,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales",2|1224|1236|72274|135621|286;2|1224|1236|135625|712|416916;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1508657;2|1224|28216|80840|119060|47670;2|976|200643|171549|815|909656;2|976|200643|171549|815|816;2|976|200643|171549|171552;2|1224|1236|72274|135621|351;2|976|200643|171549|815;2|1224|28216|80840|119060;2|1224|28216|80840;2|1224|28211;2|1224|28211|766,Complete,Fatima Zohra
bsdb:150/1/2,Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Healthy controls,Throat cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",29,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,"Lwaldron,WikiWorks",Variations in oral microbiota composition associated with a risk of Throat Cancer,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|1236|135625|712|713;2|1239|186801|3082720|3030910|109326;2|976|117743|200644|2762318|59735;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|363464;2|95818;2|1239|186801;2|201174|1760|85007|1653;2|201174|1760|85007;2|201174|1760|85007|1653|1716;2|29547;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1506553;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1239|909932;2|1224|28216|206351|481|482;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|201174|1760|85006|1268|32207;2|1239|909932|909929;2|1239|909932|909929|1843491|970;2|203691|203692|136|137;2|203691|203692|136;2|203691|203692;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Fatima
bsdb:150/2/1,Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Vocal cord polyp,Cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",9,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota composition associated with a risk of Throat Cancer,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",2|1224|1236|91347|543|547;2|1224|1236|135625|712|416916;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351,Complete,Fatima Zohra
bsdb:150/2/2,Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Vocal cord polyp,Cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",9,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota composition associated with a risk of Throat Cancer,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|186801|3082720|3118655|44259;2|1224|1236|135625|712|713;2|29547|3031852|213849|72293|209;2|976|200643|171549|171550;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|841;2|1239|186801|3082720|3030910|109326;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|43994;2|32066|203490;2|32066;2|32066|203490|203491;2|32066|203490|203491|203492;2|32066|203490|203491|1129771;2|1239|186801|3082720|186804;2|95818;2|976|117747|200666;2|976|117747;2|976|200643|171549|1840213;2|29547|3031852|213849|72293;2|363464;2|1224|28211|204458|76892;2|1224|28211|204458;2|1239|186801|3085636|1185407;2|200940|3031449|213115|194924;2|200940|3031449|213115,Complete,Fatima Zohra
bsdb:151/1/1,Study 151,case-control,30081953,10.1186/s40168-018-0515-3,NA,"Zhu J, Liao M, Yao Z, Liang W, Li Q, Liu J, Yang H, Ji Y, Wei W, Tan A, Liang S, Chen Y, Lin H, Zhu X, Huang S, Tian J, Tang R, Wang Q , Mo Z",Breast cancer in postmenopausal women is associated with an altered gut metagenome,Microbiome,2018,"Breast cancer, Gut microbiota, Immunity, Metabolism, Metagenomic analyses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,controls,Postmenopausal breast cancer patients,Postmenopausal breast cancer patients,46,44,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,unchanged,Signature 1,Table 2 and Supplementary Table S4,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of the different species between postmenopausal breast cancer patients and postmenopausal healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio cholerae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia rettgeri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia amylovora,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis|s__Sodalis glossinidius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia enterocolitica,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella putrefaciens",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|620|624;2|1224|1236|91347|1903414|583|584;2|1224|1236|91347|543|620|621;2|1224|1236|135623|641|662|666;2|1224|1236|91347|543|561|564;2|1224|1236|91347|543|620|623;2|1224|1236|2887326|468|469|470;2|1224|1236|2887326|468|469|40214;2|1224|1236|91347|1903414|586|587;2|1239|91061|186826|33958|2742598|97478;2|976|200643|171549|171551|836|281920;2|32066|203490|203491|203492|848|851;2|1224|1236|91347|543|544|545;2|200940|3031449|213115|194924|872|901;2|1239|91061|186826|81852|1350|1353;2|1224|1236|91347|543|590|28901;2|1224|1236|91347|1903409|551|552;2|1224|1236|91347|2812006|84565|63612;2|1224|1236|2887326|468|469|40216;2|32066|203490|203491|203492|848|856;2|1239|909932|1843488|909930|904|187327;2|976|200643|171549|171552|838|419005;2|1224|1236|91347|1903411|629|630;2|1239|1737404|1737405|1570339|165779|33037;2|1224|1236|135622|267890|22|24,Complete,Fatima Zohra
bsdb:151/1/2,Study 151,case-control,30081953,10.1186/s40168-018-0515-3,NA,"Zhu J, Liao M, Yao Z, Liang W, Li Q, Liu J, Yang H, Ji Y, Wei W, Tan A, Liang S, Chen Y, Lin H, Zhu X, Huang S, Tian J, Tang R, Wang Q , Mo Z",Breast cancer in postmenopausal women is associated with an altered gut metagenome,Microbiome,2018,"Breast cancer, Gut microbiota, Immunity, Metabolism, Metagenomic analyses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,controls,Postmenopausal breast cancer patients,Postmenopausal breast cancer patients,46,44,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,unchanged,Signature 2,Table 2 and Supplementary Table S4,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of the different species between postmenopausal breast cancer patients and postmenopausal healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella melitensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",2|1239|186801|3085636|186803|28050|39485;2|1224|1236|91347|543|561|208962;2|29547|3031852|213849|72294|194|199;2|1239|186801|3085636|186803|841|360807;2|1224|28211|356|118882|234|29459;2|1239|91061|186826|33958|2742598|1633,Complete,Fatima Zohra
bsdb:152/1/1,Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|1239|186801|3085636|186803|189330;2|1224|1236|91347|1903414|581;2|1224|1236|91347|1903414|583;2|1239|186801|186802|216572|1263;2|1224|1236|135622|267890|22;2|1224|1236|135624|83763|83770,Complete,Claregrieve1
bsdb:152/1/2,Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1224|1236|135619|28256|2745;2|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:152/2/1,Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patients,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Table 3, Figure 5",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",2|976|200643|171549|815|816|46506;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561|562;2|1224|1236;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|310297;2|1224;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|360807,Complete,Claregrieve1
bsdb:152/2/2,Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patients,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Table 3, Figure 5",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales",2|1239|909932|1843488|909930;2|1239|909932;2|1239|909932|1843488|909930|33024;2|1239|909932|909929,Complete,Claregrieve1
bsdb:153/1/1,Study 153,"cross-sectional observational, not case-control",31379800,10.3389/fmicb.2019.01664,NA,"Ma X, Chi C, Fan L, Dong B, Shao X, Xie S, Li M , Xue W",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,"cancer, microbiome, prostate, prostate cancer, prostatic fluid",Experiment 1,China,Homo sapiens,Prostate gland secretion,UBERON:0004796,Prostate cancer,MONDO:0008315,non-prostate cancer,prostate cancer,Prostate cancer  commonest male malignant tumors determined by pathology of prostate biopsy,27,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy",Analysis of the specific microbial species differences. (A) The differences in microbial species between the two groups were explored.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826|186828|2747;2|1239|91061|1385|186817|129337;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:153/1/2,Study 153,"cross-sectional observational, not case-control",31379800,10.3389/fmicb.2019.01664,NA,"Ma X, Chi C, Fan L, Dong B, Shao X, Xie S, Li M , Xue W",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,"cancer, microbiome, prostate, prostate cancer, prostatic fluid",Experiment 1,China,Homo sapiens,Prostate gland secretion,UBERON:0004796,Prostate cancer,MONDO:0008315,non-prostate cancer,prostate cancer,Prostate cancer  commonest male malignant tumors determined by pathology of prostate biopsy,27,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,unchanged,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy",Analysis of the specific microbial species differences. (A) The differences in microbial species between the two groups were explored.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus",2|1239|186801|3082720|3118656|114627;2|1224|1236|91347|543|413496;2|1239|91061|186826|81852|1350;2|1239|91061|1385|186822|44249,Complete,Peace Sandy
bsdb:154/1/1,Study 154,case-control,31250341,10.1007/s11684-019-0695-7,NA,"Zhang H, Chang Y, Zheng Q, Zhang R, Hu C , Jia W",Altered intestinal microbiota associated with colorectal cancer,Frontiers of medicine,2019,"Devosia, Eubacterium, colorectal cancer (CRC), gut microbiota, intestinal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer,diagnosed only with colorectal cancer with endoscopy,14,9,30 days,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3, Supplementary table 2, table 2",10 January 2021,Fatima Zohra,WikiWorks,Altered intestinal microbiota associated with colorectal cancer,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium",2|1224|28211|356|45401;2|1224|28211|356|2831106|46913;2|1224|28211|356;2|1224|28211;2|1239|91061|1385|186822|44249;2|1239|91061|1385|186822;2|976|117743|200644|2762318|59732,Complete,Atrayees
bsdb:154/1/2,Study 154,case-control,31250341,10.1007/s11684-019-0695-7,NA,"Zhang H, Chang Y, Zheng Q, Zhang R, Hu C , Jia W",Altered intestinal microbiota associated with colorectal cancer,Frontiers of medicine,2019,"Devosia, Eubacterium, colorectal cancer (CRC), gut microbiota, intestinal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer,diagnosed only with colorectal cancer with endoscopy,14,9,30 days,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3, Supplementary table 2, table 2",10 January 2021,Fatima Zohra,WikiWorks,Altered intestinal microbiota associated with colorectal cancer,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|186801|186802|31979;2|28221;2|200940|3031449|213115;2|1239|186801|186802|186806|1730;2|1224|1236|91347|543|570;2|32066|203490|203491|1129771|32067;2|1239|909932|1843488|909930|33024;2|1239|186801|3082720|3030910|86331;2|1224|1236|91347|1903411|613,Complete,Atrayees
bsdb:155/1/1,Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Adenocarcinoma (EAC),diagnosed with easophageal cancer anytime after oral wash sample collection,160,81,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|976|200643|171549|2005525|195950|28112;2|201174|1760|2037|2049|2529408|181487;2|1239|909932|1843489|31977|29465;2|1239|909932|909929|1843491|970,Complete,Fatima Zohra
bsdb:155/1/2,Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Adenocarcinoma (EAC),diagnosed with easophageal cancer anytime after oral wash sample collection,160,81,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|976|200643|171549|171552|1283313;2|1239|186801|3085636|186803|265975;2|1239|526524|526525|128827|123375;2|1224|28216|206351|481|482;2|201174|1760|85007|1653|1716|61592;2|976|200643|171549|171552|2974257|425941;2|1239|91061|186826|1300|1301|1313;2|1239|186801|3085636|186803|1164882|617123;2|1239|186801|3085636|186803|265975|1501329;2|1239|526524|526525|128827|123375|102148;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|490;2|1224|1236|135625|712|724,Complete,Fatima Zohra
bsdb:155/2/1,Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),diagnosed with easophageal cancer anytime after oral wash sample collection,50,25,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria weaveri,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii",2|976|200643|171549|171552|2974257|425941;2|976|117743|200644|2762318|59735;2|1224|28216|206351|481|482|28091;2|203691|203692|136|2845253|157|69710,Complete,Fatima Zohra
bsdb:155/2/2,Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),diagnosed with easophageal cancer anytime after oral wash sample collection,50,25,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus",2|1239|186801|3085636|186803;2|976|200643|171549|171552|838;2|1224|1236|135625|712|416916|732,Complete,Fatima Zohra
bsdb:156/1/1,Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,88,116,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543;2|1224;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061;2|1239|91061|186826;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|976|200643|171549|171551;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|201174|1760;2|201174;2|1239|909932|1843489|31977|29465;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3082768|990719|990721;2|1239|186801|3082768|990719;2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:156/1/2,Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,88,116,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|186801|186802;2|1239|186801;2|1239;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|1506553,Complete,Shaimaa Elsafoury
bsdb:156/2/1,Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,48,48,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary figure 3,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",2|1239|526524|526525|128827|1729679;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061;2|1239|91061|186826;2|1224|1236|91347|543|570;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|201174|1760;2|201174;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|29465;2|1239|186801|3082768|990719,Complete,Shaimaa Elsafoury
bsdb:156/2/2,Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,48,48,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary figure 3,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1224|28216|80840;2|1224|28216;2|1239|186801;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|1506553,Complete,Shaimaa Elsafoury
bsdb:157/1/1,Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Dysplasia,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,63,87,1 month,16S,34,Roche454,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,number of teeth measurement,oral hygiene,sex,smoking status",NA,decreased,unchanged,NA,NA,NA,Signature 1,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Relative abundance of significant microbiota in the ESCC group compared to the Dysplasia group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|186801|3082720|3118655|44259;2|1239|91061|186826|33958|1578;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|91061|186826|186827|46123,Complete,ChiomaBlessing
bsdb:157/1/2,Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Dysplasia,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,63,87,1 month,16S,34,Roche454,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,number of teeth measurement,oral hygiene,sex,smoking status",NA,decreased,unchanged,NA,NA,NA,Signature 2,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Relative abundance of significant microbiota in the ESCC group compared to the Dysplasia group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|1224|1236|135625|712|416916;2|201174|84998|84999|1643824|1380;2|1239|526524|526525|128827|118747;2|29547|3031852|213849|72294|194;2|1239|186801|3085636|186803|43996;2|201174|1760|85007|1653|1716;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28216|80840|75682|963;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|186807|2740;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465;2|1224|1236|135615|868|2717,Complete,ChiomaBlessing
bsdb:157/2/1,Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Healthy controls,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,85,87,1 month,16S,34,Roche454,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,oral hygiene,sex,smoking status",NA,decreased,decreased,NA,NA,NA,Signature 1,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",2|976|200643|171549|815|816;2|976|117743|200644|49546|1016;2|976|117743|200644|2762318|308865;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|830,Complete,ChiomaBlessing
bsdb:157/2/2,Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Healthy controls,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,85,87,1 month,16S,34,Roche454,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,oral hygiene,sex,smoking status",NA,decreased,decreased,NA,NA,NA,Signature 2,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group,decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|544448|31969|186329|2146|2147;2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|416916;2|201174|84998|84999|1643824|1380;2|1239|526524|526525|128827|118747;2|1239|186801|3085636|186803|830;2|29547|3031852|213849|72294|194;2|1224|1236|135615|868|2717;2|1239|186801|3085636|186803|43996;2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|39948;2|1239|186801|3082720|3118655|44259;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|201174|1760|85006|1268|32207;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|32067,Complete,ChiomaBlessing
bsdb:158/1/1,Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,Metastats,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Significant differences of the predominant taxa from lung cancer patients and healthy volunteers,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976;2|32066;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|203492|848;2|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:158/1/2,Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,Metastats,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Significant differences of the predominant taxa from lung cancer patients and healthy volunteers,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1239;2|1224|1236|91347|543|579;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|547;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,Claregrieve1
bsdb:158/2/1,Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,LEfSe,0.05,TRUE,4,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbiota from patients with lung cancer and healthy volunteers,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549;2|976;2|976|200643;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1224|1236|91347|543|570;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:158/2/2,Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,LEfSe,0.05,TRUE,4,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbiota from patients with lung cancer and healthy volunteers,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239|186801;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|547;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239;2|1224|1236;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|1224;2|1224|1236|91347|543|620;2|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:159/1/1,Study 159,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R, Liu H, Li X, Yang Q, Jia L, Zheng Y , Li W",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,NA,Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Gingival disease,EFO:0009670,before,1 month after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of microbiota that showed statistically significant differences among three different time points,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|1224|1236|135625|712|713;2|976|117743|200644|49546|1016,Complete,NA
bsdb:159/2/1,Study 159,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R, Liu H, Li X, Yang Q, Jia L, Zheng Y , Li W",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Gingival disease,EFO:0009670,before,3 months after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of microbiota that showed statistically significant differences among three different time points,increased,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,2|976|117743|200644|49546|1016,Complete,NA
bsdb:159/2/2,Study 159,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R, Liu H, Li X, Yang Q, Jia L, Zheng Y , Li W",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Gingival disease,EFO:0009670,before,3 months after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Relative abundance of microbiota that showed statistically significant differences among three different time points,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus",2|1239|91061|186826|186828|117563;2|1239|91061|186826|1300|1301|1303|1077464,Complete,NA
bsdb:160/1/1,Study 160,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M , Punyadeera C",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,"biomarker, oral cancer, oral microbiome, oral rinse, saliva",Experiment 1,Australia,Homo sapiens,Mouth,UBERON:0000165,Head and neck carcinoma,MONDO:0002038,High-risk individuals,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),11,32,NA,16S,678,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1B, Supp. Table 2, Text",10 January 2021,Utsav Patel,WikiWorks,The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",2|976|200643|171549|2005523|346096;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836;2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|713;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|416916;2|1224|28216|80840|119060|47670,Complete,Atrayees
bsdb:160/2/1,Study 160,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M , Punyadeera C",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,"biomarker, oral cancer, oral microbiome, oral rinse, saliva",Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Head and neck carcinoma,MONDO:0002038,Normal Healthy Controls,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),20,31,NA,16S,678,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Supp. Table 2, Text",10 January 2021,Utsav Patel,"WikiWorks,Atrayees",The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,2|1239|186801|3085636|186803|265975,Complete,Atrayees
bsdb:160/2/2,Study 160,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M , Punyadeera C",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,"biomarker, oral cancer, oral microbiome, oral rinse, saliva",Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Head and neck carcinoma,MONDO:0002038,Normal Healthy Controls,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),20,31,NA,16S,678,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 1B, Supp. Table 2, Text",10 January 2021,Utsav Patel,WikiWorks,The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|724;2|201174|1760|85007|1653|1716;2|976|200643|171549|2005523|346096;2|976|200643|171549|171551|836;2|976|117743|200644|49546|1016,Complete,Atrayees
bsdb:161/1/1,Study 161,case-control,31205521,10.7150/jca.28077,NA,"Zhang W, Luo J, Dong X, Zhao S, Hao Y, Peng C, Shi H, Zhou Y, Shan L, Sun Q, Li Y , Zhao X",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,Healthy controls,NSCLC,Newly diagnosed NSCLC (non-small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 3 (B),10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","(b) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant bacterial
taxa between non-small cell lung cancer patients and healthy controls. Only taxa meeting an LDA significant threshold > 4.0 are shown. Red (HC) indicates the healthy controls, and green (NSCLC), non-small cell lung cancer group",increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",2|1224;2|1224|28216;2|1224|28216|80840;2|1239|91061;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826;2|1224|28216|80840|119060;2|1224|28216|80840|119060|47670,Complete,Peace Sandy
bsdb:161/1/2,Study 161,case-control,31205521,10.7150/jca.28077,NA,"Zhang W, Luo J, Dong X, Zhao S, Hao Y, Peng C, Shi H, Zhou Y, Shan L, Sun Q, Li Y , Zhao X",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,Healthy controls,NSCLC,Newly diagnosed NSCLC (non-small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 3 (B),10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","(b) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant bacterial taxa between non-small cell lung cancer patients and healthy controls. Only taxa meeting an LDA significant threshold > 4.0 are shown. Red (HC) indicates the healthy controls, and green (NSCLC), non-small cell lung cancer group",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552;2|976;2|976|200643;2|976|200643|171549,Complete,Peace Sandy
bsdb:162/1/1,Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy control,lung cancer group,newly diagnosed lung cancer patients by histopathology and computed tomography,16,30,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,WikiWorks,Comparison of relative abundant microbiome at family level between cancer groups and healthy controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:162/2/1,Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls + other lung cancer groups,CEA group,newly diagnosed lung cancer patients who are CEA-positive,35,11,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of relatively abundant microbiota between CEA group and other study groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|976|200643|171549|815;2|1239|91061|186826|1300,Complete,Claregrieve1
bsdb:162/3/1,Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls + other lung cancer groups,NSE group,newly diagnosed lung cancer patients who are NSE positive,37,9,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant microbiota between NSE group and the other study groups,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|91347|543;2|32066|203490|203491|203492;2|74201|203494|48461|203557,Complete,Claregrieve1
bsdb:162/4/1,Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy controls,CYF group,newly diagnosed lung cancer patients who are CYFRA positive,16,10,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Relative microbial abundance between CYF group and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|91347|543;2|32066|203490|203491|203492;2|74201|203494|48461|203557,Complete,Claregrieve1
bsdb:162/5/1,Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy controls + other lung cancer groups,CYF group,newly diagnosed lung cancer patients who are CYFRA positive,36,10,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,11 November 2022,Claregrieve1,Claregrieve1,Relative microbial abundance between CYF group and other study groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:163/1/1,Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 1,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 3, Text",10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|872;2|32066|203490|203491|1129771;2|1239|186801|3085636|186803|437755;2|1239|909932|909929|1843491|55506;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157,Complete,Atrayees
bsdb:163/1/2,Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 1,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 3, Text",10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|186801|3085636|186803|43996;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|1224|1236|135625|712;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:163/2/1,Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 2,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Supplementary Figure S4,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174;2|1224|1236|135624;2|1224|28211;2|976|200643|171549;2|976|200643;2|976;2|201174|1760|85004;2|201174|1760|85007|1653;2|28221;2|1239|526524|526525;2|1239|526524;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743;2|1239|909932;2|1224|1236|135625|712;2|976|200643|171549|171552;2|1224;2|1239|909932|909929;2|976|117747|200666;2|976|117747;2|203691|203692|136|137|146;2|203691|203692|136|137;2|203691|203692|136;2|203691;2|1224|1236|135624|83763;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Atrayees
bsdb:163/2/2,Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 2,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Supplementary Figure S4,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239|91061;2|1224|1236;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:164/1/1,Study 164,case-control,26457297,10.1155/2015/173729,NA,"Hu J, Han S, Chen Y , Ji Z",Variations of Tongue Coating Microbiota in Patients with Gastric Cancer,BioMed research international,2015,NA,Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,16,34,2 months,16S,234,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Table 4, text",10 January 2021,Rimsha Azhar,WikiWorks,Relative abundances of selected tongue coating microbial taxa in 34 gastric cancer subjects and 16 control subjects.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota",2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049|1654;2|32066|203490|203491|1129771|32067;2|201174,Complete,Atrayees
bsdb:164/1/2,Study 164,case-control,26457297,10.1155/2015/173729,NA,"Hu J, Han S, Chen Y , Ji Z",Variations of Tongue Coating Microbiota in Patients with Gastric Cancer,BioMed research international,2015,NA,Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,16,34,2 months,16S,234,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Table 4, text",10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",Relative abundances of selected tongue coating microbial taxa in 34 gastric cancer subjects and 16 control subjects.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|28216|206351|481|482;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|976|200643|171549|171551|836;2|1224;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:165/1/1,Study 165,case-control,31245306,10.3389/fcimb.2019.00206,NA,"Li F, Wang M, Wang J, Li R , Zhang Y",Alterations to the Gut Microbiota and Their Correlation With Inflammatory Factors in Chronic Kidney Disease,Frontiers in cellular and infection microbiology,2019,"16S rDNA deep sequencing, Akkermansia, chronic kidney disease, gut microbiota, inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease patients,individuals diagnosed with chronic kidney disease because they exhibited an effective glomerular filtration rate of <60mL/min for a 3 month period,22,50,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Taxonomic differences in fecal microbiota exhibited by patients with chronic kidney disease compared with healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|201174;2|201174|1760|2037;2|201174|1760;2|976|200643|171549|171552|1283313;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107;2|201174|84998|84999;2|200940|3031449|213115|194924|872;2|1224|28211|356|119045;2|1224|28211|356|119045|407;2|976|200643|171549|171552|577309,Complete,Claregrieve1
bsdb:165/1/2,Study 165,case-control,31245306,10.3389/fcimb.2019.00206,NA,"Li F, Wang M, Wang J, Li R , Zhang Y",Alterations to the Gut Microbiota and Their Correlation With Inflammatory Factors in Chronic Kidney Disease,Frontiers in cellular and infection microbiology,2019,"16S rDNA deep sequencing, Akkermansia, chronic kidney disease, gut microbiota, inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease patients,individuals diagnosed with chronic kidney disease because they exhibited an effective glomerular filtration rate of <60mL/min for a 3 month period,22,50,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2a,10 January 2021,Fatima Zohra,"Lwaldron,Claregrieve1,WikiWorks",Taxonomic differences in fecal microbiota exhibited by patients with chronic kidney disease compared with healthy controls,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Deferribacterota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Synergistota,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",2|74201|203494|48461|1647988|239934;2|1239|526524|526525|128827|174708;2|1239|91061;2|1224|28216;2|1224|28216|80840;2|29547|3031852|213849;2|200930|68337|191393|191394;2|200930|68337|191393;2|200930|68337;2|200930;2|201174|84998|1643822|1643826|580024;2|29547;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|201174|1760|85006|1268;2|200930|68337|191393|2945020|248038;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|265975;2|1224|28216|80840|995019|577310;2|201174|84998|84999|84107|1427376;2|508458|649775|649776|3029088|638847;2|201174|1760|85006|1268|32207;2|1224|28216|80840|995019;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775|649776|649777|2753;2|508458;2|508458|649775;2|74201;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461,Complete,Claregrieve1
bsdb:166/1/1,Study 166,case-control,30088332,10.1002/mbo3.678,NA,"Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F , Wang Y",Altered gut microbiota and microbial biomarkers associated with chronic kidney disease,MicrobiologyOpen,2019,"chronic kidney disease, gut microbiota, hemodialysis, intestinal dysbiosis, microbial biomarker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,patients with chronic kidney disease,24,49,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of gut bacteria between the HC and chronic kidney disease groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976;2|976|200643;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|526524|526525|2810280|1505663;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|946234;2|1224|1236;2|1239|91061|186826|81850;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|1769710;2|1224|1236|91347|543|620;2|1239|91061|186826|33958|46255;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|33039;2|1239|526524|526525|128827|1522,Complete,Claregrieve1
bsdb:166/1/2,Study 166,case-control,30088332,10.1002/mbo3.678,NA,"Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F , Wang Y",Altered gut microbiota and microbial biomarkers associated with chronic kidney disease,MicrobiologyOpen,2019,"chronic kidney disease, gut microbiota, hemodialysis, intestinal dysbiosis, microbial biomarker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,patients with chronic kidney disease,24,49,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,10 January 2021,Fatima Zohra,WikiWorks,Comparison of gut bacteria between the HC and chronic kidney disease groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota",2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1506577;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|186802|541000;2|201174|84998|84999|84107|102106;2|1239|186801|186802|3085642|580596;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|186828|2747;2|1239|186801|3085636|186803|1766253|39491;2|976|200643|171549|171552;2|1239|909932|1843489|31977|39948;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977;2|1239|186801;2|1239|186801|186802;2|1239,Complete,Claregrieve1
bsdb:167/1/1,Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 1,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 4,OSCC  confirmed by biopsy and pathological findings,51,90,No antibiotics treatment at the time of sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 4 group compared to healthy control group,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus",2|1224|1236|135625|712|416916|739;2|976|200643|171549|171552|1283313|1872471;2|201174|1760|85004|31953|419014|419015;2|1239|909932|1843489|31977|156454|156456;2|976|200643|171549|815|816|28113;2|29547|3031852|213849|72294|194|824;2|29547|3031852|213849|72294|194|205;2|1239|909932|909929|1843491|82202;2|1239|909932|1843489|31977|39948|39950;2|1224|28216|206351|481|538|539;2|1224|1236|91347|543|561|562;2|1239|186801|3082720|3118655|44259|143361;2|32066|203490|203491|203492|848|860;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|724|727;2|32066|203490|203491|1129771|32067|104608;2|1224|28216|206351|481|482|495;2|1224|28216|206351|481|482|1107316;2|1239|186801|3085636|186803|265975|1969407;2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|3082720|186804;2|976|200643|171549|171551|836|1924944;2|1239|909932|909929|1843491|970|2053611;2|1239|909932|909929|1843491|970|69823;2|1239|91061|186826|1300|1301|76860,Complete,Atrayees
bsdb:167/1/2,Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 1,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 4,OSCC  confirmed by biopsy and pathological findings,51,90,No antibiotics treatment at the time of sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 4 group compared to healthy control group,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae",2|201174|1760|2037|2049|1654|52769;2|1239|91061|186826|186828|117563|46124;2|976|200643|171549|171552|2974257|425941;2|976|200643|171549|171552|838|28132;2|32066|203490|203491|1129771|2755140|157692;2|201174|1760|2037|2049|2529408|52768,Complete,Atrayees
bsdb:167/2/1,Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 2,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 1,OSCC  confirmed by biopsy and pathological findings,51,41,No antibiotics treatment at the time of sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Supplementary Figure 5A,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging  in Stage 1 group compared to healthy control group,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus",2|29547|3031852|213849|72294|194|205;2|1239|186801|3082720|3118655|44259|143361;2|32066|203490|203491|203492|848|860;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|724|727;2|1224|28216|206351|481|482|1107316;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|171551|836|1924944;2|1239|91061|186826|1300|1301|76860,Complete,ChiomaBlessing
bsdb:167/2/2,Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 2,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 1,OSCC  confirmed by biopsy and pathological findings,51,41,No antibiotics treatment at the time of sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Supplementary Figure 5A,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 1 group compared to healthy control group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",2|1224|1236|135625|712|724|729;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|2529408|1660;2|1239|909932|1843489|31977|29465|29466,Complete,ChiomaBlessing
bsdb:167/3/1,Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 3,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 2 & 3,OSCC  confirmed by biopsy and pathological findings,51,66,No antibiotics treatment at the time of sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 1,Supplementary Figure 5B,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stages 2 & 3 group compared to healthy control group,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus",2|1224|1236|135625|712|416916|739;2|1239|909932|1843489|31977|156454|156456;2|29547|3031852|213849|72294|194|824;2|29547|3031852|213849|72294|194|205;2|1239|186801|186802|186806|1730;2|1239|186801|3082720|3118655|44259|143361;2|32066|203490|203491|203492|848|860;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|724|727;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|171551|836|1924944;2|1239|909932|909929|1843491|970|69823;2|1239|91061|186826|1300|1301|76860,Complete,ChiomaBlessing
bsdb:167/3/2,Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 3,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 2 & 3,OSCC  confirmed by biopsy and pathological findings,51,66,No antibiotics treatment at the time of sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 2,Supplementary Figure 5B,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stages 2 & 3 group compared to healthy control group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875",2|1224|1236|135625|712|724|729;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|2529408|1660;2|1239|91061|186826|1300|1301|28037;2|1239|909932|1843489|31977|29465|29466;2|221235|1226342,Complete,ChiomaBlessing
bsdb:168/1/1,Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",22,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow tongue coating patients and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota",2|1224|28216|80840|119060;2|1224|1236|135615|868;2|1224|28216|80840|80864;2|1224|28216|80840|80864|283;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224,Complete,Claregrieve1
bsdb:168/1/2,Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",22,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow tongue coating patients and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",2|201174|1760|85004|31953;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|95818|2093818|2093825|2171986|1331051;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|3120161|1481960;2|201174|1760|85004|31953|196081,Complete,Claregrieve1
bsdb:168/2/1,Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,chronic hepatitis B white tongue coating patients,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",25,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Fatima,Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow and white tongue coating patients,increased,"k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota",2|363464;2|544448|31969|2085|2092|2093;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224,Complete,Claregrieve1
bsdb:168/2/2,Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,chronic hepatitis B white tongue coating patients,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",25,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow and white tongue coating patients,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976;2|1239|186801|3085636|186803|43996;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:168/3/1,Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 3,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B white tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a white tongue coating",22,25,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between healthy controls and chronic hepatitis B white tongue coating patients,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|117743|200644|2762318|59735;2|1239|526524|526525|128827|118747;2|1239|909932|909929|1843491|82202;2|976|200643|171549|171551;2|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:168/3/2,Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 3,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B white tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a white tongue coating",22,25,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between healthy controls and chronic hepatitis B white tongue coating patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1224|28216|206351|481|194195;2|1224|1236|135615|868;2|544448|31969|2085|2092;2|1239|186801|186802|186806|113286;2|201174|1760|85004|31953|196081,Complete,Claregrieve1
bsdb:169/1/1,Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thin tongue coating GC patient,gastric cancer with different tongue coatings,90,25,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 1,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Ampelomyces",2|1224|28216|80840|119060|47670;2|976|117743|200644|49546|1016|327575;2759|4751|4890|147541|92860|5020|50729,Complete,Atrayees
bsdb:169/1/2,Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thin tongue coating GC patient,gastric cancer with different tongue coatings,90,25,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 1,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium equiseti",2|1239|186801|3085636|186803|1213720;2|1239|909932|1843489|31977|906|187326;2|1239|186801|186802|186806|1730|142586;2759|4751|5204|162481|231213;2759|4751|4890|147550|5125|110618|5506|61235,Complete,Atrayees
bsdb:169/2/1,Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thick tongue coating GC patient,gastric cancer with different tongue coatings,72,43,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,increased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum",2|95818;2|1239|186801|186802|541000;2|1239|909932|1843489|31977|906|187326;2|1239|909932|909929|1843491|970|69823;2|976|200643|171549|171552|2974251|439703;2|1239|186801|186802|543314|35518,Complete,Atrayees
bsdb:169/2/2,Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thick tongue coating GC patient,gastric cancer with different tongue coatings,72,43,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales",2|1224|1236|2887326|468|469|108980;2|1239|91061|186826|33958|2767887|1624;2759|4751|4890|147550|5125,Complete,Atrayees
bsdb:169/3/1,Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 3,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,yellow-thick tongue coating GC patient,gastric cancer with different tongue coatings,95,20,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 4,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter sp. NP39,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",2|1239|186801|186802|541000;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|539738|1378|84135;2|976|117743|200644|49546|1016|1019;2|1224|1236|135625|712|724|729;2|1224|1236|72274|2887365|2742|479370;2|1224|28216|80840|119060,Complete,Atrayees
bsdb:169/4/1,Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 4,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,yellow-thin coating GC patient,gastric cancer with yellow thin coating,88,27,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,18 August 2023,Atrayees,Atrayees,LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium halotolerans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma",2759|4751|4890|147541|2726946|452563|5498|1052096;2759|4751|4890|147550|5125|5129|5543,Complete,Atrayees
bsdb:170/1/1,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,none,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85007;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:170/1/2,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,none,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|1236|2887326|468;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:170/2/1,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,paired contralateral non-cancerous site in lung cancer patients,paired contralateral non-cancerous site samples from patients with diagnosis of lung cancer established by histological confirmation,18,24,none,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743|200644|49546|237;2|1224|1236|135625|712|724;2|1239|91061|186826;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:170/2/2,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,paired contralateral non-cancerous site in lung cancer patients,paired contralateral non-cancerous site samples from patients with diagnosis of lung cancer established by histological confirmation,18,24,none,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|1224|1236|2887326|468|469;2|1239|186801|3085636|186803;2|1224|1236|2887326|468;2|1224|1236|72274,Complete,Claregrieve1
bsdb:170/3/1,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 3,China,Homo sapiens,Lung,UBERON:0002048,Sampling site,EFO:0000688,paired contralateral non-cancerous site (TN),cancerous site (T),patients with diagnosis of lung cancer established by histological confirmation,24,24,none,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",Differentially abundant taxa between T (patients in cancerous site) and TN (contralateral non-cancerous site) groups,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1239|91061|1385;2|95818;2|1239|909932|1843489|31977|39948,Complete,Folakunmi
bsdb:170/4/1,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 4,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics,cancerous site with no antibiotics,patients who have diagnosis of lung cancer established by histological confirmation,8,13,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 1,Supplemental Figure S1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics),increased,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,2|976|117743|200644|49546|1016,Complete,Folakunmi
bsdb:170/4/2,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 4,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics,cancerous site with no antibiotics,patients who have diagnosis of lung cancer established by histological confirmation,8,13,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 2,Supplemental Figure S1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics),decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Hydrotalea",2|1224|28216|80840|80864;2|28221;2|1224|1236|2887326|468;2|2818505|32015|29;2|1224|28211|204455|31989|265;2|1224|28211|204455|31989;2|1224|28211|204455;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1224|1236|72274;2|1224|28216|80840;2|1224|28211;2|976|1853228|1853229|563835;2|1239|186801;2|1239|186801|186802|1898207;2|976;2|976|1853228|1853229|563835|1004300,Complete,Folakunmi
bsdb:170/5/1,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 5,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics (No),contralateral non-cancerous site with no antibiotics (TNo),contralateral non-cancerous site samples from lung cancer patients who received no antibiotics in  the prior three months,8,13,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,supplementary figure 1,3 February 2024,Folakunmi,Folakunmi,Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics),increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061;2|1239|91061|186826;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:170/5/2,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 5,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics (No),contralateral non-cancerous site with no antibiotics (TNo),contralateral non-cancerous site samples from lung cancer patients who received no antibiotics in  the prior three months,8,13,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 2,supplementary figure 1,3 February 2024,Folakunmi,Folakunmi,Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics),decreased,"k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Hydrotalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|77133;2|1239|186801|3085636|186803|33042;2|1224|1236|2887326|468|469;2|1224|28211|204458|76892;2|1224|1236|2887326|468;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|28216|80840;2|1224|1236|72274;2|1224|28211;2|976|1853228|1853229|563835|1004300;2|1239|186801|3085636|186803;2|1239|186801;2|1239|186801|186802|1898207,Complete,Folakunmi
bsdb:170/6/1,Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 6,China,Homo sapiens,Lung,UBERON:0002048,Sampling site,EFO:0000688,contralateral non-cancerous site with no antibiotics (TNo),Cancerous site with no antibiotics (To),cancerous site samples from lung cancer patients who received no antibiotics in  the prior three months,13,13,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 1,supplementary figure 1,4 February 2024,Folakunmi,Folakunmi,Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and To (cancerous site samples of lung cancer patients who received no antibiotics prior to 3 months),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|201174|1760|85007|1653;2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:171/1/1,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Digestive system cancer,MONDO:0002516,controls,digestive tract cancer patients,"patients with digestive tract cancers (tongue/pharynx, esophagus, stomach and/or large intestine)",118,59,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 1,"Figure 3, Figure S1",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|495;2|976|200643|171549|171551|836|837;2|201174|1760|2037|2049|2529408|1660;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1306;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:171/1/2,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Digestive system cancer,MONDO:0002516,controls,digestive tract cancer patients,"patients with digestive tract cancers (tongue/pharynx, esophagus, stomach and/or large intestine)",118,59,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 2,"Figure 3, Figure S1",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2047;2|1239|526524|526525|128827|123375|102148,Complete,Claregrieve1
bsdb:171/2/1,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Tongue neoplasm,EFO:0003871,controls,tongue/pharyngeal cancer patients,patients with tongue/pharyngeal cancer,26,13,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between tongue/pharyngeal cancer patients and control subjects,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",2|1224|1236|135625|712|416916|739;2|201174|1760|85007|1653|1716;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1305,Complete,Claregrieve1
bsdb:171/2/2,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Tongue neoplasm,EFO:0003871,controls,tongue/pharyngeal cancer patients,patients with tongue/pharyngeal cancer,26,13,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between tongue/pharyngeal cancer patients and control subjects,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis",2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|113107,Complete,Claregrieve1
bsdb:171/3/1,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,controls,esophageal cancer patients,patients with esophageal cancer,24,12,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,increased,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,WikiWorks,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",2|1224|1236|135625|712|416916|739;2|201174|1760|85007|1653|1716;2|32066|203490|203491|1129771|32067|157688;2|32066|203490|203491|1129771|32067|104608;2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171551|836|837;2|1239|91061|186826|1300|1301|1306,Complete,Claregrieve1
bsdb:171/3/2,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,controls,esophageal cancer patients,patients with esophageal cancer,24,12,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,increased,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis",2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|1300|1301;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301|113107,Complete,Claregrieve1
bsdb:171/4/1,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,controls,colorectal cancer patients,patients with colorectal cancer,48,24,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between colorectal cancer patients and control subjects,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces paraguayensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|906|187326;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975|237576;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|59823;2|201174|1760|2037|2049|2529408|1660;2|201174|1760|85011|2062|1883|68251;2|1239|91061|186826|1300|1301|1318,Complete,Claregrieve1
bsdb:171/4/2,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,controls,colorectal cancer patients,patients with colorectal cancer,48,24,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between colorectal cancer patients and control subjects,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:171/5/1,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,controls,gastric cancer patients,patients with gastric cancer,20,10,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between gastric cancer patients and control subjects,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|32066|203490|203491|203492|848|860;2|1239|91061|1385|539738|1378|84135;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836|837;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:171/5/2,Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,controls,gastric cancer patients,patients with gastric cancer,20,10,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,WikiWorks,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between gastric cancer patients and control subjects,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803;2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:172/1/1,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the lateral border of the tongue in the marijuana usage group VS controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea vestrisii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",2|201174|1760|2037|2049|1654|55565;2|1224|28211|356|2831100|85413;2|1224|28211|356|2831100|85413|151416;2|1224|28216|80840|80864;2|1224|28216|80840|80864|80865;2|1224|28216|80840|80864|80865|80866;2|1224|28216|80840|2975441|88;2|201174|1760|85006|1268;2|1239|186801|3082720|3030910|86331;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465|39777,Complete,Atrayees
bsdb:172/1/2,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the lateral border of the tongue in the marijuana usage group VS controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976;2|976|117743|200644|2762318|59735;2|976|117743|200644|2762318|59735|1962306;2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|2974257|425941;2|976|200643|171549|171551;2|976|200643|171549|171551|836,Complete,Atrayees
bsdb:172/2/1,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the oral pharynx in the marijuana usage group VS controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales",2|1239|186801|3082720|3030910|86331;2|1239|909932;2|1239|186801|186802|541000;2|1239|909932|909929|1843491;2|1239|909932|909929;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|909932|1843489,Complete,Atrayees
bsdb:172/2/2,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the oral pharynx in the marijuana usage group VS controls,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|117743|200644|2762318|59735;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:172/3/1,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,DESeq2,NA,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,table 1,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",DESeq2 differentiation of taxa on the genus level at the lateral border of tongue in the marijuana usage group VS controls,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1224|28211|356|2831100|85413;2|1224|28216|80840|80864|80865;2|1224|28216|80840|119060|47670;2|1224|28216|80840|2975441|88;2|1224|1236|72274|135621|286;2|201174|1760|85006|1268|32207,Complete,Atrayees
bsdb:172/3/2,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,DESeq2,NA,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",DESeq2 differentiation of taxa on the genus level at the lateral border of tongue in the marijuana usage group VS controls,decreased,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,2|976|117743|200644|2762318|59735,Complete,Atrayees
bsdb:172/4/1,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,DESeq2,0.05,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1,24 July 2023,Atrayees,"Atrayees,ChiomaBlessing",DESeq2 differentiation of taxa on the genus level at the oral pharynx in the marijuana usage group VS controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:172/4/2,Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,DESeq2,0.05,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1,24 July 2023,Atrayees,"Atrayees,ChiomaBlessing",DESeq2 differentiation of taxa on the genus level at the oral pharynx in the marijuana usage group VS controls,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus",2|976|117743|200644|2762318|59735;2|1239|91061|1385|186817|400634,Complete,Atrayees
bsdb:173/1/1,Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,healthy controls,pancreatic cancer,patients with pancreatic cancer diagnosed according to international guidelines by comprehensive consideration of clinical symptoms,57,85,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbial communities between PC patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Paraliobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|909932|1843488|909930|904;2|1224|1236|135625|712|416916;2|29547|3031852|213849|72294|194;2|1239|526524|526525|2810280|135858;2|1239|909932|909929|1843491|82202;2|1224|1236|91347|543|413496;2|1224|1236|91347|543|547;2|976|200643|171549|171552|52228;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067;2|1239|91061|1385|186817|200903;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:173/1/2,Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,healthy controls,pancreatic cancer,patients with pancreatic cancer diagnosed according to international guidelines by comprehensive consideration of clinical symptoms,57,85,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbial communities between PC patients and healthy controls,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|244127;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1224|28211|204458|76892|41275;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|216572|946234;2|1239|186801|186802|204475;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1239|186801|3082720|3030910|86331;2|201174|84998|1643822|1643826|651554;2|1224|28216|80840|995019|577310;2|1224|1236|91347|1903414|583;2|1224|28211|356|82115|379;2|1239|186801|186802|216572|44748,Complete,Claregrieve1
bsdb:173/2/1,Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,pancreatic head cancer without obstruction,pancreatic head cancer with obstruction,pancreatic head cancer with obstruction of common bile duct,32,22,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between pancreatic cancer patients with bile obstruction vs without obstruction,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|28216|80840|80864|283;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|140625;2|32066|203490|203491|1129771|32067;2|1239|186801|3085636|186803|115543;2|1239|186801|3085636|186803|46205;2|1239|186801|186802|216572|1200657;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:173/2/2,Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,pancreatic head cancer without obstruction,pancreatic head cancer with obstruction,pancreatic head cancer with obstruction of common bile duct,32,22,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between pancreatic cancer patients with bile obstruction vs without obstruction,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1239|526524|526525|128827|118966;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,Claregrieve1
bsdb:174/1/1,Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Valentina Pineda,WikiWorks,Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Actinomycetota|c__Thermoleophilia,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Bacillota",2|1224|28211|356;2|201174|1497346;2|57723;2|1239|909932|909929|1843491|970;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|28135;2|1239|186801|3085636|186803|1164882;2|1239|91061|186826|1300|1301;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803;2|1224|28211|204457|41297|13687;2|201174;2|1239|186801|3082720|186804;2|976|200643|171549|171552|838|28129;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468;2|976|200643|171549|171552;2|1224|1236|2887326|468|469|470;2|1239|186801|186802;2|1239|186801;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|976|200643|171549;2|976|200643;2|1239|91061;2|976;2|1239|91061|1385;2|1224|1236|72274|135621|286|287;2|1239,Complete,Folakunmi
bsdb:174/1/2,Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure3,10 January 2021,Valentina Pineda,WikiWorks,Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Niveispirillum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus|s__Levilactobacillus brevis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales",2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|1903411|613;2|29547|3031852|213849|72293|209|210;2|29547|3031852|213849|72293;2|29547|3031852|213849|72293|209;2|1224|1236|91347|1903411|613|615;2|29547|3031852|213849;2|29547;2|1224|28211|204441|2829815|1543704;2|1224|28211|204441|41295;2|1224|28211|204441;2|1239|91061|186826|33958|2767886|1580;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1357|1358;2|1224|1236|135614,Complete,Folakunmi
bsdb:174/2/1,Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,H-pylori sequencing negative,H-pylori sequencing positive,H-pylori sequencing positive non-cancerous samples while studying the correlation between non-cancerous tissue microbiota and gastric cancer risk factors,44,18,1 month,16S,45,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,supplementary figure 2,29 February 2024,Folakunmi,Folakunmi,Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Holosporales|f__Candidatus Hepatincolaceae|g__Candidatus Hepatincola,k__Bacteria|p__Myxococcota|o__Polyangiales|f__Polyangiaceae|g__Sorangium|s__Sorangium cellulosum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Methylococcales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Geodermatophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Candidatus Melainabacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii",2|1224|1236|91347|1903411|613;2|1224|1236|91347|1903411|613|615;2|1224|1236|91347|543;2|1224|1236|91347;2|29547|3031852|213849;2|29547|3031852;2|29547|3031852|213849|72293;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293|209|210;2|976|200643|171549|171552|2974257|425941;2|1239|91061;2|1239|91061|186826;2|1224|1236|135622|72275;2|1239;2|1224|28211|1921002|1921003|263960;2|2818505|3031712|49|39643|56;2|1239|91061|1385|90964|69965;2|1224|1236|135622|72275|111142;2|201174|1760|2037|2049|1654|55565;2|1239|91061|186826|186828|292480;2|1224|1236|135618;2|544448|31969|2085|2092|2093;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|201174|1497346|588673|320599|207599;2|201174|1760|85006|85023|110932;2|201174|1760|1643682|85030|1860;2|1224|1236|135625|712|416916;2|1798710;2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654|1655,Complete,Folakunmi
bsdb:174/2/2,Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,H-pylori sequencing negative,H-pylori sequencing positive,H-pylori sequencing positive non-cancerous samples while studying the correlation between non-cancerous tissue microbiota and gastric cancer risk factors,44,18,1 month,16S,45,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,supplementary figure 2,29 February 2024,Folakunmi,Folakunmi,Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552;2|1224|1236|72274|135621|286|287;2|1224;2|1224|1236;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621;2|1224|1236|72274,Complete,Folakunmi
bsdb:174/3/1,Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,supplementary table S5,29 February 2024,Folakunmi,Folakunmi,Significantly differential bacteria identified among the top 20 abundant genera of the cancer  and non-cancer groups,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1224|1236|2887326|468|469;2|1239|91061|1385|186817|1386;2|976|200643|171549|815|816;2|1224|28211|204457|41297|13687;2|1239|186801|3082720|186804|1257;2|1239|91061|186826|1300|1301;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:174/3/2,Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,supplementary table S5,29 February 2024,Folakunmi,Folakunmi,Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|29547|3031852|213849|72293|209;2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:175/1/1,Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the two cohorts with incident primary pancreatic adenocarcinoma,371,361,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and pancreatic cancer cases,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota",2|976|200643|171549|171552|1283313;2|976,Complete,Claregrieve1
bsdb:175/1/2,Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the two cohorts with incident primary pancreatic adenocarcinoma,371,361,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and pancreatic cancer cases,decreased,"k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|32066;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771,Complete,Claregrieve1
bsdb:175/2/1,Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the CPSII cohorts with incident primary pancreatic adenocarcinoma,170,170,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|976|200643|171549|171552|1283313;2|32066;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771,Complete,Claregrieve1
bsdb:175/3/1,Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the PLCO cohorts with incident primary pancreatic adenocarcinoma,201,191,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771,Complete,ChiomaBlessing
bsdb:176/1/1,Study 176,case-control,28320465,10.1186/s40168-017-0250-1,NA,"Chua LL, Rajasuriar R, Azanan MS, Abdullah NK, Tang MS, Lee SC, Woo YL, Lim YA, Ariffin H , Loke P",Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation,Microbiome,2017,"Acute lymphoblastic leukemia, Adult survivors of childhood cancer, Alpha diversity, Immune activation, Inflammation, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Caecum,UBERON:0001153,Leukemia,EFO:0000565,controls,survivors of acute lymphoblastic leukemia,adult surviors of childhood leukemia,61,73,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Figure 2,Supplementary table S1",10 January 2021,Fatima Zohra,WikiWorks,Alterations to microbial communities in adult survivors of acute lymphoblastic leukemia,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Archaea,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|150022;2157;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|201174|1760|2037|2049|1654,Complete,NA
bsdb:176/1/2,Study 176,case-control,28320465,10.1186/s40168-017-0250-1,NA,"Chua LL, Rajasuriar R, Azanan MS, Abdullah NK, Tang MS, Lee SC, Woo YL, Lim YA, Ariffin H , Loke P",Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation,Microbiome,2017,"Acute lymphoblastic leukemia, Adult survivors of childhood cancer, Alpha diversity, Immune activation, Inflammation, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Caecum,UBERON:0001153,Leukemia,EFO:0000565,controls,survivors of acute lymphoblastic leukemia,adult surviors of childhood leukemia,61,73,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,"Figure 2,Supplementary table S1",10 January 2021,Fatima Zohra,WikiWorks,Alterations to microbial communities in adult survivors of acute lymphoblastic leukemia,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",2|976|200643|171549;2|976|200643;2|976;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|976|200643|171549|171550;2|1239|186801|3085636|186803|28050;2|200940|3031449|213115;2|28221;2|200940|3031449|213115|194924,Complete,NA
bsdb:177/1/1,Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 1,Sweden,Homo sapiens,Mucosa of ascending colon,UBERON:0004990,Colorectal cancer,EFO:0005842,control group,colon cancer patients,patients diagnosed with stage I-III colon cancer,14,12,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Table 2, supplemental table S1",10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",Microbiota alterations in colon cancer mucosa samples compared with non cancer control mucosa at colonoscopy,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Mycoplasmatota",2|976;2|200940|3031449|213115|194924|35832;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2157|28890;2|32066;2|32066|203490|203491|203492|848;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|119852;2|1239|186801|3082720|186804|1257;2|544448,Complete,Claregrieve1
bsdb:177/1/2,Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 1,Sweden,Homo sapiens,Mucosa of ascending colon,UBERON:0004990,Colorectal cancer,EFO:0005842,control group,colon cancer patients,patients diagnosed with stage I-III colon cancer,14,12,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Table 2, supplemental table S1",10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",Microbiota alterations in colon cancer mucosa compared with non cancer control mucosa at colonoscopy,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:177/2/1,Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 2,Sweden,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,control group,colon cancer patients (tumor samples),patients diagnosed with stage I-III colon cancer,14,12,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Table 2, supplemental table S1",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Microbiota alterations in colon cancer tumor samples compared with non cancer control mucosa at colonoscopy,increased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2157|28890|183925|2158|2159|2172;2|1239|186801|3082720|186804|1257;2|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:177/3/1,Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 3,Sweden,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control group,colon cancer patients (fecal samples),patients diagnosed with stage I-III colon cancer,21,14,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supppemental table S2, text",10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",Microbiota alterations in colon cancer fecal samples compared with non cancer control fecal samples at colonoscopy,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|186801|3085636|186803|189330;2|1239|186801|3082720|186804|1257,Complete,Claregrieve1
bsdb:177/3/2,Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 3,Sweden,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control group,colon cancer patients (fecal samples),patients diagnosed with stage I-III colon cancer,21,14,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supppemental table S2,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Microbiota alterations in colon cancer fecal samples compared with non cancer control fecal samples at colonoscopy,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Mycoplasmatota",2|1239|186801|3085636|186803|841;2|544448,Complete,NA
bsdb:178/1/1,Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer peritumor group,gastric cancer,60,61,1 month,16S,34,Illumina,LEfSe,2,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae",2|1224|1236|135619;2|1224|1236|135619|28256|2745;2|1224|1236|135619|28256;2|1224|1236|135622|267890;2|1224|1236|135622|267890|22;2|1224|1236|135622;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1224|28211|204458|76892|41275;2|201174|1760|85006|1268|1663;2|201174|1760|85007|1762|1763;2|201174|1760|85007|1762,Complete,Atrayees
bsdb:178/1/2,Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer peritumor group,gastric cancer,60,61,1 month,16S,34,Illumina,LEfSe,2,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales",2|1224|28216|80840|119060|106589;2|1224|28216|80840|119060;2|976|200643|171549|171551;2|1224|1236|118969|444;2|1224|1236|118969|444|445;2|1224|1236|118969,Complete,Atrayees
bsdb:178/2/1,Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor,gastric cancer tumor group,gastric cancer,61,59,1 month,16S,34,Illumina,LEfSe,2,TRUE,2,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|91061;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|909932|909929|1843491|970;2|1224|1236|135619;2|1224|1236|135619|28256|2745;2|1224|1236|135619|28256;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|1224|1236|91347|543;2|1224|1236|91347;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|1263;2|976|200643|171549|171550;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977|906;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:178/2/2,Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor,gastric cancer tumor group,gastric cancer,61,59,1 month,16S,34,Illumina,LEfSe,2,TRUE,2,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota",2|1224|28211|356|82115|379;2|1224|28211|356|82115;2|976;2|1239|909932|909929|1843491|158846;2|1224|1236|135622|267890;2|1224|1236|135622|267890|22;2|1224|1236|135622;2|201174|1760|85007|1762|1763;2|201174|1760|85007|1762;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1224,Complete,Atrayees
bsdb:178/3/1,Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer tumor group,gastric cancer,60,59,1 month,16S,34,Illumina,LEfSe,2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174;2|1224|1236|135622;2|1224|28216|80840|92793;2|1239|91061;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1224|28216|80840;2|1239|91061|186826|186828;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1224|1236|91347;2|1224|1236|91347|543;2|1239;2|1239|91061|1385|539738|1378;2|1239|186801|186802|204475;2|1239|91061|186826|186828|117563;2|1224|2008785|119069|206349;2|1224|2008785|119069;2|1224|2008785|119069|206349|70774;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045;2|1224|28211|356|119045|407;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1239|186801|186802|541000;2|1224|28216|80840|75682;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|1239|186801|3085636|186803|841;2|201174|84995|84996|84997|42255;2|201174|84995|84996|84997;2|201174|84995|84996;2|1239|186801|186802|216572|1263;2|1224|1236|135622|267890|22;2|1224|1236|135622|267890;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Atrayees
bsdb:178/3/2,Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer tumor group,gastric cancer,60,59,1 month,16S,34,Illumina,LEfSe,2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|976;2|976|200643|171549|171551;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|1224|28216|80840|119060;2|1224|28216|80840|119060|106589;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,Atrayees
bsdb:179/1/1,Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1224|1236|135615|868|2717,Complete,Folakunmi
bsdb:179/1/2,Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836,Complete,Folakunmi
bsdb:179/2/1,Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|84998|84999|1643824;2|201174|84998|84999|1643824|1380;2|201174|84998|84999;2|201174|84998,Complete,Folakunmi
bsdb:179/2/2,Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|976|200643|171549|171551;2|976|200643|171549|171551|836,Complete,Folakunmi
bsdb:180/1/1,Study 180,"cross-sectional observational, not case-control",29102920,10.1136/gutjnl-2017-314205,NA,"Ferreira RM, Pereira-Marques J, Pinto-Ribeiro I, Costa JL, Carneiro F, Machado JC , Figueiredo C",Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota,Gut,2018,"Helicobacter pylori, bacterial infection, gastric carcinoma, gastritis",Experiment 1,Portugal,Homo sapiens,Stomach,UBERON:0000945,Gastric carcinoma,EFO:0000178,chronic gastritis,gastric carcinoma,gastric carcinoma,81,54,NA,16S,56,Ion Torrent,LEfSe,0.05,TRUE,4,age,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3, Figure S4",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp.,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium sp.,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales",2|1224|28216|80840|506|222|134375;2|201174;2|1224|28216|80840;2|976|117743|200644|2762318|59732|1871047;2|1224|1236|91347|543|544|1896336;2|1239|186801|186802|31979|1485|1506;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|201174|1760|85007|85025;2|1224|28211|356|69277|28100|1871046;2|1224;2|1224|1236|72274|135621|286|306;2|201174|1760|85007|85025|1827|1831;2|1224|1236|135614|32033;2|1224|1236|135614,Complete,Claregrieve1
bsdb:180/1/2,Study 180,"cross-sectional observational, not case-control",29102920,10.1136/gutjnl-2017-314205,NA,"Ferreira RM, Pereira-Marques J, Pinto-Ribeiro I, Costa JL, Carneiro F, Machado JC , Figueiredo C",Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota,Gut,2018,"Helicobacter pylori, bacterial infection, gastric carcinoma, gastritis",Experiment 1,Portugal,Homo sapiens,Stomach,UBERON:0000945,Gastric carcinoma,EFO:0000178,chronic gastritis,gastric carcinoma,gastric carcinoma,81,54,NA,16S,56,Ion Torrent,LEfSe,0.05,TRUE,4,age,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3, Figure S4",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter sp.,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.",2|1239|91061;2|976|200643;2|976;2|29547|3031852|213849;2|29547;2|1239;2|32066;2|32066|203490;2|29547|3031852|213849|72293|209|218;2|29547|3031852|213849|72293;2|1239|91061|186826;2|1224|28216|206351|481|482|192066;2|1224|28216|206351;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301|1306;2|1239|91061|1385|539738|1378|1966354,Complete,Claregrieve1
bsdb:181/1/1,Study 181,"cross-sectional observational, not case-control",33429936,https://doi.org/10.3390/jpm11010035,NA,"Barandouzi ZA, Lee J, Maas K, Starkweather AR , Cong XS",Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components,Journal of personalized medicine,2021,"food components, irritable bowel syndrome, microbiome, microbiota, nutrients",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy control,IBS,The patient's who have been diagnosed from irritable bowel syndrome(IBS).,21,80,current,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,Figure 2(b),25 October 2022,Fatima,"Fatima,Aiyshaaaa",Taxonomic differences of fecal microbiota between IBS and HC groups,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia",2|74201|203494|48461|1647988|239934;2|1239|91061;2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803;2|1239|91061|186826;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239|909932|1843489|31977|29465;2|74201|203494|48461;2|74201;2|1239|186801|3085636|186803;2|74201|203494,Complete,Aiyshaaaa
bsdb:181/1/2,Study 181,"cross-sectional observational, not case-control",33429936,https://doi.org/10.3390/jpm11010035,NA,"Barandouzi ZA, Lee J, Maas K, Starkweather AR , Cong XS",Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components,Journal of personalized medicine,2021,"food components, irritable bowel syndrome, microbiome, microbiota, nutrients",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy control,IBS,The patient's who have been diagnosed from irritable bowel syndrome(IBS).,21,80,current,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 2,Figure 2,25 October 2022,Fatima,Fatima,Taxonomic differences of fecal microbiota between IBS and HC groups,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Aiyshaaaa
bsdb:182/1/1,Study 182,"cross-sectional observational, not case-control",31215600,10.1590/1678-7757-2018-0635,NA,"Yokoi A, Ekuni D, Hata H, Yamane-Takeuchi M, Maruyama T, Yamanaka R , Morita M",Relationship between acetaldehyde concentration in mouth air and characteristics of microbiota of tongue dorsum in Japanese healthy adults: a cross-sectional study,Journal of applied oral science : revista FOB,2019,NA,Experiment 1,Japan,Homo sapiens,Mouth,UBERON:0000165,Acetaldehyde,CHEBI:15343,low acetaldehyde concentration group,high acetaldehyde concentration group,"The Sensor Gas Chromatograph SGEA-P2 (FIS Inc., Itami, Japan) was used to measure acetaldehyde concentrations in mouth air.",6,6,current use,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Difference in relative abundance of tongue microbiome between High acetaldehyde concentration group and Low acetaldehyde concentration group.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens",2|1239|91061|1385|539738|1378|84135;2|1239|909932|1843489|31977|29465|29466;2|1224|28216|206351|481|482|484,Complete,NA
bsdb:182/1/2,Study 182,"cross-sectional observational, not case-control",31215600,10.1590/1678-7757-2018-0635,NA,"Yokoi A, Ekuni D, Hata H, Yamane-Takeuchi M, Maruyama T, Yamanaka R , Morita M",Relationship between acetaldehyde concentration in mouth air and characteristics of microbiota of tongue dorsum in Japanese healthy adults: a cross-sectional study,Journal of applied oral science : revista FOB,2019,NA,Experiment 1,Japan,Homo sapiens,Mouth,UBERON:0000165,Acetaldehyde,CHEBI:15343,low acetaldehyde concentration group,high acetaldehyde concentration group,"The Sensor Gas Chromatograph SGEA-P2 (FIS Inc., Itami, Japan) was used to measure acetaldehyde concentrations in mouth air.",6,6,current use,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Difference in relative abundance of tongue microbiome between High acetaldehyde concentration group and Low acetaldehyde concentration group.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",2|1239|91061|186826|1300|1301|1318;2|976|200643|171549|171552|838|470565,Complete,NA
bsdb:183/1/1,Study 183,case-control,31764438,10.1097/MPG.0000000000002461,NA,"Kansal S, Catto-Smith AG, Boniface K, Thomas S, Cameron DJ, Oliver M, Alex G, Kirkwood CD , Wagner J",Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease,Journal of pediatric gastroenterology and nutrition,2019,NA,Experiment 1,Australia,Homo sapiens,Ileum,UBERON:0002116,Crohn's disease,EFO:0000384,crohn disease ASCA negative patients,crohn disease ASCA positive patients,Crohn disease anti-Saccharomyces cerevisiae antibody status,39,38,3 months,16S,2,Non-quantitative PCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,2|1239|186801|3085636|186803|2316020|33039,Complete,Atrayees
bsdb:183/1/2,Study 183,case-control,31764438,10.1097/MPG.0000000000002461,NA,"Kansal S, Catto-Smith AG, Boniface K, Thomas S, Cameron DJ, Oliver M, Alex G, Kirkwood CD , Wagner J",Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease,Journal of pediatric gastroenterology and nutrition,2019,NA,Experiment 1,Australia,Homo sapiens,Ileum,UBERON:0002116,Crohn's disease,EFO:0000384,crohn disease ASCA negative patients,crohn disease ASCA positive patients,Crohn disease anti-Saccharomyces cerevisiae antibody status,39,38,3 months,16S,2,Non-quantitative PCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1224|1236|91347|543|547|550;2|1239|186801|186802|216572|216851|853,Complete,Atrayees
bsdb:184/1/1,Study 184,"cross-sectional observational, not case-control,prospective cohort",30117171,10.1002/pros.23713,NA,"Alanee S, El-Zawahry A, Dynda D, Dabaja A, McVary K, Karr M , Braundmeier-Fleming A",A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis,The Prostate,2019,"benign prostate, microbiota, prostate cancer",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Prostate cancer,MONDO:0008315,controls,prostate cancer patients,the association of urinary and fecal microbiota with prostate cancer diagnosis,16,14,28 days,16S,345,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 1, Text",10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",Significant differential OTU frequencies in urine samples of patients with or without prostate cancer,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Atrayees
bsdb:184/1/2,Study 184,"cross-sectional observational, not case-control,prospective cohort",30117171,10.1002/pros.23713,NA,"Alanee S, El-Zawahry A, Dynda D, Dabaja A, McVary K, Karr M , Braundmeier-Fleming A",A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis,The Prostate,2019,"benign prostate, microbiota, prostate cancer",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Prostate cancer,MONDO:0008315,controls,prostate cancer patients,the association of urinary and fecal microbiota with prostate cancer diagnosis,16,14,28 days,16S,345,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 1, text",26 June 2023,Atrayees,Atrayees,Significant differential OTU frequencies in urine samples of patients with or without prostate cancer,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|258514,Complete,Atrayees
bsdb:185/1/1,Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,unchanged,NA,increased,Signature 1,"Figure 2, Sup. figure 2A, Sup. figure 2B",10 January 2021,Valentina Pineda,WikiWorks,Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1224;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|29465;2|1224|1236;2|1224|1236|91347,Complete,Claregrieve1
bsdb:185/1/2,Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,unchanged,NA,increased,Signature 2,"Figure 2, Sup. figure 2A, Sup. figure 2B",10 January 2021,Valentina Pineda,WikiWorks,Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643;2|976|200643|171549,Complete,Claregrieve1
bsdb:185/2/1,Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy gastric cancer (post surgery),gastric cancer,gastric cancer patients,6,20,1 month,16S,NA,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,10 January 2021,Valentina Pineda,WikiWorks,LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group,increased,"k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|508458;2|1239|186801|3085636|186803;2|1224|1236|91347|543|570,Complete,Claregrieve1
bsdb:185/2/2,Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy gastric cancer (post surgery),gastric cancer,gastric cancer patients,6,20,1 month,16S,NA,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,10 January 2021,Valentina Pineda,WikiWorks,LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|74201|203494;2|74201|203494|48461;2|74201|203494|48461|203557;2|74201;2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543|620;2|95818;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552,Complete,Claregrieve1
bsdb:186/2/1,Study 186,laboratory experiment,35387878,http://dx.doi.org/10.1136/gutjnl-2021-325021,https://gut.bmj.com/content/71/12/2439,"Bai X, Wei H, Liu W, Coker OO, Gou H, Liu C, Zhao L, Li C, Zhou Y, Wang G, Kang W, Ng EK , Yu J",Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites,Gut,2022,"BACTERIAL PATHOGENESIS, BILE ACID METABOLISM, COLORECTAL CANCER",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Smoke-free control group intraperitoneally injected with carcinogen azoxymethane (AOM) (10 mg/kg),"Smoke-exposed group intraperitoneally injected with carcinogen, AOM (AOM + Smoking)",Mice exposed to cigarette smoke directly (4% of 2000 mL/ min airflow) 2 hours per day for 28 weeks (at end time point),15,15,NA,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2c,8 March 2023,Busayo,"Busayo,Mcarlson,ChiomaBlessing",Differentially abundant bacteria in smoke-free and smoke-exposed mice (AOM vs AOM + Smoking),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus thuringiensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus velezensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium choerinum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter massiliensis (ex Traore et al. 2017),k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum gordoncarteri,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis",2|1239|91061|1385|186817|1386|1428;2|1239|91061|1385|186817|1386|492670;2|201174|1760|85004|31953|1678|35760;2|201174|84998|1643822|1643826|84111|84112;2|1224|1236|91347|543|561|562;2|201174|84998|1643822|1643826|644652|1841863;2|201174|84998|1643822|1643826|644652|471189;2|201174|84998|1643822|1643826|644652|1335613;2|976|200643|171549|2005473|1918540|2530390;2|201174|84998|84999|1643824|2082587|1871022;2|1239|91061|1385|90964|1279|29388,Complete,ChiomaBlessing
bsdb:186/2/2,Study 186,laboratory experiment,35387878,http://dx.doi.org/10.1136/gutjnl-2021-325021,https://gut.bmj.com/content/71/12/2439,"Bai X, Wei H, Liu W, Coker OO, Gou H, Liu C, Zhao L, Li C, Zhou Y, Wang G, Kang W, Ng EK , Yu J",Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites,Gut,2022,"BACTERIAL PATHOGENESIS, BILE ACID METABOLISM, COLORECTAL CANCER",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Smoke-free control group intraperitoneally injected with carcinogen azoxymethane (AOM) (10 mg/kg),"Smoke-exposed group intraperitoneally injected with carcinogen, AOM (AOM + Smoking)",Mice exposed to cigarette smoke directly (4% of 2000 mL/ min airflow) 2 hours per day for 28 weeks (at end time point),15,15,NA,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2c,8 March 2023,Busayo,"Busayo,Mcarlson,ChiomaBlessing",Differentially abundant bacteria in smoke-free and smoke-exposed mice (AOM vs AOM + Smoking),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium GAM147,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CT06,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis",2|976|200643|171549|815|816|246787;2|1239|186801|186802|2109688;2|1239|526524|526525|128827|2109692;2|1239|91061|186826|33958|2742598|1598;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|375288|2025876;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|821;2|1239|91061|186826|1300|1301|1307,Complete,ChiomaBlessing
bsdb:187/1/1,Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,depot medroxyprogesterone acetate vaginal microbiome (visit 2) among black participants,naive black participants (baseline visit),participants who had not yet been given the medroxyprogesterone acetate treatment at baseline,16,16,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:187/2/1,Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black naive vaginal microbiome (baseline visit ),white naiive vaginal microbiome (baseline),white participants at baseline,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at baseline,increased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,2|1239|1737404|1737405|1570339|150022,Complete,Claregrieve1
bsdb:187/2/2,Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black naive vaginal microbiome (baseline visit ),white naiive vaginal microbiome (baseline),white participants at baseline,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at baseline,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella",2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|177971,Complete,Claregrieve1
bsdb:187/3/1,Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 2),white participants after using depot medroxyprogesterone (visit 2),white participants at visit 2,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at visit 2,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:187/3/2,Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 2),white participants after using depot medroxyprogesterone (visit 2),white participants at visit 2,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at visit 2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|1239|186801|186802|31979|1485;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|168808,Complete,Claregrieve1
bsdb:187/4/1,Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 3),white participants after using depot medroxyprogesterone (visit 3),white participants at visit 3,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differentially abundant genera between Hispanic White and Black women at visit 3,increased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,2|1239|1737404|1737405|1570339|150022,Complete,Claregrieve1
bsdb:187/4/2,Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 3),white participants after using depot medroxyprogesterone (visit 3),white participants at visit 3,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differentially abundant genera between Hispanic White and Black women at visit 3,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|91061|186826|186827|1375;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:188/1/1,Study 188,case-control,30854760,10.1111/1471-0528.15600,NA,"Brown RG, Chan D, Terzidou V, Lee YS, Smith A, Marchesi JR, MacIntyre DA , Bennett PR",Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage,BJOG : an international journal of obstetrics and gynaecology,2019,"Infection, preterm birth, rescue cerclage, vaginal microbiome",Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Cervical cerclage,NCIT:C102763,Vaginal microbiome of asymptomatic women prior to cerclage,Vaginal microbiome of symptomatic women prior ro cerclage,NA,13,7,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Cladogram describing differentially abundant vaginal microbial clades and nodes observed between asymptomatic women and those with symptoms as identified using LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|1239|91061|186826|1300|1301|257758;2|976|200643|171549|171552|838|28130;2|201174|1760|85004|31953|2701|2702;2|201174|1760|85004|31953|2701,Complete,NA
bsdb:188/1/2,Study 188,case-control,30854760,10.1111/1471-0528.15600,NA,"Brown RG, Chan D, Terzidou V, Lee YS, Smith A, Marchesi JR, MacIntyre DA , Bennett PR",Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage,BJOG : an international journal of obstetrics and gynaecology,2019,"Infection, preterm birth, rescue cerclage, vaginal microbiome",Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Cervical cerclage,NCIT:C102763,Vaginal microbiome of asymptomatic women prior to cerclage,Vaginal microbiome of symptomatic women prior ro cerclage,NA,13,7,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Cladogram describing differentially abundant vaginal microbial clades and nodes observed between asymptomatic women and those with symptoms as identified using LEfSe analysis,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,NA
bsdb:189/1/1,Study 189,case-control,29180991,10.3389/fmicb.2017.02222,NA,"Wang J, Wang Y, Zhang X, Liu J, Zhang Q, Zhao Y, Peng J, Feng Q, Dai J, Sun S, Zhao Y, Zhao L, Zhang Y, Hu Y , Zhang M",Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients,Frontiers in microbiology,2017,"16S rRNA gene sequencing, aromatic amino acids, chronic hepatitis B, gut sysbiosis, serum metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B patients,Chronic hepatitis B patients,22,85,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between chronic hepatitis patients and controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|909932|909929|1843491|158846;2|201174|1760|2037|2049|1654;2|1239|186801|186802|31979|1485|1506;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:189/1/2,Study 189,case-control,29180991,10.3389/fmicb.2017.02222,NA,"Wang J, Wang Y, Zhang X, Liu J, Zhang Q, Zhao Y, Peng J, Feng Q, Dai J, Sun S, Zhao Y, Zhao L, Zhang Y, Hu Y , Zhang M",Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients,Frontiers in microbiology,2017,"16S rRNA gene sequencing, aromatic amino acids, chronic hepatitis B, gut sysbiosis, serum metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B patients,Chronic hepatitis B patients,22,85,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2,10 January 2021,Rimsha Azhar,"Fatima,Claregrieve1,WikiWorks",Differential microbial abundance between chronic hepatitis patients and controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|815|816;2|976|200643|171549|1853231|574697;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1224|1236|91347|543;2|1239|186801|3085636|186803;2|1239|186801|186802|1898207;2|201174|84998|1643822|1643826|553372;2|201174|84998|84999|84107;2|1224|1236|91347|543|1940338;2|1224|1236|91347|543;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:190/1/1,Study 190,prospective cohort,30813950,10.1186/s40168-019-0645-2,NA,"Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, González A, Midtvedt T , Eggesbø M",Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month,Microbiome,2019,"Birth cohort, Breast milk, Infant gut microbiome, Short-chain fatty acids, Toxicants",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,one-month age infants exposed to low chemical breast milk (<20th percentile),one-month age infants exposed to high chemical breast milk,infants with high chemical exposure (≥ 80th percentile breast milk toxicant exposure),45,45,2 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,gestational age,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,"Fatima,LGeistlinger,WikiWorks",Differentially abundant sequences in the high vs. low chemical exposure groups.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300,Complete,Claregrieve1
bsdb:190/1/2,Study 190,prospective cohort,30813950,10.1186/s40168-019-0645-2,NA,"Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, González A, Midtvedt T , Eggesbø M",Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month,Microbiome,2019,"Birth cohort, Breast milk, Infant gut microbiome, Short-chain fatty acids, Toxicants",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,one-month age infants exposed to low chemical breast milk (<20th percentile),one-month age infants exposed to high chemical breast milk,infants with high chemical exposure (≥ 80th percentile breast milk toxicant exposure),45,45,2 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,gestational age,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentially abundant sequences in the high vs. low chemical exposure groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:191/1/1,Study 191,"cross-sectional observational, not case-control",30791484,10.3390/nu11020433,NA,"Iino C, Shimoyama T, Iino K, Yokoyama Y, Chinda D, Sakuraba H, Fukuda S , Nakaji S",Daidzein Intake Is Associated with Equol Producing Status through an Increase in the Intestinal Bacteria Responsible for Equol Production,Nutrients,2019,"Asaccharobacter celatus, Slackia isoflavoniconvertens, daidzein, equol, gut microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Equol,CHEBI:34741,equol non-producers,equol producers,The equol production status was defined by a urinary log 10 - transformed equol/daidzein ratio of −1.75 or more as described previously,586,458,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative abundance of species (percentage of the total bacterial 16sRNA).,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens",2|201174|84998|1643822|1643826|447020|446660|394340;2|201174|84998|1643822|1643826|84108|572010,Complete,Atrayees
bsdb:192/1/1,Study 192,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll IM, Ringel-Kulka T, Siddle JP , Ringel Y",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,123,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that differ between D-IBS patients and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347;2|1224|1236|91347|543,Complete,Atrayees
bsdb:192/1/2,Study 192,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll IM, Ringel-Kulka T, Siddle JP , Ringel Y",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,123,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Table 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that differ between D-IBS patients and healthy controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:192/2/1,Study 192,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll IM, Ringel-Kulka T, Siddle JP , Ringel Y",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,6,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that differ between D-IBS patients and healthy controls,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens",2|1224;2|1224|1236;2|1224|1236|91347|543;2|1239|186801|186802|216572|253238,Complete,Atrayees
bsdb:193/1/1,Study 193,prospective cohort,25052961,10.1111/hel.12145,NA,"Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS , Kim JF","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,"16S ribosomal RNA, H. pylori, carcinogenesis, gastric cancer",Experiment 1,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Gastric cancer,MONDO:0001056,chronic gastritis and intestinal metaplasia,gastric cancer,noncardia gastric cancer patients whose diagnosis were confirmed by histopathology,20,11,6 months,16S,5,Roche454,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplemental Fig S1, S2",10 January 2021,Fatima Zohra,WikiWorks,"Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|91061;2|1239|91061|186826|1300,Complete,Folakunmi
bsdb:193/1/2,Study 193,prospective cohort,25052961,10.1111/hel.12145,NA,"Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS , Kim JF","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,"16S ribosomal RNA, H. pylori, carcinogenesis, gastric cancer",Experiment 1,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Gastric cancer,MONDO:0001056,chronic gastritis and intestinal metaplasia,gastric cancer,noncardia gastric cancer patients whose diagnosis were confirmed by histopathology,20,11,6 months,16S,5,Roche454,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Supplemental Fig S1, S2",10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi","Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer",decreased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,2|29547|3031852|213849|72293,Complete,Folakunmi
bsdb:193/2/1,Study 193,prospective cohort,25052961,10.1111/hel.12145,NA,"Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS , Kim JF","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,"16S ribosomal RNA, H. pylori, carcinogenesis, gastric cancer",Experiment 2,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Gastric cancer,MONDO:0001056,H. pylori negative chronic gastritis,H. pylori positive chronic gastritis,H. pylori positive chronic gastritis patients who were diagnosed by conventional laboratory method including rapid urease test and histopathology,0,7,6 months,16S,5,Roche454,NA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Fig S3,10 January 2021,Fatima Zohra,WikiWorks,Comparison of the gastric microbial profiles between H. pylori positive and H. pylori negative chronic gastritis patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",2|1224|28211|356|41294;2|1224|28211|204458|76892;2|1239|91061|186826|33958;2|1224|28216|80840|119060,Complete,Folakunmi
bsdb:194/1/1,Study 194,case-control,30737418,10.1038/s41598-018-38031-2,NA,"Zhou B, Sun C, Huang J, Xia M, Guo E, Li N, Lu H, Shan W, Wu Y, Li Y, Xu X, Weng D, Meng L, Hu J, Gao Q, Ma D , Chen G",The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,normal tissue,ovarian cancer,women diagnosed with high grade ovarian cancer,25,25,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 1,"Figure 2, Fig S3",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","LEfSe was performed to identify the most differentially abundant taxons between ovarian cancer tissues and normal distal fallopian tube tissues.  

(A,C) Histogram of the LDA scores for differentially abundant phyla and genera, respectively. Only taxa meeting an LDA significant threshold of 3.5 are shown. *P < 0.05; **P < 0.01; ***P < 0.001.",increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella osloensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia vermicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter lwoffii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas azotifigens",2|1224;2|1224|28211|356|212791;2|1224|28216|80840|80864|283;2|1239|91061|1385|90964|1279;2|1224|28211|204457|41297|165695;2|1224|28211|356|119045|407;2|1224|28216|80840|119060|106589;2|1224|1236|91347|1903414|586;2|1224|28216|80840|2975441|196013;2|976|1853228|1853229|563835|504481;2|1224|28216|80840|80864|12916;2|1224|28211|204457|41297|13687;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|475|34062;2|1224|28211|204457|41297|165695|13690;2|1224|1236|91347|1903414|586|333965;2|1224|1236|2887326|468|469|28090;2|1224|28211|204457|41297|13687|330920,Complete,Peace Sandy
bsdb:194/1/2,Study 194,case-control,30737418,10.1038/s41598-018-38031-2,NA,"Zhou B, Sun C, Huang J, Xia M, Guo E, Li N, Lu H, Shan W, Wu Y, Li Y, Xu X, Weng D, Meng L, Hu J, Gao Q, Ma D , Chen G",The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,normal tissue,ovarian cancer,women diagnosed with high grade ovarian cancer,25,25,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 2,"Figure 2, Fig S3",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","LEfSe was performed to identify the most differentially abundant taxons between ovarian cancer tissues and normal distal fallopian tube tissues.

(A,C) Histogram of the LDA scores for differentially abundant phyla and genera, respectively. Only taxa meeting an LDA significant threshold of 3.5 are shown. *P < 0.05; **P < 0.01; ***P < 0.001.",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus piscium",2|1239;2|201174;2|57723;2|1239|186801|186802|216572|236752;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1357|1364,Complete,Peace Sandy
bsdb:195/1/1,Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,increased,NA,decreased,Signature 1,"Figure 3, Text",10 January 2021,Rimsha Azhar,WikiWorks,LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia",2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|1903411|629;2|1224|1236|135614;2|1239|186801|3082720|3118655|44259;2|1224|1236|135614|32033;2|1239|186801|3082720|186804;2|1239|186801|186802;2|1239|186801,Complete,Claregrieve1
bsdb:195/1/2,Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,increased,NA,decreased,Signature 2,"Figure 3, Text",10 January 2021,Rimsha Azhar,WikiWorks,LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067;2|976|117743|200644;2|976|117743|200644|49546;2|976|117743;2|976|117743|200644|49546|1016,Complete,Claregrieve1
bsdb:195/2/1,Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,liver cirrhosis,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Figure 4, Text",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic differences in oral microbiota of the CHB and LC groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|186801|3082720|3118655|44259;2|203691|203692|136|137;2|203691|203692|136;2|203691;2|203691|203692;2|203691|203692|136|2845253|157,Complete,Claregrieve1
bsdb:195/2/2,Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,liver cirrhosis,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Figure 4, Text",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic differences in oral microbiota of the CHB and LC groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales",2|1224|28216;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351,Complete,Claregrieve1
bsdb:196/1/1,Study 196,case-control,29525681,10.1016/j.intimp.2018.03.003,NA,"Wang X, Zhang L, Wang Y, Liu X, Zhang H, Liu Y, Shen N, Yang J , Gai Z",Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, IgA, Microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,70,85,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 6b,10 January 2021,Rimsha Azhar,WikiWorks,The most differentially abundant taxa between Henoch-Schönlein Purpura (HSP) and controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|909932|1843489|31977|29465;2|32066|203490;2|32066;2|32066|203490|203491;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|909932|1843489|31977;2|1239|909932|909929|1843491|158846;2|976|200643|171549|171551;2|976|200643|171549|2005525|375288,Complete,Claregrieve1
bsdb:196/1/2,Study 196,case-control,29525681,10.1016/j.intimp.2018.03.003,NA,"Wang X, Zhang L, Wang Y, Liu X, Zhang H, Liu Y, Shen N, Yang J , Gai Z",Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, IgA, Microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,70,85,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 6b,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",The most differentially abundant taxa between Henoch-Schönlein Purpura (HSP) and controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1224|28216|80840|506;2|1224|28216;2|1224|28216|80840;2|1239|186801|3082768|990719;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803;2|1224|28216|80840|995019|577310;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:197/1/1,Study 197,case-control,29031597,10.1016/j.jaci.2017.09.018,NA,"Goldman DL, Chen Z, Shankar V, Tyberg M, Vicencio A , Burk R",Lower airway microbiota and mycobiota in children with severe asthma,The Journal of allergy and clinical immunology,2018,NA,Experiment 1,United States of America,Homo sapiens,Right lung middle lobe bronchiole,UBERON:0012068,Asthma,MONDO:0004979,non-asthma,severe asthma,severe asthma,11,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1a, 1b",10 January 2021,Rimsha Azhar,"Fatima,Claregrieve1,WikiWorks",Differentially abundant genera between severe asthma and non-asthma patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Leucosporidiales|f__Leucosporidiaceae|g__Leucosporidium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pneumocystomycetes|o__Pneumocystales|f__Pneumocystaceae|g__Pneumocystis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|976|117743|200644|49546|1016;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2759|4751|5204|162481|231212|1163720|5277;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2759|4751|4890|147553|37987|44281|4753;2759|4751|5204|162481|231213|1799696|5533;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:197/1/2,Study 197,case-control,29031597,10.1016/j.jaci.2017.09.018,NA,"Goldman DL, Chen Z, Shankar V, Tyberg M, Vicencio A , Burk R",Lower airway microbiota and mycobiota in children with severe asthma,The Journal of allergy and clinical immunology,2018,NA,Experiment 1,United States of America,Homo sapiens,Right lung middle lobe bronchiole,UBERON:0012068,Asthma,MONDO:0004979,non-asthma,severe asthma,severe asthma,11,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1a, 1b",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant genera between severe asthma and non-asthma patients,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricostilbomycetes|o__Agaricostilbales|f__Agaricostilbaceae|g__Sterigmatomyces",2759|4751|5204|155616|5234|1884633|5206;2759|4751|4890|147541|2726946|452563|237557;2|1224|1236|91347|1903414|583;2759|4751|5204|162480|48846|48847|5615,Complete,Claregrieve1
bsdb:198/1/1,Study 198,case-control,30342346,10.1016/j.intimp.2018.10.017,NA,"Chen B, Wang J, Wang Y, Zhang J, Zhao C, Shen N, Yang J, Gai Z , Zhang L",Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, Immunoglobulin, Oral microbiota",Experiment 1,China,Homo sapiens,Mouth,UBERON:0000165,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,66,98,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 6b, 6c",10 January 2021,Rimsha Azhar,WikiWorks,"Histogram of the LDA scores computed for different abundance levels between children with HSP and healthy children, as detected by the LEfSe tool",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|1224|28216|206351;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|1239|909932|1843489|31977|29465;2|1239|909932;2|1239|909932|1843489;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976;2|976|200643;2|976|200643|171549,Complete,NA
bsdb:198/1/2,Study 198,case-control,30342346,10.1016/j.intimp.2018.10.017,NA,"Chen B, Wang J, Wang Y, Zhang J, Zhao C, Shen N, Yang J, Gai Z , Zhang L",Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, Immunoglobulin, Oral microbiota",Experiment 1,China,Homo sapiens,Mouth,UBERON:0000165,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,66,98,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 6b, 6c",10 January 2021,Rimsha Azhar,WikiWorks,"Histogram of the LDA scores computed for different abundance levels between children with HSP and healthy children, as detected by the LEfSe tool",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota",2|1224|1236|135625|712|724;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|28211;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468;2|1224|1236|72274;2|1224|1236;2|1224,Complete,NA
bsdb:199/1/1,Study 199,case-control,31954395,10.1186/s13048-019-0603-4,NA,"Wang Q, Zhao L, Han L, Fu G, Tuo X, Ma S, Li Q, Wang Y, Liang D, Tang M, Sun C, Wang Q, Song Q , Li Q",The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ,Journal of ovarian research,2020,"16S rRNA sequencing, Bacteria, KEGG, Lipopolysaccharide, Ovarian cancer",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,controls,ovarian cancer,preliminary diagnosis of suspected ovarian cancer and undergoing laparotomy,10,6,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 3, Table 2",10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks,LGeistlinger",Differential relative abundance of taxa in ovarian communities between patients in cancer an control group.,increased,"k__Bacteria|p__Aquificota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacteria|p__Chloroflexota|c__Ktedonobacteria|o__Thermogemmatisporales|f__Thermogemmatisporaceae",2|200783;2|29547|3031852|213849;2|1224|1236|91347;2157|28890|183925|2158|2159;2157|28890|183925|2158;2|201174|1760|85006|85023;2|1224|1236|2887326|468;2|203682|203683|112;2|203682;2|1224|1236|72274;2|74201|134549;2|1239|91061|1385|90964;2|1297|188787|68933|188786;2|200795|388447|768667|768668,Complete,Lwaldron
bsdb:199/1/2,Study 199,case-control,31954395,10.1186/s13048-019-0603-4,NA,"Wang Q, Zhao L, Han L, Fu G, Tuo X, Ma S, Li Q, Wang Y, Liang D, Tang M, Sun C, Wang Q, Song Q , Li Q",The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ,Journal of ovarian research,2020,"16S rRNA sequencing, Bacteria, KEGG, Lipopolysaccharide, Ovarian cancer",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,controls,ovarian cancer,preliminary diagnosis of suspected ovarian cancer and undergoing laparotomy,10,6,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3, Table 2",10 January 2021,Fatima Zohra,WikiWorks,Differential relative abundance of taxa in ovarian communities between patients in cancer an control group,decreased,"k__Archaea|p__Thermoproteota,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Archaea|p__Euryarchaeota|c__Archaeoglobi|o__Archaeoglobales|f__Archaeoglobaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanocorpusculaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax",2157|28889;2|976|117747;2157|28890|183963|2235;2|976|117743|200644|49546;2157|28890|183980|2231|2232;2|32066|203490|203491|1129771;2157|28890|224756|2191|88404;2|201174|1760|1643682|85030;2|1239|91061|1385|186822|44249;2157|28890|183963|2235|1644056|2251,Complete,Lwaldron
bsdb:200/1/2,Study 200,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A , Walther-Antonio MRS",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Lower part of vagina,UBERON:0015243,Postmenopausal,EFO:0002721,Pre-menopausal patients,Post-menopausal patients,Post-menopausal patients without Endometrial cancer,49,14,2 weeks,16S,345,Illumina,Wald Test,0.1,TRUE,NA,NA,"obesity,vaginal pH",NA,increased,NA,NA,NA,increased,Signature 2,Figure 2 + Table S1,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Bacterial OTUs differentially enriched among Post-menopausal patients without endometrial cancer compared to Pre-menopausal patients,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Luteococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|29547|3031852|213849|72294|194;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|1737404|1737405|1570339|162290;2|201174|1760|85009|31957|33983;2|1239|186801|186802|186807|2740;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|1239|1737404|1737405|2992719|285105;2|201174|1760|85009|31957|72763;2|201174|1760|2037|2049|184869;2|1239|1737404|1737405|1570339|165779;2|1239;2|201174|1760|85004|31953|419014;2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|437755,Complete,ChiomaBlessing
bsdb:200/2/1,Study 200,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A , Walther-Antonio MRS",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Lower part of vagina,UBERON:0015243,Endometrial cancer,MONDO:0011962,Benign,Endometrial cancer,Patients undergoing hysterectomy for endometrial cancer,67,57,2 weeks,16S,345,Illumina,Wald Test,0.1,TRUE,NA,NA,"body mass index,menopause,vaginal pH",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4 + Table S2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:200/2/2,Study 200,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A , Walther-Antonio MRS",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Lower part of vagina,UBERON:0015243,Endometrial cancer,MONDO:0011962,Benign,Endometrial cancer,Patients undergoing hysterectomy for endometrial cancer,67,57,2 weeks,16S,345,Illumina,Wald Test,0.1,TRUE,NA,NA,"body mass index,menopause,vaginal pH",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4 + Table S2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|28263;2|29547|3031852|213849|72294|194;2|1239|1737404|1737405|1570339|150022;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|162290;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186807|2740;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|2037|2049|184869;2|1239|1737404|1737405|1570339|165779,Complete,ChiomaBlessing
bsdb:201/1/1,Study 201,time series / longitudinal observational,30988420,10.1038/s41598-019-42652-6,NA,"Rashidi A, Kaiser T, Shields-Cutler R, Graiziger C, Holtan SG, Rehman TU, Wasko J, Weisdorf DJ, Dunny G, Khoruts A , Staley C",Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,repeat therapy,induction,acute leukemia patients undergoing chemotherapy,7,13,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2b,10 January 2021,Fatima Zohra,"WikiWorks,Claregrieve1",Composition of microbial communities during induction and repeat therapy in leukemia patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:201/1/2,Study 201,time series / longitudinal observational,30988420,10.1038/s41598-019-42652-6,NA,"Rashidi A, Kaiser T, Shields-Cutler R, Graiziger C, Holtan SG, Rehman TU, Wasko J, Weisdorf DJ, Dunny G, Khoruts A , Staley C",Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,repeat therapy,induction,acute leukemia patients undergoing chemotherapy,7,13,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2b,10 January 2021,Fatima Zohra,"WikiWorks,Claregrieve1",Composition of microbial communities during induction and repeat therapy in leukemia patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|1239|526524|526525|128827|1573536;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|292632;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:202/1/1,Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,children with autism non-mental regression (ANMR),children with autism mental regression (AMR),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5 who had development regression during the first two years of life.,30,18,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1224;2|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:202/2/1,Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism non-mental regression (ANMR),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5 who did not have development regression during the first two years of life.,57,30,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 & Table 3",10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Relative abundances of bacteria in fecal microbiota of children with ANMR ASD and healthy children.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|201174;2|201174|1760;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|2719313|208479;2|201174|1760|85006|85023;2|1239|186801|68295|186814;2|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:202/3/1,Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism mental regression (AMR),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5 who had development regression during the first two years of life.,57,18,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 & Table 3",10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Relative abundances of bacteria in fecal microbiota of children with AMR ASD and healthy children.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|2719313|208479;2|1239|91061|186826|81852|1350;2|201174|1760|85006|85023;2|1224;2|1239|186801|68295|186814,Complete,Claregrieve1
bsdb:202/4/1,Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism spectrum disorders (ASD),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5,57,48,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",2|1239|91061|1385|186817;2|201174|1760|85004|31953;2|201174|1760|85007|1653;2|200940|3031449|213115|213117;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|526524|526525|128827;2|201174|1760|85006|85023;2|1239|91061|1385|186824;2|32066|203490|203491|203492,Complete,Claregrieve1
bsdb:202/4/2,Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism spectrum disorders (ASD),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5,57,48,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:203/1/1,Study 203,case-control,30707176,10.1097/CM9.0000000000000086,NA,"Bai W, Chen S, Tang CS, Qi JG, Cui QH, Xu M, Du JB , Jin HF",Gut microbiota analysis and its significance in vasovagal syncope in children,Chinese medical journal,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Syncope,HP:0001279,healthy children,children with vasovagal syncope,children ages 5-18 who meet diagnostic criteria for vasovagal syncope,20,20,8 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and children with VVS,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,Claregrieve1
bsdb:204/1/1,Study 204,case-control,29791775,10.1111/1471-0528.15299,NA,"Tabatabaei N, Eren AM, Barreiro LB, Yotova V, Dumaine A, Allard C , Fraser WD",Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case-control study,BJOG : an international journal of obstetrics and gynaecology,2019,"16S rRNA, Lactobacillus, bacterial vaginosis, preterm birth, vaginal microbiome",Experiment 1,Canada,Homo sapiens,Vagina,UBERON:0000996,Premature birth,EFO:0003917,mothers whose newborns were delivered at ≥37 getastional weeks,mothers whose newborns were delivered at <34 gestational week,NA,365,17,NA,16S,4,Illumina,NLMIXED,0.05,TRUE,NA,NA,"body mass index,ethnic group,maternal age,parity,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Vaginal microbial oligotype differential relative abundance composition between pregnant women who had early (<34 weeks of gestation) preterm versus full term (≥37 weeks gestation) deliveries,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia solanacearum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1578|33959;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|1685;2|1239|91061|186826|33958|1578|1579;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|147802;2|1224|28216|80840|119060|48736|305;2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:205/1/1,Study 205,"cross-sectional observational, not case-control",23758857,10.1186/1471-2334-13-271,NA,"Gao W, Weng J, Gao Y , Chen X",Comparison of the vaginal microbiota diversity of women with and without human papillomavirus infection: a cross-sectional study,BMC infectious diseases,2013,NA,Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV negative women,HPV positive women,women positive for HPV infection,38,32,1 month,16S,23,NA,Chi-Square,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HPV positive and HPV negative women,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|201174|1760|85004|31953|2701|2702;2|1239|91061|186826|33958|1578|1596,Complete,Claregrieve1
bsdb:206/1/1,Study 206,"cross-sectional observational, not case-control",29317709,10.1038/s41598-017-18596-0,NA,"Hsieh YY, Tung SY, Pan HY, Yen CW, Xu HW, Lin YJ, Deng YF, Hsu WT, Wu CS , Li C",Increased Abundance of Clostridium and Fusobacterium in Gastric Microbiota of Patients with Gastric Cancer in Taiwan,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,patients diagnosed with gastritis,patients diagnosed with gastric cancer,Patients with gastric cancer,16,11,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Valentina Pineda,"Claregrieve1,WikiWorks",Bacteria specifically found in patients with gastric cancer compared with the average counts in gastritis specimens,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium colicanis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|1239|186801|186802|31979|1485|179628;2|32066|203490|203491|203492|848|285729;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|2742598|1598;2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|2974251|28135;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1318,Complete,Claregrieve1
bsdb:207/1/1,Study 207,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu MB, Xu SR, He Y, Deng GH, Sheng HF, Huang XM, Ouyang CY , Zhou HW",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginitis,EFO:1001240,Normal controls,Women with BV,BV assessment with a gram-stain score => 7,30,10,1 month,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between normal controls and women with BV,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|201174;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|526524|526525|128827|118747;2|1239|186801;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802;2|32066;2|32066|203490|203491;2|201174|1760|85004|31953|2701;2|201174|1760|2037|2049|2050;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1224;2|32066|203490|203491|1129771|168808;2|1239|909932|1843489|31977;2|32066|203490|203491|1129771,Complete,Claregrieve1
bsdb:207/1/2,Study 207,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu MB, Xu SR, He Y, Deng GH, Sheng HF, Huang XM, Ouyang CY , Zhou HW",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginitis,EFO:1001240,Normal controls,Women with BV,BV assessment with a gram-stain score => 7,30,10,1 month,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Figure 1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between normal controls and women with BV,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:207/2/1,Study 207,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu MB, Xu SR, He Y, Deng GH, Sheng HF, Huang XM, Ouyang CY , Zhou HW",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginitis,EFO:1001240,Normal controls,Women with BV and VVC,Women infected with both BV and VVC,30,16,1 month,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between normal controls and women with candida vulvovaginitis and BV,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549;2|976;2|976|200643;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Claregrieve1
bsdb:208/1/1,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1a, Text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|186801|186802|31979;2|976|768503|768507|89373;2|201174|1760|85007|85025;2|1239;2|32066;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,Atrayees
bsdb:208/1/2,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1a, Text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|28216|80840|506;2|1239|186801|186802|543314;2|1224|28211|356|69277;2|1224|1236|135614|32033;2|976|117743|200644|49546;2|1224|1236|2887326|468;2|976;2|1224;2|201174;2|74201;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1239|186801|3082720|186804;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:208/2/1,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,LEfSe,2,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1d, Text",10 January 2021,Lucy Mellor,"Merit,WikiWorks",Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae",2|201174|1760|2037;2;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|976|768503|768507|89373;2|201174|1760|85007|85025,Complete,Atrayees
bsdb:208/2/2,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,LEfSe,2,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1d, Text",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",2|1239|909932|1843489|31977|906;2|1239|186801|186802|541000;2|976|117743|200644|49546;2|1224|28211|356|69277;2|1224|28211|356|69277|68287;2|1224|28216|80840|506|222;2|1224|28216|80840|506;2|976|117743|200644;2|201174|84998|1643822|1643826|84111;2|976|117743|200644|49546|237;2|1224|1236|135614|32033;2|1224|1236|135614|32033|40323;2|1239|186801|3082720|3030910|86331;2|976|117743|200644|2762318|59732;2|1239|186801|186802|543314;2|1224|1236|135614;2|1224|28211|204458|76892;2|1224|28216|80840|80864|283,Complete,Atrayees
bsdb:208/3/1,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,LEfSe,2,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia",2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802;2|1239|186801,Complete,Atrayees
bsdb:208/3/2,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,LEfSe,2,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text",10 January 2021,Lucy Mellor,"Merit,WikiWorks",Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|3085636|186803;2|201174|1760|85007|85025,Complete,Atrayees
bsdb:208/4/1,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2c, Text",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:208/4/2,Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2c, Text",10 January 2021,Lucy Mellor,"Merit,WikiWorks",Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|815|816;2|976|200643|171549,Complete,Atrayees
bsdb:209/1/1,Study 209,prospective cohort,32012716,10.3390/microorganisms8020179,NA,"Wong WSW, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE , Hourigan SK",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,"antibiotics, delivery mode, infant, microbiome, neonate, pediatrics",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,"meconium defined as the first stool passed, other than meconium staining of amniotic fluid.",62,43,"Mothers of infants born by CS received significantly more peripartum antibiotics than those born by VD (43/43 (100%) in CS vs. 19/62 (31%) in VD, p < 0.001).",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,Figure 4 & text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentially abundant OTUs(FDR< 0.05) according to deliverymode,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Rubrivivax,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium",2|1239|909932|1843489|31977|29465;2|1224|28211|356|119045|407;2|1224|1236|91347|543|544;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|1224|28216|80840|80864|12916;2|201174|1760|85009|31957|1743;2|1239|91061|186826|186828|117563;2|1224|1236|2887326|468|469;2|1224|28211|356|41294|374;2|1224|28216|80840|80864|80865;2|201174|1760|85004|31953|1302778;2|1239|91061|186826|33958|1578;2|1224|28216|80840|506|222;2|1297|188787|68933|188786|65551;2|1224|28211|356|2036754|28209;2|1224|1236|135614|32033|40323;2|1224|28216|80840|114248;2|1224|1236|135625|712|724;2|1224|28216|80840|2975441|88;2|1224|28216|80840|80864|283;2|1224|28216|80840|2975441|28067;2|976|1853228|1853229|563835|504481;2|1239|91061|186826|1300|1357;2|1224|1236|91347|543|547;2|1239|91061|1385|186817|150247;2|1224|28211|356|82115|357,Complete,NA
bsdb:209/1/2,Study 209,prospective cohort,32012716,10.3390/microorganisms8020179,NA,"Wong WSW, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE , Hourigan SK",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,"antibiotics, delivery mode, infant, microbiome, neonate, pediatrics",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,"meconium defined as the first stool passed, other than meconium staining of amniotic fluid.",62,43,"Mothers of infants born by CS received significantly more peripartum antibiotics than those born by VD (43/43 (100%) in CS vs. 19/62 (31%) in VD, p < 0.001).",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,Figure 4 & text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentially abundant OTUs(FDR< 0.05) according to deliverymode,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|91347|543|561;2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|544;2|1224|1236|91347|543|570;2|1224|1236|91347|543|158851;2|1224|1236|91347|543|620;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:210/1/1,Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,T-Test,0.01,FALSE,NA,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table 2, Text (Alterations at the family and genus levels)",10 January 2021,Lucy Mellor,"Fatima,WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297|13687;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572;2|1239|186801|186802|31979|1485|59620,Complete,Folakunmi
bsdb:210/1/2,Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,T-Test,0.01,FALSE,NA,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Table 2, Text (Alterations at the family and genus levels)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:210/2/1,Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 3, Text (Comparison of relative abundance through LDA score and cladogram analysis)",10 January 2021,Lucy Mellor,"Fatima,WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|28211;2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572,Complete,Folakunmi
bsdb:210/2/2,Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 3, Text (Comparison of relative abundance through LDA score and cladogram analysis)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:211/1/1,Study 211,case-control,33718259,10.3389/fcimb.2021.549678,NA,"Long Y, Liang F, Guo R, Zhu C, Zhao X, Wang X, Liu F, Jiang M, Liang Q, Zeng S, Han M, Qin J, Li S, Li S , Yang H",Gut Microbiota Signatures in Gestational Anemia,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, gestational anemia, gut microbiota, microbial dysbiosis, pregnant women",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,healthy controls(HC1 group),gestational anemia (GA1 group),Gestational diseases are associated with altered intestinal microbiota in pregnant women in the first trimester.,54,24,4 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,gestational age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,FIGURE 2B.,10 January 2021,Lora Kasselman,"WikiWorks,Chinelsy,ChiomaBlessing",Bacterial genera significantly enriched in the GA1 group compared to the HC1 group (first trimester).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|265975;2|1239|1737404|1737405|1570339|543311;2|1239|526524|526525|2810281|191303,Complete,Chinelsy
bsdb:211/2/1,Study 211,case-control,33718259,10.3389/fcimb.2021.549678,NA,"Long Y, Liang F, Guo R, Zhu C, Zhao X, Wang X, Liu F, Jiang M, Liang Q, Zeng S, Han M, Qin J, Li S, Li S , Yang H",Gut Microbiota Signatures in Gestational Anemia,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, gestational anemia, gut microbiota, microbial dysbiosis, pregnant women",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,healthy controls (HC3 group),gestational anemia (GA3 group),Gestational diseases are associated with altered intestinal microbiota in pregnant women in the third trimester.,56,30,4 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,gestational age,sex",NA,unchanged,decreased,NA,NA,NA,decreased,Signature 1,FIGURE 2C.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Bacterial genera significantly enriched in the GA3 group compared to the HC3 group (third trimester).,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|201174|84998|84999|1643824|1380;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979;2|201174|84998|1643822|1643826|84111,Complete,Chinelsy
bsdb:211/2/2,Study 211,case-control,33718259,10.3389/fcimb.2021.549678,NA,"Long Y, Liang F, Guo R, Zhu C, Zhao X, Wang X, Liu F, Jiang M, Liang Q, Zeng S, Han M, Qin J, Li S, Li S , Yang H",Gut Microbiota Signatures in Gestational Anemia,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, gestational anemia, gut microbiota, microbial dysbiosis, pregnant women",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,healthy controls (HC3 group),gestational anemia (GA3 group),Gestational diseases are associated with altered intestinal microbiota in pregnant women in the third trimester.,56,30,4 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,gestational age,sex",NA,unchanged,decreased,NA,NA,NA,decreased,Signature 2,FIGURE 2C.,1 February 2024,ChiomaBlessing,ChiomaBlessing,Bacterial genera significantly enriched in the GA3 group compared to the HC3 group (third trimester).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572;2|1239|186801|186802;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|204475;2|201174|84998|1643822|1643826|447020,Complete,ChiomaBlessing
bsdb:212/1/1,Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low quartile of TOTAL fiber intake,Higher quartile of TOTAL fiber intake,Subjects who had a higher total fiber intake,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Supplemental Table 1",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks,ChiomaBlessing",Forest plot of the fold change of microbial abundance in both New York University and National Cancer Institute study populations with significant association with higher fibre intake subjects,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|201174|1760|2037|2049|1654;2|1239|526524|526525|128827|2749846|31971;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:212/1/2,Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low quartile of TOTAL fiber intake,Higher quartile of TOTAL fiber intake,Subjects who had a higher total fiber intake,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Supplemental Table 1",10 January 2021,Lora Kasselman,"Claregrieve1,Merit,WikiWorks,ChiomaBlessing,Davvve",Forest plot of the fold change of microbial abundance in both New York University and National Cancer Institute study populations with significant association with higher fibre intake subjects.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:212/2/1,Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from FRUITS/ VEGETABLES,Higher fiber intake from FRUITS/ VEGETABLES,Subjects who had a higher fiber intake from FRUITS/ VEGETABLES,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplemental Table 2, Figure 3",28 October 2023,ChiomaBlessing,ChiomaBlessing,Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from FRUIT/ VEGETABLE  in the NCI and NYU study population,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",2|201174|1760|2037|2049|1654;2|976|200643|171549|815|816|820;2|201174|84998|84999;2|1239|91061|186826;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|1263|40518,Complete,Folakunmi
bsdb:212/2/2,Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from FRUITS/ VEGETABLES,Higher fiber intake from FRUITS/ VEGETABLES,Subjects who had a higher fiber intake from FRUITS/ VEGETABLES,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental Table 2,28 October 2023,ChiomaBlessing,ChiomaBlessing,Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from FRUIT/ VEGETABLE  in the NCI and NYU study population,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,2|1239|186801|3082720|186804,Complete,Folakunmi
bsdb:212/3/1,Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from BEANS,Higher fiber intake from BEANS,Subjects who had a higher fiber intake from BEANS,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplemental Table 4, Figure 3",28 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from BEANS in the NCI and NYU study population,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853,Complete,Folakunmi
bsdb:212/3/2,Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from BEANS,Higher fiber intake from BEANS,Subjects who had a higher fiber intake from BEANS,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 3, supplementary table 4",28 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Heatmap analysis representing fold changes of taxa in higher fiber intake from BEANS in the meta-analysis of NCI and NYU study populations,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",2|201174|1760|2037;2|1239|526524|526525|128827|2749846|31971;2|976|200643|171549|815|816;2|28221;2|200940|3031449|213115;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231;2|1239|186801|186802|216572|1263;2|200940|3031449|213115|194924,Complete,Folakunmi
bsdb:212/4/1,Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from GRAINS,Higher fiber intake from GRAINS,Subjects who had a higher fiber intake from GRAINS,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table 3,28 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from GRAINS in the NCI and NYU study population,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:213/4/1,Study 213,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang YS, Li SH, Guo Y, Lu JH, He JR, Luo BJ, Jiang FJ, Shen H, Papasian CJ, Pang H, Xia HM, Deng HW , Qiu X",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Neonates,2-month-old infants,Samples from 2-month-old infants,15,14,NA,16S,345,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3,24 October 2023,OdigiriGreat,OdigiriGreat,Comparison of microbial community composition at the phylum (a) and genus (b) levels for neonates and 2-month-old infants.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|31979|1485;2|1239|91061|186826|1300;2|1239|526524|526525|2810280;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|1678,Complete,Folakunmi
bsdb:213/5/1,Study 213,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang YS, Li SH, Guo Y, Lu JH, He JR, Luo BJ, Jiang FJ, Shen H, Papasian CJ, Pang H, Xia HM, Deng HW , Qiu X",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered neonates,Vaginally delivered neonates,samples from neonates delivered by Vagina,9,6,NA,16S,345,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 5,25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|1239|909932|909929|1843491|158846;2|976|200643|171549|2005525|375288,Complete,Folakunmi
bsdb:213/5/2,Study 213,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang YS, Li SH, Guo Y, Lu JH, He JR, Luo BJ, Jiang FJ, Shen H, Papasian CJ, Pang H, Xia HM, Deng HW , Qiu X",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered neonates,Vaginally delivered neonates,samples from neonates delivered by Vagina,9,6,NA,16S,345,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 5,25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella",2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|158851,Complete,Folakunmi
bsdb:213/6/1,Study 213,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang YS, Li SH, Guo Y, Lu JH, He JR, Luo BJ, Jiang FJ, Shen H, Papasian CJ, Pang H, Xia HM, Deng HW , Qiu X",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered 2-month-olds,Vaginally delivered 2-month-olds,Two months infants that were delivered vaginally,7,7,NA,16S,345,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Figure 5, within text result (Effects of delivery modes on infant gut microbiota, line 12)",25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Comparison of the microbial community of vaginal and cesarean delivery subjects for 2-month-old infants,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|815|816;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|216572,Complete,Folakunmi
bsdb:213/6/2,Study 213,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang YS, Li SH, Guo Y, Lu JH, He JR, Luo BJ, Jiang FJ, Shen H, Papasian CJ, Pang H, Xia HM, Deng HW , Qiu X",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered 2-month-olds,Vaginally delivered 2-month-olds,Two months infants that were delivered vaginally,7,7,NA,16S,345,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Comparison of the microbial community of vaginal and cesarean delivery subjects for 2-month-old infants,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|186802|31979|1485;2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:214/1/1,Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,"16s rRNA sequencing, Bacteroidetes, Clostridia, Cow's milk allergy, Firmicutes, fatty acid, food allergy, metagenome, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy at age 8,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1a,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differentially abundant taxa in children with milk allergy persistence versus milk allergy resolution at age 8,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella",2|976|200643|171549;2|976|200643;2|976;2|1224|1236|91347|543|547;2|1224|1236|91347|543|590;2|1224|1236|91347|543|158851,Complete,Claregrieve1
bsdb:214/1/2,Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,"16s rRNA sequencing, Bacteroidetes, Clostridia, Cow's milk allergy, Firmicutes, fatty acid, food allergy, metagenome, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy at age 8,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1a,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differentially abundant taxa in children with milk allergy persistence versus milk allergy resolution at age 8,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|572511;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|186806|1730;2|1239;2|1239|186801|3082720|186804;2|976|200643|171549|171552;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:215/1/1,Study 215,case-control,27812181,10.1371/journal.pone.0166026,NA,"Zheng H, Liang H, Wang Y, Miao M, Shi T, Yang F, Liu E, Yuan W, Ji ZS , Li DK",Altered Gut Microbiota Composition Associated with Eczema in Infants,PloS one,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control infants,infants with eczema,infants with eczema,51,50,NA,16S,34,Roche454,Metastats,1e-5,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 3, Supplemental Table S2, Supplemental Table S3",10 January 2021,Lucy Mellor,"Fatima,Claregrieve1,WikiWorks",Differentially abdundant species in the gut of infants with and without eczema,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Archaea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|186803|207244;2157;2|976|200643|171549|815|816|626929;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|33042;2|1224|1236|91347|543|413496|28141;2|200940|3024418|213118|213119;2|200940|3031449|213115|194924|872;2|1224|1236|91347|543|547;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|946234;2|1239|186801|186802|204475;2|1239|186801|186802|204475|745368;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|1239|91061|1385|186822;2|1239|91061|1385|186822|44249;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171552|577309;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|171552|2974251|28126;2|1224|28211|356|82115;2|1224|28211|356|82115|379;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977|29465;2|74201|203494|48461|203557;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|186801|186802|31979|1485,Complete,Claregrieve1
bsdb:215/1/2,Study 215,case-control,27812181,10.1371/journal.pone.0166026,NA,"Zheng H, Liang H, Wang Y, Miao M, Shi T, Yang F, Liu E, Yuan W, Ji ZS , Li DK",Altered Gut Microbiota Composition Associated with Eczema in Infants,PloS one,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control infants,infants with eczema,infants with eczema,51,50,NA,16S,34,Roche454,Metastats,1e-5,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 3, Supplemental Table S2, Supplemental Table S3",10 January 2021,Lucy Mellor,"Fatima,Claregrieve1,WikiWorks",Differentially abundant species in the gut of infants with and without eczema,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|904;2|1239|909932|1843489|31977|209879;2|1239|909932|1843489|31977|156454;2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816|817;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696;2|1239|186801|186802|3085642|580596;2|1239|91061|186826|186828;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|1760|85006|85020;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1224|28216|206351|481|538;2|1239|526524|526525|128827;2|1239|526524;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1239|526524|526525|128827|1573535|1735;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|459786;2|1224|1236|135625|712;2|1239|186801|3082720|186804;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1304;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:216/1/1,Study 216,"cross-sectional observational, not case-control",27362264,10.1371/journal.pone.0158498,NA,"Martin R, Makino H, Cetinyurek Yavuz A, Ben-Amor K, Roelofs M, Ishikawa E, Kubota H, Swinkels S, Sakai T, Oishi K, Kushiro A , Knol J","Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota",PloS one,2016,NA,Experiment 1,Netherlands,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,babies that were delivered by c-section,80,28,"use of antibiotics between 2 weeks prior to delivery and 2 weeks after delivery, for any reason except for prophylactic use (e.g. cesarean section).",16S,NA,RT-qPCR,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential microbial abundance between infants born by vaginal delivery or C-section.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|201174|1760|85004|31953|1678|1686;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|186802|31979|1485|1502;2|1239|91061|186826|81852|1350;2|976|200643|171549|815|909656|821;2|201174|1760|85004|31953|1678|1681;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|2742598|1598,Complete,Claregrieve1
bsdb:217/1/1,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,child with eczema,19,15,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,"Fatima,WikiWorks",Differences in microbiota of healthy and eczematous children at 18 months of age,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi",2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|29343,Complete,Folakunmi
bsdb:217/1/2,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,child with eczema,19,15,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Table 2,10 January 2021,Lucy Mellor,WikiWorks,Differences in microbiota of healthy and eczematous children at 18 months of age,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota",2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|820;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|1283313|76122;2|976,Complete,Folakunmi
bsdb:217/2/1,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Figure 1,10 January 2021,Lucy Mellor,"WikiWorks,Merit,Folakunmi,Aleru Divine",Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,2|1239|186801|3085636|186803|572511|1532,Complete,Folakunmi
bsdb:217/2/2,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Figure 1,10 January 2021,Lucy Mellor,WikiWorks,Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli",2|201174;2|1239|91061,Complete,Folakunmi
bsdb:217/3/1,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Table 1,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi","Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by
HITChip analysis",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium",2|1239|186801|3085636|186803|3342669|45851;2|1239|526524|526525|2810280|100883|100884;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|140625|140626;2|1239|909932|1843488|909930|33024|33025;2|1224|1236|91347|1903414|583;2|1239|186801|186802|216572|1263|40518;2|1224|28216|80840|995019|40544|40545;2|1239|186801|3085636|186803|1506553|1512;2|544448|31969|220137,Complete,Folakunmi
bsdb:217/3/2,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Table 1,10 January 2021,Lucy Mellor,WikiWorks,"Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by
HITChip analysis",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|2767842|1590,Complete,Folakunmi
bsdb:217/4/1,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Lactobacillus rhamnosus GG,NCBITAXON:568703,placebo group at 18 months,children supplemented with LGG at 18 months,children who have been supplemented with L. rhamnosus GG at the age of 18 months i.e. a year after the cessation of the probiotic supplementation,15,19,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 9,25 February 2024,Folakunmi,Folakunmi,"The microbiota differences between the intervention groups (LGG or
placebo) at the age of 18 months as assessed by HITChip analysis.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",2|1239|186801|3085636|186803|207244|105841;2|1239|186801|186802|186806|1730|39496,Complete,Folakunmi
bsdb:217/4/2,Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Lactobacillus rhamnosus GG,NCBITAXON:568703,placebo group at 18 months,children supplemented with LGG at 18 months,children who have been supplemented with L. rhamnosus GG at the age of 18 months i.e. a year after the cessation of the probiotic supplementation,15,19,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 9,25 February 2024,Folakunmi,Folakunmi,"The microbiota differences between the intervention groups (LGG or
placebo) at the age of 18 months as assessed by HITChip analysis.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,2|1239|186801|3082720|186804|1870884|1496,Complete,Folakunmi
bsdb:218/1/1,Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,healthy controls,non-HBV non-HCV related HCC,HCC patients whose disease is not related to hepatitis B/hepatitis virus,33,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and non-hepatitis virus related hepatocellular carcinoma patients,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,2|1239|186801|186802|216572|244127,Complete,Claregrieve1
bsdb:218/1/2,Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,healthy controls,non-HBV non-HCV related HCC,HCC patients whose disease is not related to hepatitis B/hepatitis virus,33,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance comparing healthy controls to non-hepatitis virus related hepatocellular carcinoma patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846,Complete,Claregrieve1
bsdb:218/2/1,Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,healthy controls,HBV-related HCC patients,HBV-related HCC patients,33,35,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance comparing healthy controls to HBV-related hepatocellular carcinoma patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|186802|216572|244127;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:218/3/1,Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,HBV related HCC patients,non-HBV non-HCV patients,HCC patients whose disease is not related to hepatitis B/hepatitis virus,35,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HBV-related hepatocellular carcinoma patients and non-hepatitis virus related HCC patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1224|1236|91347|1903409|32199;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|28050;2|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:219/1/1,Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds) - at baseline,"lower fiber (cracker), at baseline",students eating crackers,38,35,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Table 1,10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,2|976|200643|171549|815|816|817,Complete,NA
bsdb:219/2/1,Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds) - 8 wk after intervention,lower fiber (cracker) - 8 wk after intervention,students eating crackers,38,35,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Table 1,10 January 2021,Lora Kasselman,"Lwaldron,WikiWorks,Atrayees",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups 8 wk after the intervention,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Mycoplasmatota|c__Mollicutes",2|1239|186801|3085636|186803|28050;2|544448|31969,Complete,NA
bsdb:219/2/2,Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds) - 8 wk after intervention,lower fiber (cracker) - 8 wk after intervention,students eating crackers,38,35,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,Table 1,10 January 2021,Lora Kasselman,"Lwaldron,WikiWorks,Atrayees",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups 8 wk after the intervention,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|976|200643|171549|171550|239759;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005473,Complete,NA
bsdb:219/3/1,Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds),lower fiber (cracker),students eating crackers,35,38,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Lora Kasselman,WikiWorks,ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline and 8 wk after the intervention,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,2|1224|28216|80840|995019|40544,Complete,NA
bsdb:220/1/1,Study 220,case-control,29791788,10.1111/jam.13929,NA,"Jugé R, Rouaud-Tinguely P, Breugnot J, Servaes K, Grimaldi C, Roth MP, Coppin H , Closs B",Shift in skin microbiota of Western European women across aging,Journal of applied microbiology,2018,"16S rRNA gene sequencing, Western European women, age-related changes, alpha diversity, beta diversity, microbiota, skin",Experiment 1,France,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,younger age,older age European women,aging,17,17,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Figure S1, Figure s2",10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic analysis of forehead microbiota using LEfSe between older and younger european women,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota",2|201174|1760|85006|1268|1663;2|32066|203490|203491|1129771|168808;2|1224|1236|2887326|468;2|1224|1236|72274;2|201174|1760|85007|1653|1716;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|1224|1236|135619;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|28216;2|1224,Complete,NA
bsdb:220/1/2,Study 220,case-control,29791788,10.1111/jam.13929,NA,"Jugé R, Rouaud-Tinguely P, Breugnot J, Servaes K, Grimaldi C, Roth MP, Coppin H , Closs B",Shift in skin microbiota of Western European women across aging,Journal of applied microbiology,2018,"16S rRNA gene sequencing, Western European women, age-related changes, alpha diversity, beta diversity, microbiota, skin",Experiment 1,France,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,younger age,older age European women,aging,17,17,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Figure S1, Figure s2",10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic analysis of forehead microbiota using  LEfSe between older and younger european women,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales",2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|201174|1760|85009,Complete,NA
bsdb:221/1/1,Study 221,case-control,30006660,10.1007/s10096-018-3322-7,NA,"Paalanne N, Husso A, Salo J, Pieviläinen O, Tejesvi MV, Koivusaari P, Pirttilä AM, Pokka T, Mattila S, Jyrkäs J, Turpeinen A, Uhari M, Renko M , Tapiainen T",Intestinal microbiome as a risk factor for urinary tract infections in children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2018,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,healthy controls,urinary tract infection,urinary tract infection,69,37,NA,16S,45,Ion Torrent,LEfSe,3,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Comaprison between UTI patients and Health controls using linear discriminant analysis,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia flexa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus dispar,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea",2|1224|1236|91347|543|547;2|1239|526524|526525|128827|61170|1468449;2|1239|91061|1385|186817|2800373|86664;2|1239|186801|3085636|186803|2719313|333367;2|1239|91061|186826|81852|1350|44009;2|1239|186801|3085636|186803|572511|536633,Complete,Atrayees
bsdb:221/1/2,Study 221,case-control,30006660,10.1007/s10096-018-3322-7,NA,"Paalanne N, Husso A, Salo J, Pieviläinen O, Tejesvi MV, Koivusaari P, Pirttilä AM, Pokka T, Mattila S, Jyrkäs J, Turpeinen A, Uhari M, Renko M , Tapiainen T",Intestinal microbiome as a risk factor for urinary tract infections in children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2018,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,healthy controls,urinary tract infection,urinary tract infection,69,37,NA,16S,45,Ion Torrent,LEfSe,3,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Comaprison between UTI patients and Health controls using linear discriminant analysis,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tertium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia aurea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia lituseburensis",2|1239|186801|186802|31979|1485|1559;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|150022|1260;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|28216|80840|75682|149698;2|1224|28216|80840|75682;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3082720|186804;2|976|200643|171549|171552|2974257|386414;2|1224|28216|80840|75682|149698|373040;2|1239|186801|3082720|186804|1501226|1537,Complete,Atrayees
bsdb:222/1/1,Study 222,"cross-sectional observational, not case-control",26729566,10.1038/srep18594,NA,"Yang I, Woltemate S, Piazuelo MB, Bravo LE, Yepez MC, Romero-Gallo J, Delgado AG, Wilson KT, Peek RM, Correa P, Josenhans C, Fox JG , Suerbaum S",Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia,Scientific reports,2016,NA,Experiment 1,Colombia,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,low gastric cancer risk patients (Tumaco residents),high gastric cancer risk patients (Tuquerres residents),individuals from Tuquerres with high gastric cancer risk,20,20,30 days,16S,NA,Illumina,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Valentina Pineda,"Claregrieve1,WikiWorks",Differential microbial abundance between Tuquerres and Tumaco residents,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",2|32066|203490|203491|1129771|32067|157687;2|1239|909932|1843489|31977|29465|1926307,Complete,Claregrieve1
bsdb:222/1/2,Study 222,"cross-sectional observational, not case-control",26729566,10.1038/srep18594,NA,"Yang I, Woltemate S, Piazuelo MB, Bravo LE, Yepez MC, Romero-Gallo J, Delgado AG, Wilson KT, Peek RM, Correa P, Josenhans C, Fox JG , Suerbaum S",Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia,Scientific reports,2016,NA,Experiment 1,Colombia,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,low gastric cancer risk patients (Tumaco residents),high gastric cancer risk patients (Tuquerres residents),individuals from Tuquerres with high gastric cancer risk,20,20,30 days,16S,NA,Illumina,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Valentina Pineda,"Lwaldron,Claregrieve1,WikiWorks,Merit",Differential microbial abundance between Tuquerres and Tumaco residents,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter|s__uncultured Haematobacter sp.",2|201174|1760|2037|2049|1654|29317;2|976|117743|200644|49546|1016|1017;2|976|117743|200644|49546;2|976|117743|200644|49546|237|239;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|192066;2|976|200643|171549|171551;2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|2974251|28135;2|201174|1760|85006|1268|32207|1885016;2|1224|28211|204457|41297;2|1239|91061|1385|90964|1279|29387;2|1239|91061|186826|1300|1301|1303;2|1224|28211|204455|31989|366614|1310087,Complete,Claregrieve1
bsdb:223/1/1,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients,patients infected with HIV,35,33,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 5b,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differentially abundant microbial taxa in HIV infected patients compared with healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",2|1239|91061;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|1236;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|2316020|33038;2|1224;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1343,Complete,Claregrieve1
bsdb:223/1/2,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients,patients infected with HIV,35,33,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 5b,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differentially abundant microbial taxa in HIV infected patients compared with healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|1843488|909930;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|1239|909932;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171552|2974251|165179;2|1239|909932|909929;2|1239|186801|186802|216572|292632;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:223/2/1,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients who are homosexual,homosexual patients infected with HIV,35,4,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who were infected through homosexual sex and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|1239|91061;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|526524|526525|2810280|1505663;2|1239|526524|526525|2810280|3025755|1547;2|1239|91061|186826,Complete,Claregrieve1
bsdb:223/2/2,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients who are homosexual,homosexual patients infected with HIV,35,4,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who were infected through homosexual sex and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales",2|1239|909932|1843488|909930;2|976|200643|171549;2|976;2|976|200643;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|909932;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552;2|1239|909932|909929,Complete,Claregrieve1
bsdb:223/3/1,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,Intravenous drug abuse HIV patients,Intravenous drug abuse patients infected with HIV,35,3,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who were infected through intravenous drug use and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|3085636|186803;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:223/4/1,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,heterosexual subjects with HIV,homosexual subjects with HIV,homosexual patients infected with HIV,26,4,4 weeks,16S,4,Illumina,Metastats,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6d,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Relative abundance bacteria with significance between heterosexual and homosexual subjects,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803|1506553;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:223/5/1,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HAART-treated HIV+ patients,HIV infected patients treated with highly active antiretroviral therapy (HAART),35,14,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 7c,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients treated with HAART and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",2|976|200643|171549|815|816|817;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|3085636|186803|1506553;2|1224|1236|91347|543|620;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33038;2|1239|91061|186826|1300|1301|1308,Complete,Claregrieve1
bsdb:223/5/2,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HAART-treated HIV+ patients,HIV infected patients treated with highly active antiretroviral therapy (HAART),35,14,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 7c,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients treated with HAART and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|1843488|909930;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976;2|976|200643;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|909932|909929|1843491|158846;2|1239|909932;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|909929;2|1239|186801|186802|216572|292632;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:223/6/1,Study 223,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HAART untreated,HIV infected patients not treated with HAART,35,19,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 7c,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who are HAART-treatment naive and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota",2|1239|91061;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|1236;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1224,Complete,Claregrieve1
bsdb:224/1/1,Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,barley (WGB),subjects who took a daily 60g dose of barley,28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",10 January 2021,Lora Kasselman,"Fatima,Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley study group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|418240;2|1239;2|1239|186801|3085636|186803|841|301302;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:224/1/2,Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,barley (WGB),subjects who took a daily 60g dose of barley,28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley study group,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|976;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171551;2|976;2|976|200643|171549|815;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977|39948,Complete,Claregrieve1
bsdb:224/2/1,Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice (BR),subjects who took a daily 60g dose of brown rice fiber,28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for brown rice study group,increased,k__Bacteria|p__Bacillota,2|1239,Complete,Claregrieve1
bsdb:224/2/2,Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice (BR),subjects who took a daily 60g dose of brown rice fiber,28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for brown rice study group,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Claregrieve1
bsdb:224/3/1,Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice + barley (BR + WGB),subjects who took a daily dose of 30g barley + 30g brown rice,28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley+brown rice study group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota",2|1239|186801|3085636|186803|572511;2|1239,Complete,Claregrieve1
bsdb:224/3/2,Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice + barley (BR + WGB),subjects who took a daily dose of 30g barley + 30g brown rice,28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley+brown rice study group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota",2|976|200643|171549|815;2|976|200643|171549|815|816;2|976,Complete,Claregrieve1
bsdb:225/1/1,Study 225,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L , Jenmalm MC",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema- at 12 months,20,20,None,16S,34,Roche454,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|91061|186826|81852|1350;2|1239|186801|3082720|186804,Complete,ChiomaBlessing
bsdb:225/1/2,Study 225,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L , Jenmalm MC",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema- at 12 months,20,20,None,16S,34,Roche454,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life,decreased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,ChiomaBlessing
bsdb:225/2/1,Study 225,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L , Jenmalm MC",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,NA,Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema- at 1 month,20,20,None,16S,34,Roche454,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Relative abundance of dominant taxa in stool samples obtained at 1 month from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815|816,Complete,ChiomaBlessing
bsdb:226/1/1,Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV-1 infected patients,HIV-1 diagnosed patients,16,67,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2B,2C, 2D, 2E",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1224|28216;2|1224|28216|80840;2|1239|186801|186802|3085642|580596;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|543|547;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|216572|216851;2|1239;2|1239|909932|909929|1843491|158846;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1224;2|1224|28216|80840|995019;2|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:226/1/2,Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV-1 infected patients,HIV-1 diagnosed patients,16,67,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 2B,2C, 2D, 2E",10 January 2021,Fatima Zohra,WikiWorks,Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|3085636|186803|33042;2|976|200643|171549|2005519|397864;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:226/2/1,Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HAART-naive HIV-1 patients,HAART-treated HIV-1 patients,HIV-1 diagnosed patients,35,32,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of microbial abundance in HIV+ HAART-naive and HIV+ HAART-treated individuals,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|1239|186801|3085636|186803|572511;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239;2|1239|909932|909929|1843491|158846;2|1239|909932;2|1224;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:226/2/2,Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HAART-naive HIV-1 patients,HAART-treated HIV-1 patients,HIV-1 diagnosed patients,35,32,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of microbial abundance in HIV+ HAART-naive and HIV+ HAART-treated individuals,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota",2|976|200643|171549|171550|239759;2|976|200643|171549;2|976;2|976|200643;2|976|200643|171549|2005519|397864;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|508458|649775|649776|3029088|638847;2|976|200643|171549|171550;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775;2|508458,Complete,Claregrieve1
bsdb:227/1/1,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, Text",10 January 2021,Lucy Mellor,WikiWorks,Phylum level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls,increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Folakunmi
bsdb:227/1/2,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|201174|1760|85004|31953|1678;2|74201|203494|48461|1647988|239934,Complete,Folakunmi
bsdb:227/2/1,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:227/2/2,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:227/3/1,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:227/3/2,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis,decreased,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,Folakunmi
bsdb:227/4/1,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1a,10 January 2021,Lucy Mellor,WikiWorks,LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|91061;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|216572|216851;2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|1239|186801|3082720|186804|1505652;2|1239|186801|3082720|186804|1501226;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186827;2|1239|526524|526525|2810280|100883,Complete,Folakunmi
bsdb:227/4/2,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1a,10 January 2021,Lucy Mellor,"WikiWorks,Merit",LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|1224|1236|91347|543|544;2|1239|526524|526525|2810280|100883;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|547;2|1224|1236|91347|543|1330547;2|1224|1236|91347|543|1504576;2|1224|1236|91347|543|160674;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:227/5/1,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1b,10 January 2021,Lucy Mellor,"WikiWorks,Merit,Folakunmi",LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1239;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1224|1236|2887326|468;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1224|1236|72274|135621;2|1224|1236|72274;2|1239|186801|3082720|186804|1501226;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|2887326|468|469,Complete,Folakunmi
bsdb:227/5/2,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1b,10 January 2021,Lucy Mellor,"WikiWorks,Merit",LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium",2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543|547;2|1224|1236|91347|543|1330547;2|1224|1236|91347|543|160674;2|74201|203494;2|74201|203494|48461;2|74201;2|74201|203494|48461|203557|2735,Complete,Folakunmi
bsdb:227/6/1,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1c,10 January 2021,Lucy Mellor,"Fatima,WikiWorks,Folakunmi",LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678,Complete,Folakunmi
bsdb:227/6/2,Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1c,10 January 2021,Lucy Mellor,WikiWorks,LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales",2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006,Complete,Folakunmi
bsdb:228/1/1,Study 228,randomized controlled trial,30139999,10.1038/s41598-018-30783-1,NA,"Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z , Alm EJ",Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort,Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,day 6 of PECTIN spike-in,day 3 of PECTIN spike-in,before pectin spike-in,9,9,6 months,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1b and text,10 January 2021,Lora Kasselman,WikiWorks,"OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - PECTIN",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|976|200643|171549|815|816;2|1239|186801|186802|216572|44748;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:228/2/1,Study 228,randomized controlled trial,30139999,10.1038/s41598-018-30783-1,NA,"Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z , Alm EJ",Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort,Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,day 6 of INULIN spike-in,day 3 of INULIN spike-in,before pectin spike-in,9,9,6 months,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1b and text,10 January 2021,Lora Kasselman,WikiWorks,"OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - INULIN",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|3085636|186803;2|976|200643|171549|815|816|820;2|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:229/1/1,Study 229,time series / longitudinal observational,29909506,10.1186/s13568-018-0629-9,NA,"Bang SJ, Kim G, Lim MY, Song EJ, Jung DH, Kum JS, Nam YD, Park CS , Seo DH",The influence of in vitro pectin fermentation on the human fecal microbiome,AMB Express,2018,"Fecal microbiota, Fermentation, Pectin, Prebiotic, Short chain fatty acids",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,late pectin incubation time,early pectin incubation time,before/early pectin incubation,3,3,6 months,16S,12,Ion Torrent,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 and text,10 January 2021,Lora Kasselman,WikiWorks,Significantly changed taxa according to pectin incubation time (q value < 0.1),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107;2|1239|526524|526525|2810280|100883;2|1239|186801|3082720|186804;2|1224|28216|80840|75682|846;2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|976|200643|171549|1853231|283168;2|1239|186801|3085636|186803|33042;2|976|200643|171549|1853231|574697;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|976|200643|171549|171550;2|976|200643|171549|815|816,Complete,Folakunmi
bsdb:229/1/2,Study 229,time series / longitudinal observational,29909506,10.1186/s13568-018-0629-9,NA,"Bang SJ, Kim G, Lim MY, Song EJ, Jung DH, Kum JS, Nam YD, Park CS , Seo DH",The influence of in vitro pectin fermentation on the human fecal microbiome,AMB Express,2018,"Fecal microbiota, Fermentation, Pectin, Prebiotic, Short chain fatty acids",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,late pectin incubation time,early pectin incubation time,before/early pectin incubation,3,3,6 months,16S,12,Ion Torrent,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 and text,10 January 2021,Lora Kasselman,WikiWorks,Significantly changed taxa according to pectin incubation time (q value < 0.1),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|1239|186801|3085636|186803|28050;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|31979|1485;2|1224|28216|80840;2|976|200643|171549,Complete,Folakunmi
bsdb:230/1/1,Study 230,prospective cohort,28903469,10.1093/femsec/fix099,NA,"Tanaka M, Korenori Y, Washio M, Kobayashi T, Momoda R, Kiyohara C, Kuroda A, Saito Y, Sonomoto K , Nakayama J",Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood,FEMS microbiology ecology,2017,"16S rRNA gene, Clostridium, fecal microbiota, food allergies, infant",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-allergy,infant with food allergy,infant with food allergy,27,14,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of gut microbiota of infants at 2 months of age in food allergy (FA) and non-allergy (NA) groups,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1243;2|1239|91061|186826|33958|46255;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:230/1/2,Study 230,prospective cohort,28903469,10.1093/femsec/fix099,NA,"Tanaka M, Korenori Y, Washio M, Kobayashi T, Momoda R, Kiyohara C, Kuroda A, Saito Y, Sonomoto K , Nakayama J",Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood,FEMS microbiology ecology,2017,"16S rRNA gene, Clostridium, fecal microbiota, food allergies, infant",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-allergy,infant with food allergy,infant with food allergy,27,14,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4c, text",10 January 2021,Lucy Mellor,WikiWorks,Relative abundances of genera in infants at 1 year of age which were statistically signficant differences between the food allergy (FA) and non-allergy (NA) groups,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|1236|91347|543;2|1239|186801|186802|31979|1485,Complete,NA
bsdb:231/1/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renatta canada apple - at 10 hr,Healthy donors administered with Renetta Canada apple,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Lora Kasselman,"WikiWorks,ChiomaBlessing",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|200940|3031449|213115|194924|35832;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263;2|1239|186801|186802;2|1239|186801|3082720|3030910|86331,Complete,ChiomaBlessing
bsdb:231/1/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renatta canada apple - at 10 hr,Healthy donors administered with Renetta Canada apple,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:231/2/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Lora Kasselman,"WikiWorks,ChiomaBlessing",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|1239|186801|186802;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263;2|1239|186801|186802;2|976|200643|171549|2005525|375288;2|200940|3031449|213115|194924|35832,Complete,ChiomaBlessing
bsdb:231/2/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:231/3/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Pink lady apple - at 10 hr,Healthy donors administered with Pink lady apple at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Lora Kasselman,"WikiWorks,ChiomaBlessing",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Pink lady apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|1239|186801|186802;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263;2|1239|186801|186802;2|976|200643|171549|2005525|375288;2|200940|3031449|213115|194924|35832,Complete,ChiomaBlessing
bsdb:231/4/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renetta Canada apple- at 24 hr,Healthy donors administered with Renetta Canada apple at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|976|200643|171549|1853231|574697;2|1239|186801|186802,Complete,ChiomaBlessing
bsdb:231/4/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renetta Canada apple- at 24 hr,Healthy donors administered with Renetta Canada apple at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:231/5/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple- at 24 hr,Healthy donors administered with Golden delicious apple at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|976|200643|171549|1853231|574697;2|1239|186801|186802,Complete,ChiomaBlessing
bsdb:231/5/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple- at 24 hr,Healthy donors administered with Golden delicious apple at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:231/6/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 6,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Pink lady apple- at 24 hr,Healthy donors administered with Pink lady apple at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Pink lady apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",2|1239|186801|186802;2|976|200643|171549|1853231|574697,Complete,ChiomaBlessing
bsdb:231/6/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 6,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Pink lady apple- at 24 hr,Healthy donors administered with Pink lady apple at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Pink lady apple compared to those administered with poorly fermentable fiber (cellulose),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:231/7/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Renatta canada apple - at 10 hr,Healthy donors administered with Renatta canada apple - at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renatta canada apple compared to those administered with inulin,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|1239|186801|186802;2|1239|186801|186802|216572|119852;2|1239|186801|3082720|3030910|86331,Complete,ChiomaBlessing
bsdb:231/7/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Renatta canada apple - at 10 hr,Healthy donors administered with Renatta canada apple - at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renatta canada apple compared to those administered with inulin,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:231/8/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple - at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with inulin,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572|119852;2|1239|186801|186802,Complete,ChiomaBlessing
bsdb:231/8/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple - at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with inulin,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:231/9/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 9,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Golden delicious apple - at 24 hr,Healthy donors administered with Golden delicious apple - at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Golden delicious apple compared to those administered with inulin,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:231/10/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 10,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Pink Lady apple - at 10 hr,Healthy donors administered with Pink Lady apple at 10 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Pink lady apple compared to those administered with inulin,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572|119852;2|1239|186801|186802,Complete,ChiomaBlessing
bsdb:231/11/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 11,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Pink Lady apple - at 24 hr,Healthy donors administered with Pink Lady apple at 24 hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Pink lady apple compared to those administered with inulin,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:231/12/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 12,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Cellulose - at 10hr,Donors administered with cellulose at 10hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with cellulose compared to those administered with inulin,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|200940|3031449|213115|194924|35832;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1239|186801|186802,Complete,ChiomaBlessing
bsdb:231/13/1,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 13,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Cellulose - at 24hr,Donors administered with cellulose at 24hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with cellulose compared to those administered with inulin,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:231/13/2,Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 13,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Cellulose - at 24hr,Donors administered with cellulose at 24hr,3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table 2,26 February 2024,ChiomaBlessing,ChiomaBlessing,Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with cellulose compared to those administered with inulin,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,ChiomaBlessing
bsdb:232/1/1,Study 232,"cross-sectional observational, not case-control",24451087,10.1186/2049-2618-1-26,NA,"McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P , Braun J",HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota,Microbiome,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV infected cART negative,HIV infected patients not on combined anti-retroviral therapy,20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.15,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Phylogenetic differences between HIV subjects not on combination anti-retroviral therapy and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|1239|1737404|1737405|1570339|165779;2|32066;2|32066|203490|203491|203492;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:232/1/2,Study 232,"cross-sectional observational, not case-control",24451087,10.1186/2049-2618-1-26,NA,"McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P , Braun J",HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota,Microbiome,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV infected cART negative,HIV infected patients not on combined anti-retroviral therapy,20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.15,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Phylogenetic differences between HIV subjects not on combination anti-retroviral therapy and healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|171550|239759;2|1239|186801;2|1239|186801|3085636|186803|33042;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|1239;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:233/1/1,Study 233,"cross-sectional observational, not case-control",24399150,10.1038/mi.2013.116,NA,"Dillon SM, Lee EJ, Kotter CV, Austin GL, Dong Z, Hecht DK, Gianella S, Siewe B, Smith DM, Landay AL, Robertson CE, Frank DN , Wilson CC",An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia,Mucosal immunology,2014,NA,Experiment 1,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,HIV infection,EFO:0000764,uninfected controls,HIV-infected subjects,Subjects with untreated chronic HIV-1 infection,14,18,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 1, Supplemental table S1",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks","Differential microbial abundance in the colonic mucosa comparing healthy controls to subjects with chronic, untreated HIV-1 infections",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1224|1236|2887326|468|469;2|1224|28211|356|118882;2|1224|1236|2887326|468;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1224;2|1224|1236|135614|32033,Complete,Claregrieve1
bsdb:233/1/2,Study 233,"cross-sectional observational, not case-control",24399150,10.1038/mi.2013.116,NA,"Dillon SM, Lee EJ, Kotter CV, Austin GL, Dong Z, Hecht DK, Gianella S, Siewe B, Smith DM, Landay AL, Robertson CE, Frank DN , Wilson CC",An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia,Mucosal immunology,2014,NA,Experiment 1,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,HIV infection,EFO:0000764,uninfected controls,HIV-infected subjects,Subjects with untreated chronic HIV-1 infection,14,18,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 1, Supplemental table S1",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks","Differential microbial abundance in the colonic mucosa comparing healthy controls to subjects with chronic, untreated HIV-1 infections",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239;2|976|200643|171549|171551;2|976|200643|171549|171550,Complete,Claregrieve1
bsdb:234/1/1,Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 1,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,adult with atopic dermatitis,adult with moderate-to-severe chronic atopic dermatitis,115,82,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,Folakunmi
bsdb:234/1/2,Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 1,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,adult with atopic dermatitis,adult with moderate-to-severe chronic atopic dermatitis,115,82,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.",2|1224|28216|80840|119060|32008|36773;2|201174|1760|85009|31957|1912216|1747;2|1239|1737404|1737405|1570339|150022|1981334;2|1239|91061|186826|33958|1578|1591;2|1224|28216|80840|2975441|93681|1909303;2|1239|91061|1385|90964|1279|29387,Complete,Folakunmi
bsdb:234/2/1,Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 2,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,healthy control,adult with psoriasis,adult with psoriasis,115,119,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1239|1737404|1737405|1570339|165779|1872515;2|201174|1760|85007|1653|1716|161879;2|201174|1760|85007|1653|1716|146827;2|1239|1737404|1737405|1570339|150022|1981334;2|1224|28216|206351|481,Complete,Folakunmi
bsdb:234/2/2,Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 2,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,healthy control,adult with psoriasis,adult with psoriasis,115,119,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles sp.",2|1224|28216|80840|119060|32008|36773;2|1239|91061|186826|33958|1578|1591;2|1224|28216|80840|2975441|93681|1909303,Complete,Folakunmi
bsdb:234/3/1,Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 3,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,adult with atopic dermatitis,adult with moderate-to-severe chronic atopic dermatitis,115,82,2 weeks,16S,NA,Roche454,"Mann-Whitney (Wilcoxon),Kruskall-Wallis,Spearman Correlation",0.01,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,supplementary table 2,26 February 2024,Folakunmi,Folakunmi,Abundant OTUs that were significantly associated with disease and also significantly associated with a confounded effect.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax paradoxus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",2|1239|1737404|1737405|1570339|150022|1981334;2|1224|28211|356|41294|374|376;2|1239|1737404|1737405|1570339|165779|1872515;2|1224|28216|80840|80864|34072|34073;2|1239|91061|186826|33958|1578|1591;2|1239|91061|1385|90964|1279|1280,Complete,Folakunmi
bsdb:234/4/1,Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 4,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,adults with psoriasis,adult with moderate-to-severe chronic plaque-type psoriasis,115,119,2 weeks,16S,NA,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Spearman Correlation",0.01,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,supplementary table 2,26 February 2024,Folakunmi,Folakunmi,Abundant OTUs that were significantly associated with disease and also significantly associated with a confounded effect.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii",2|1239|1737404|1737405|1570339|150022|1981334;2|1224|28211|356|41294|374|376;2|201174|1760|85007|1653|1716|1720;2|201174|1760|85007|1653|1716|161879,Complete,Folakunmi
bsdb:235/1/1,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,child with food allergy,child with food allergy,21,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Merit,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|216572|459786|351091,Complete,Atrayees
bsdb:235/1/2,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,child with food allergy,child with food allergy,21,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|1239|186801|3085636|186803|572511|1955243;2|1224|1236|135625|712|724|729,Complete,Atrayees
bsdb:235/2/1,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy sibling,child with food allergy,child with food allergy,25,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Merit,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",2|1239|186801|186802|216572|459786|351091;2|1239|186801|186802|216572|216851|1971605,Complete,Atrayees
bsdb:235/2/2,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy sibling,child with food allergy,child with food allergy,25,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.",2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|572511|1955243;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|1872444,Complete,Atrayees
bsdb:235/3/1,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,healthy sibling,sibling with no food allergy,21,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.",2|1239|186801|186802|216572|459786|351091;2|1239|186801|186802|216572|216851|1971605;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|1872444,Complete,Atrayees
bsdb:235/3/2,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,healthy sibling,sibling with no food allergy,21,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|1239|186801|3085636|186803|572511|1955243;2|1224|1236|135625|712|724|729,Complete,Atrayees
bsdb:235/4/1,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,<7 years,7-18 years,child age 7-18,26,42,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant taxons in children <7 years compared to children 7-18 years,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",2|976;2|1239|186801|186802|216572|459786|351091,Complete,Atrayees
bsdb:235/4/2,Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,<7 years,7-18 years,child age 7-18,26,42,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons in children <7 years compared to children 7-18 years,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239;2|1224;2|1239|526524|526525|128827;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804,Complete,Atrayees
bsdb:236/1/1,Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,after walnut diet,before walnut diet,before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Figure 4b, 5a, and text",10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:236/1/2,Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,after walnut diet,before walnut diet,before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Figure 4b, 5a, and text",10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|541000;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:236/2/1,Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,replace both,carbohydrate replacement (with walnuts),before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,5a and text,10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|204475;2|1239|186801|3085636|186803|1407607;2|976|200643|171549|815|816,Complete,Atrayees
bsdb:236/3/1,Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,fat replacement (with walnuts),replace both,before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,5a and text,10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|204475;2|1239|186801|3085636|186803|1407607;2|976|200643|171549|815|816,Complete,Atrayees
bsdb:237/1/1,Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,cirrhosis patients,hepatitis C patients with cirrhosis,50,38,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,NA,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,Folakunmi,MyleeeA",Genera with distinct patterns and their mean abundance in predefinded groups,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171552|1283313;2|1224|1236|91347|543|544;2|1224|1236|91347|543|1940338;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|1269;2|1239|91061|186826|33958|1253;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|46255;2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:237/1/2,Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,cirrhosis patients,hepatitis C patients with cirrhosis,50,38,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,NA,Signature 2,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Merit,Atrayees,Folakunmi",Genera with distinct patterns and their mean abundance in predefinded groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",2|1239|186801|186802|216572|35829;2|200940|3031449|213115|194924|35832;2|976|200643|171549|1853231|574697;2|1239|909932|909929|1843491|52225;2|1239|186801|186802|216572|1017280;2|1798710|3118680|2211217|213484;2|256845|1313211|278082|255528|172900,Complete,Atrayees
bsdb:237/2/1,Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,no cirrhosis,cirrhosis patients,heatitis C patients with cirrhosis,57,38,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees",Genera with distinct patterns and their mean abundance in predefinded groups,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465;2|201174|1760|85004|31953|1678;2|74201|203494|48461|1647988|239934;2|1224|1236|135625|712|724;2|201174|1760|85006|1268|1269;2|1239|91061|186826|33958|46255,Complete,Atrayees
bsdb:237/2/2,Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,no cirrhosis,cirrhosis patients,heatitis C patients with cirrhosis,57,38,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 2,Table 3,14 July 2023,Atrayees,Atrayees,Genera with distinct patterns and their mean abundance in predefinded groups,decreased,k__Bacteria|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,2|1798710|3118680|2211217|213484,Complete,Atrayees
bsdb:237/3/1,Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,No cirrhosis,Hepatitis C patients with no cirrhosis,50,57,3 months,16S,12,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",Genera with distinct patterns and their mean abundance in predefinded groups,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio",2|1239|909932|909929|1843491|52225;2|1239|186801|186802|216572|946234;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|35829,Complete,Atrayees
bsdb:237/3/2,Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,No cirrhosis,Hepatitis C patients with no cirrhosis,50,57,3 months,16S,12,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 3,21 February 2024,Folakunmi,"Folakunmi,MyleeeA",Genera with distinct patterns and their differential mean abundance between healthy control and hepatitis C patients with no cirrhosis,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|171552|1283313;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:238/1/1,Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4A,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|1506553;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810280|1505663;2|1239|186801|3085636|186803|437755;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|459786;2|1239|91061|186826|1300|1301,Complete,Fatima Zohra
bsdb:238/1/2,Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4A,10 January 2021,Cynthia Anderson,"Fatima,WikiWorks",The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|3082768|990719;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803|1407607;2|1239|186801|3082720|186804|1505657;2|976|200643|171549|2005525|375288;2|1239|186801|3082720|186804|1501226;2|1224|1236|91347|543|620;2|976|200643|171549|1853231|574697,Complete,Fatima Zohra
bsdb:238/2/1,Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,age,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4B,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for age,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|1506553;2|1239|526524|526525|2810280|1505663;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|437755,Complete,Fatima Zohra
bsdb:238/2/2,Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,age,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4B,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for age,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|976|200643|171549|171550|239759,Complete,Fatima Zohra
bsdb:238/3/1,Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,race,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4C,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for race,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810280|1505663;2|1239|186801|3085636|186803|437755,Complete,Fatima Zohra
bsdb:238/3/2,Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,race,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4C,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for race,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|3082720|186804|1505657;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|207244;2|1224|1236|91347|543|547;2|976|200643|171549|171550|239759,Complete,Fatima Zohra
bsdb:239/1/1,Study 239,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, Jones SM, Leung DYM, Sampson HA, Sicherer SH , Bunyavanich S",Early-life gut microbiome and egg allergy,Allergy,2018,"egg allergy, egg sensitization, food allergy, microbiome, purine",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Egg allergy,EFO:0007248,healthy control,children with egg allergy,children with egg allergy (ages ranging from 3 to 16 months),75,66,NA,16S,4,Illumina,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,antibiotic,atopic eczema,breast feeding",NA,increased,increased,NA,NA,increased,Signature 1,"Figure 2b, text",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera significantly associated with egg allergy,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1357,Complete,Atrayees
bsdb:239/1/2,Study 239,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, Jones SM, Leung DYM, Sampson HA, Sicherer SH , Bunyavanich S",Early-life gut microbiome and egg allergy,Allergy,2018,"egg allergy, egg sensitization, food allergy, microbiome, purine",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Egg allergy,EFO:0007248,healthy control,children with egg allergy,children with egg allergy (ages ranging from 3 to 16 months),75,66,NA,16S,4,Illumina,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,antibiotic,atopic eczema,breast feeding",NA,increased,increased,NA,NA,increased,Signature 2,"Figure 2b, text",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera significantly associated with egg allergy,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,2|1239|91061|186826|33958|1243,Complete,Atrayees
bsdb:239/2/1,Study 239,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, Jones SM, Leung DYM, Sampson HA, Sicherer SH , Bunyavanich S",Early-life gut microbiome and egg allergy,Allergy,2018,"egg allergy, egg sensitization, food allergy, microbiome, purine",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Egg allergy,EFO:0007248,healthy control,children with egg sensitization,children with egg sensitization,40,101,NA,16S,4,Illumina,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,race",NA,increased,increased,NA,NA,increased,Signature 1,"Figure 5b, text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Bacterial genera significantly associated with egg sensitization,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|74201;2|1239,Complete,Atrayees
bsdb:240/1/1,Study 240,case-control,25599982,10.1111/cea.12487,NA,"Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA , Kozyrskyj AL",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-sensitized group,sensitized group,3 months infants with food sensitization at 1 year,154,12,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant phyla in fecal microbiota of sensitized infants VS non-sensitized infants at 3 months according to food sensitization at 1 year,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota",2|1224|1236|91347|543;2|1224,Complete,ChiomaBlessing
bsdb:240/2/1,Study 240,case-control,25599982,10.1111/cea.12487,NA,"Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA , Kozyrskyj AL",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-sensitized group,sensitized group,1 year infants with food sensitization at 1 year,154,12,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant phyla in fecal microbiota of sensitized infants VS non-sensitized infants at 1 year according to food sensitization at 1 year,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:240/2/2,Study 240,case-control,25599982,10.1111/cea.12487,NA,"Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA , Kozyrskyj AL",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-sensitized group,sensitized group,1 year infants with food sensitization at 1 year,154,12,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant phyla in fecal microbiota of sensitized infants VS non-sensitized infants at 1 year according to food sensitization at 1 year,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|976;2|976|200643|171549|815,Complete,ChiomaBlessing
bsdb:241/1/1,Study 241,case-control,30418043,10.1556/030.65.2018.045,NA,"Muleviciene A, D'Amico F, Turroni S, Candela M , Jankauskiene A",Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study,Acta microbiologica et immunologica Hungarica,2018,"children, dysbiosis, gut microbiota, infants, iron deficiency anemia",Experiment 1,Lithuania,Homo sapiens,Feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,infants and young children with iron deficiency anemia,10,10,None.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Discriminant species-level taxa between iron deficiency anemia (IDA) infants and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale",2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|186802|31979|1485|137838,Complete,ChiomaBlessing
bsdb:241/1/2,Study 241,case-control,30418043,10.1556/030.65.2018.045,NA,"Muleviciene A, D'Amico F, Turroni S, Candela M , Jankauskiene A",Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study,Acta microbiologica et immunologica Hungarica,2018,"children, dysbiosis, gut microbiota, infants, iron deficiency anemia",Experiment 1,Lithuania,Homo sapiens,Feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,infants and young children with iron deficiency anemia,10,10,None.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Discriminant species-level taxa between iron deficiency anemia (IDA) infants and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|189330|39486;2|201174|1760|85004|31953|1678|1681;2|1239|909932|1843489|31977|39948,Complete,ChiomaBlessing
bsdb:242/1/1,Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,"Figure 3b, 4b, Table S2",10 January 2021,Rimsha Azhar,WikiWorks,Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239;2|1224|1236|2887326|468|475;2|1239|91061|186826|1300|1357;2|1224|1236|72274|135621|286;2|1239|91061|186826|81852|1350;2|201174|1760|85006|1268|57493;2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:242/1/2,Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,"Figure 3b, 4b, Table S2",10 January 2021,Rimsha Azhar,WikiWorks,Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|201174;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|482;2|1224|1236|135625|712|416916;2|1224|1236|135615|868|2717,Complete,Folakunmi
bsdb:242/2/1,Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 5b,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1239|91061;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239;2|201174|1760|85006|1268|57493;2|1239|91061|186826;2|1239|91061|186826|1300|1357;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1239|186801|3082720|186804;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300;2|1224|1236|72274|135621,Complete,Claregrieve1
bsdb:242/2/2,Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 5b,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients,decreased,"k__Bacteria|p__Campylobacterota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes",2|29547;2|29547|3031852|213849;2|29547|3031852|213849|72294;2|29547|3031852|213849|72294|194;2|1224|1236|135615|868;2|1224|1236|135615;2|1224|1236|135615|868|2717;2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|416916;2|1224|28216|80840|2975441|215579;2|1224|28216|80840;2|976|117743|200644|49546|1016;2|976|117743;2|976|117743|200644|49546;2|976|117743|200644;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|28216;2|201174|1760|85007;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174;2|201174|1760,Complete,Claregrieve1
bsdb:242/3/1,Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 3,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,iron deficiency anemia moderate,iron deficiency anemia severe,iron defiency anemia,16,8,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|201174|1760|85006|1268|57493;2|1224|28211|204457|335929|1111;2|201174|1760|85004|31953;2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351;2|1239;2|1224|1236;2|1239|91061|186826|1300|1357;2|1224|1236|72274,Complete,Claregrieve1
bsdb:242/3/2,Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 3,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,iron deficiency anemia moderate,iron deficiency anemia severe,iron defiency anemia,16,8,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5d,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1224|1236|135625;2|1224|1236|135625|712;2|1224|28216|206351;2|1224|28216|206351|481,Complete,Claregrieve1
bsdb:243/1/1,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,non-current H.pylori infection,current H.pylori infection,patients with H.pylori infection (bacteria were histologically detected in any one of the biopsies or it was positively indicated by C-UBT),23,24,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2D,10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",differential microbial abundance between current or non-current H.Pylori infection subjects,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|91061|1385|539738|1378;2|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:243/1/2,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,non-current H.pylori infection,current H.pylori infection,patients with H.pylori infection (bacteria were histologically detected in any one of the biopsies or it was positively indicated by C-UBT),23,24,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S2D,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between current or non-current H.Pylori infection subjects,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax facilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus erythropolis",2|1224|28216|80840|80864|12916;2|1224|28216|80840|80864|12916|12917;2|201174|1760|85007|85025;2|201174|1760|85007|85025|1827;2|201174|1760|85007|85025|1827|1833,Complete,Claregrieve1
bsdb:243/2/1,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,past H.pylori infection,current H.pylori infection patients,patients with H.pylori infection (bacteria were histologically detected in any one of the biopsies or it was positively indicated by C-UBT),8,24,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",differential microbial abundance between current and past H.Pylori infection subjects,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|28216|80840|506;2|976|200643|171549;2|976|200643|171549|815|816|820;2|976;2|976|200643;2|1224|28216;2|1224|28216|80840;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552;2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:243/3/1,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,H.pylori negative,past H.pylori infection,subjects with evidence of past H.pylori infection but no current infection,15,8,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between past H.Pylori infection subjects and individuals who are H.Pylori negative,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|820;2|976;2|976|200643;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|310298;2|976|200643|171549|171551,Complete,Claregrieve1
bsdb:243/4/1,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,gastritis cases,subjects with gastric lesions (gastritis),7,18,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,Rukky,WikiWorks",differential microbial abundance between gastritis and non-gastritis (normal) subjects,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|s__Mollicutes bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae sp. B_A14,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium EM3",2|1239|186801|186802|216572|244127;2|1239|91061;2|1239;2|1239|186801;2|1239|186801|3085636|186803|189330;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1224|1236;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|877420;2|1239|91061|186826;2|544448|31969|37628;2|1239|186801|186802|541000;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572|3023528;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|216572|2807717,Complete,Claregrieve1
bsdb:243/4/2,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,gastritis cases,subjects with gastric lesions (gastritis),7,18,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between gastritis and non-gastritis (normal) subjects,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549;2|976;2|976|200643,Complete,Claregrieve1
bsdb:243/5/1,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,subjects with metaplasia,subjects with metaplasia,7,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks,Merit",differential microbial abundance between subjects with metaplasia and normal subjects,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802;2|1239|186801|186802|186806|1730|290054;2|1239|186801|3085636|186803|1506553;2|1224|1236;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804;2|1224;2|1239|186801|3082720|186804|1501226;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979;2|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:243/5/2,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,subjects with metaplasia,subjects with metaplasia,7,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between subjects with metaplasia and normal subjects,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549;2|976;2|976|200643,Complete,Claregrieve1
bsdb:243/6/1,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,subjects with gastritis,subjects with metaplasia,subjects with metaplasia,18,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between gastritis and metaplastia subjects,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota",2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|1224,Complete,Claregrieve1
bsdb:243/6/2,Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,subjects with gastritis,subjects with metaplasia,subjects with metaplasia,18,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks,Merit",differential microbial abundance between gastritis and metaplastia subjects,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:244/1/1,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1b, Supplemental table E2, Figure 2b text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Skin microorganisms differ with age in the healthy skin,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",2|201174|1760|85007|1653|1716|1720;2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2|201174|1760|85009|31957|1743;2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|165779,Complete,Atrayees
bsdb:244/1/2,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1b, Supplemental table E2, Figure 2b text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Skin microorganisms differ with age in the healthy skin,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301|1306;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|91061|186826|186828|117563;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724,Complete,Atrayees
bsdb:244/2/1,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,text,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Atrayees
bsdb:244/2/2,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,text,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|1239|91061|186826|1300|1301;2|201174|1760|85009|31957|1743,Complete,Atrayees
bsdb:244/3/1,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E4,10 January 2021,Lucy Mellor,WikiWorks,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85009|31957|1743;2|201174|1760|85007|1653|1716;2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:244/3/2,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table E4,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|1300|1301;2|1239|91061|186826|186828|117563;2|1239|91061|1385|539738|1378;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:244/4/1,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 4,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E3,10 January 2021,Lucy Mellor,WikiWorks,Taxonomic compositions of the healthy skin microbiome at the species level,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2|1239|91061|186826|33958|1578|147802,Complete,Atrayees
bsdb:244/5/1,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 5,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin in young children,lesional skin in young children,atopic dermatitis lesional skin,69,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the species level among adults-teenagers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85007|1653|1716|38303;2|1239|91061|1385|90964|1279|29388;2|1239|91061|1385|90964|1279|29380;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|45634,Complete,Atrayees
bsdb:244/6/1,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 6,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,10 January 2021,Lucy Mellor,WikiWorks,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among children,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,Atrayees
bsdb:244/7/1,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 7,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|33958|1578|147802;2|1239|91061|1385|90964|1279|1282,Complete,Atrayees
bsdb:244/7/2,Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 7,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table E5,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",2|1239|91061|186826|1300|1301|45634;2|201174|1760|85006|1268|32207|43675,Complete,Atrayees
bsdb:245/1/1,Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,LEfSe,3,FALSE,3,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"KathyWaldron,WikiWorks",LEfSe analysis based on OTU characterizes microbiome between the Kidney Stone group and HC group.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea thiooxidans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium",2|1224|1236|2887326|468|469;2|976|200643|171549|171552|1283313;2|1224|28211|356|2831100|85413;2|1224|28211|356|2831100|85413|53254;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806|1730;2|1239|526524|526525|128827|1573534;2|1239|186801|3085636|186803|1506553;2|1239|909932|909929|1843491|158846;2|1224|1236|2887326|468;2|1224|1236|72274;2|1224|1236|72274|135621|286|287;2|1224|1236|91347|543|620;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|815|2212467,Complete,Atrayees
bsdb:245/1/2,Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,LEfSe,3,FALSE,3,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis based on OTU characterizes microbiome between the Kidney Stone group and HC group.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|1239|186801|186802|216572|1508657;2|1239|186801|3082768|990719;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827|61170;2|1224|28211|204441|2844866|168934;2|1224|28211|204441|41295;2|1224|28211|204441;2|1224|28211;2|508458|649775|649776|3029088|638847;2|508458|649775|649776|3029088|638847|638849;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|841;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803;2|976|200643|171549|171550|239759|328813;2|1224|28216|80840|995019|577310;2|976|200643|171549|815|909656|310297;2|1224|1236|91347|543|547,Complete,Atrayees
bsdb:245/2/1,Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table 2, Figure 2",10 January 2021,Rimsha Azhar,WikiWorks,List of genera that were significantly different between Kidney Stone group and HC group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",2|976|200643|171549|171552|1283313;2|1239|526524|526525|2810280|1505663;2|1239|186801|3085636|186803;2|1239|909932|1843488|909930|33024;2|1239|909932|909929|1843491|158846;2|1224|1236|2887326|468|469;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1224|28216|80840|995019|40544;2|1239|526524|526525|128827;2|1224|1236|2887326|468;2|1224|1236|72274;2|1239|526524|526525,Complete,Atrayees
bsdb:245/2/2,Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table 2, Figure 2",10 January 2021,Rimsha Azhar,WikiWorks,List of genera that were significantly different between Kidney Stone group and HC group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|216572|292632;2|1239|186801|186802|186806|1730|42322;2|1239|526524|526525|128827|1573535;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|577310;2|200940|3031449|213115|194924|35832,Complete,Atrayees
bsdb:246/1/1,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/male caucasian infants,male caucasian infants born to mothers who had prenatal asthma,504,41,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1a,10 January 2021,Lucy Mellor,"KathyWaldron,WikiWorks,Merit,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to male caucasian infants compared to no asthma group.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1239|91061|186826|1300|1357;2|1239|909932|909929|1843491|158846;2|201174|1760|2037|2049|1654;2|1239|91061|186826|1300|1357;2|1239|91061|1385|539738;2|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:246/1/2,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/male caucasian infants,male caucasian infants born to mothers who had prenatal asthma,504,41,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1a,10 January 2021,Lucy Mellor,"KathyWaldron,WikiWorks,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to male caucasian infants compared to no asthma group.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1224|1236|91347|543|158851;2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:246/2/1,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma,female caucasian infants born to mothers who had prenatal asthma,430,46,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1b,10 January 2021,Lucy Mellor,"KathyWaldron,WikiWorks,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to female caucasian infants compared to no asthma group.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643|171549|815|816|817;2|976|200643;2|976;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:246/2/2,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma,female caucasian infants born to mothers who had prenatal asthma,430,46,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1b,10 January 2021,Lucy Mellor,"WikiWorks,Merit,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to female caucasian infants compared to no asthma group.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906;2|1239|186801|186802|31979|1485|1506,Complete,Folakunmi
bsdb:246/4/1,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants,mothers of caucasian infants who had prenatal asthma,721,74,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian infants",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:246/5/1,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 5,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/female infants,"prenatal asthma mothers of female infants who were vaginally delivered, breastfed, not exposed to maternal antibiotics",186,21,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S2,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa in infant gut microbiota according to material prenatal asthma in female infants, vaginally delivered, breastfed, not exposed to materal antibiotics during birth",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|976|200643|171549|815;2|976|200643|171549|815|816;2|976;2|1239|186801|3085636|186803|189330,Complete,Folakunmi
bsdb:246/5/2,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 5,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/female infants,"prenatal asthma mothers of female infants who were vaginally delivered, breastfed, not exposed to maternal antibiotics",186,21,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S2,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa in infant gut microbiota according to material prenatal asthma in female infants, vaginally delivered, breastfed, not exposed to materal antibiotics during birth",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239;2|1224;2|1224|1236|91347|543,Complete,Folakunmi
bsdb:246/6/1,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 6,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants/allergies,"prenatal asthma mothers of caucasian infants, who had allergies during pregnancy",429,64,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with allergies during pregnancy",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|1224|1236|91347|543,Complete,Folakunmi
bsdb:246/7/1,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 7,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants/no allergies,"prenatal asthma mothers of caucasian infants, who had no allergies during pregnancy",278,10,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with no allergies during pregnancy",increased,"k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|74201;2|74201|203494|48461|203557;2|74201|203494|48461|1647988|239934,Complete,Folakunmi
bsdb:246/7/2,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 7,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants/no allergies,"prenatal asthma mothers of caucasian infants, who had no allergies during pregnancy",278,10,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S3,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with no allergies during pregnancy",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654,Complete,Folakunmi
bsdb:246/8/1,Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 8,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,overweight prenatal asthma caucasian mothers,"prenatal asthma mothers of caucasian infants, who were overweight/obese before pregnancy",291,33,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,27 February 2024,Folakunmi,Folakunmi,"Median relative abundance of bacterial taxa at phylum, family and genus level in fecal microbiota at 3-4 months according to maternal asthma during pregnancy, restricted to Caucasian mothers and stratified by maternal pre-pregnancy weight",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|1239|91061|186826|33958|1578;2|1239|91061|186826|81850;2|1239|909932|1843489|31977|906,Complete,Folakunmi
bsdb:247/1/1,Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Prebiotic,Placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|119852;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:247/1/2,Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Prebiotic,Placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:247/2/1,Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 2,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with low dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:247/3/1,Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 3,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with high dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy",Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:247/3/2,Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 3,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with high dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:247/4/1,Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 4,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Low dietary fiber,High dietary fiber,Placebo (control for prebiotic intake - representing lower fiber group),14,20,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 7,10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy","Mean genus level changes after the prebiotic intervention between the
low ( ) and high dietary fibre ( ) groups. * Significant change (P <0·05) as
analysed by a two-way repeated-measures ANOVA (blocked by participant)
and least significant difference test.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:247/4/2,Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 4,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Low dietary fiber,High dietary fiber,Placebo (control for prebiotic intake - representing lower fiber group),14,20,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 7,21 February 2024,Peace Sandy,Peace Sandy,Mean genus level changes after the prebiotic intervention between the low ( ) and high dietary fibre ( ) groups. * Significant change (P <0·05) as analysed by a two-way repeated-measures ANOVA (blocked by participant) and least significant difference test.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:248/1/1,Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 1,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,low risk hpv,high risk hpv,High risk HPV infection confirmed through HPV genotyping test,57,30,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for high-risk HPV by LefSe,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota",2|1224|1236|72274|135621|351;2|1239|91061|186826|186827;2|201174|84998|84999;2|201174|84998|84999|84107|33870;2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|32066|203490|203491;2|32066,Complete,Fatima Zohra
bsdb:248/1/2,Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 1,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,low risk hpv,high risk hpv,High risk HPV infection confirmed through HPV genotyping test,57,30,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for high-risk HPV by LefSe,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae",2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|135625|712|724;2|1224|28211;2|1224|1236;2|1224|1236|72274;2|1224|28211|356|69277|28100;2|1224|28211|356;2|1224|28211|356|69277,Complete,Fatima Zohra
bsdb:248/2/1,Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 2,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV,HPV,HPV infection confirmed through HPV genotyping test,50,37,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,supplemental figure 2,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for HPV by LefSe.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|1224|28211;2|1224|28211|766;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|2701,Complete,Fatima Zohra
bsdb:248/2/2,Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 2,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV,HPV,HPV infection confirmed through HPV genotyping test,50,37,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,supplemental figure 2,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for HPV by LefSe.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales",2|1224|1236;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|72274;2|29547|3031852|213849;2|29547;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|76761;2|1224|1236|72274|135621|351;2|1224|28211|356;2|1224|28211|356|69277;2|1224|28211|356|69277|28100;2|1224|28211|204458|76892;2|1224|28211|204458,Complete,Fatima Zohra
bsdb:249/1/1,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,alcoholics,alcoholic hepatitis,20,56,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 2B,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|28211|356|41294|374;2|201174|1760|85006|85023|33882;2|1239|186801|3085636|186803|1843210;2|201174|1760|85007|1653|1716;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803,Complete,NA
bsdb:249/1/2,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,alcoholics,alcoholic hepatitis,20,56,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 2B,10 January 2021,Fatima Zohra,WikiWorks,Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis|g__Thermicanus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|201174|1760|85007|85026|2053;2|201174|1760|85009|85015|1839;2|201174|1760|85009|85015|53387;2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|976|200643|171549|171550|239759;2|976|117743|200644|49546|237;2|1239|91061|1385|186817|182709;2|1239|91061|1385|539003|94008;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|1263;2|1224|28211|356|119045|186650;2|1224|28211|204455|31989|265;2|1224|28211|766|775|780;2|1224|28216|80840|114248;2|1224|28216|80840|80864|12916;2|1224|28216|80840|80864|47420;2|1224|28216|80840|2975441|215579;2|1224|28216|80840|75682|29580;2|1224|2008785|119069|206349|70774;2|1224|1236|135624|84642|642,Complete,NA
bsdb:249/2/1,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,HDC,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1224|1236|2887326|468|469;2|1239|1737404|1737405|1570339|165779;2|1224|28211|356|41294|374;2|976|117743|200644|2762318|59732;2|201174|1760|85006|1268|57493;2|32066|203490|203491|1129771;2|201174|1760|85006|85023|33882;2|1224|28216|206351|481|482;2|1224|28211|204458|76892|20;2|201174|1760|85011|2062|1883;2|1224|28211|204455|31989|1060;2|1239|186801|3082720|186804,Complete,NA
bsdb:249/2/2,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,HDC,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,10 January 2021,Fatima Zohra,WikiWorks,differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",2|201174|1760|85007|85026|2053;2|201174|1760|85009|85015|1839;2|201174|1760|85004|31953|1678;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|976|200643|171549|171551;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|117743|200644|49546|237;2|1239|91061|186826|1300|1301;2|1239|186801|186802|31979|1485;2|1224|28216|80840|114248;2|1224|28216|80840|80864|12916;2|1224|2008785|119069|206349|70774;2|1224|1236|72274|135621|351,Complete,NA
bsdb:249/3/1,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 3,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,MAH,alcoholic hepatitis,20,18,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",2|1239|186801|3082720|186804;2|1224|1236|2887326|468|469;2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|165779;2|1224|28211|356|41294|374;2|1239|91061|186826|186828;2|976|117743|200644|2762318|501783;2|201174|1760|85007|1653|1716;2|1224|28216|80840|80864|281915;2|1239|91061|186826|186828|117563;2|1224|28211|356|119045|407,Complete,NA
bsdb:249/3/2,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 3,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,MAH,alcoholic hepatitis,20,18,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,10 January 2021,Fatima Zohra,WikiWorks,differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",2|201174|1760|85009|85015|1839;2|201174|1760|85009|85015|53387;2|201174|1760|2037;2|976|200643|171549;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|117743|200644|49546|237;2|1239|91061|1385|186817|1386;2|1239|186801|186802|31979|1485;2|1224|28211|204457|41297;2|1224|28216|80840|75682|29580;2|1224|28216|80840;2|1224|2008785|119069|206349|70774;2|1224|1236|135624|84642;2|1224|1236|72274|135621|351,Complete,NA
bsdb:249/4/1,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 4,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,SAH,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,10 January 2021,Fatima Zohra,"Atrayees,WikiWorks",differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Gillisia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae",2|201174|1760|2037|2049|1654;2|1239|91061|186826|186828|1651;2|201174|1760|85006|85020|43668;2|201174|1760|85007|1653|1716;2|976|117743|200644|49546|244698;2|201174|1760|85006|85023|33882;2|201174|1760|85008|28056,Complete,NA
bsdb:249/4/2,Study 249,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 4,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,SAH,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,10 January 2021,Fatima Zohra,WikiWorks,differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH),decreased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae",2|201174|84992|84993;2|201174|1760|85006|85023;2|201174|1760|85009|85015|1839;2|201174|1760|2037;2|201174|1760|85004|31953|1678;2|976|200643|171549;2|976|200643|171549|2005519|397864;2|976|200643|171549|171551;2|976|200643|171549|171552;2|976|200643|171549|171550|239759;2|976|117743|200644|49546|237;2|976|1853228|1853229|563835;2|976|768503|768507|89373,Complete,NA
bsdb:250/1/1,Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 1,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,baseline,hematopoietic stem cell transplantation engraftment,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,2345678,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 8a,10 January 2021,Shaimaa Elsafoury,"WikiWorks,Atrayees,Folakunmi",Statistically significant bacteria as determined by Lefse analysis for hematopoietic stem cell transplantation patients between the baseline timepoint and engraftment timepoint,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.",2|1224|1236|135625|712|724|729;2|201174|1760|85006|1268|32207|43675;2|201174|1760|2037|2049|1654|114702;2|1239|91061|1385|539738|1378|84135;2|1239|186801|3085636|186803|265975|237576;2|976|200643|171549|171552|838|28129;2|1239|91061|1385|539738|1378|1379;2|1224|28216|206351|481|482;2|32066|203490|203491|203492|848|860;2|1239|186801|3085636|186803|1213720;2|976|200643|171549|171552|2974257|425941;2|976|200643|171549|171551|836|1924944,Complete,NA
bsdb:250/2/1,Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 2,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,baseline,hematopoietic stem cell transplantation engraftment,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,3456789,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,10 January 2021,Shaimaa Elsafoury,WikiWorks,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis",2|1224|1236|135625|712|724|729;2|201174|1760|2037|2049|1654|114702;2|1239|91061|1385|539738|1378|84135;2|1239|186801|3085636|186803|265975|237576;2|1224|28216|206351|481|482;2|976|200643|171549|171552|2974257|425941,Complete,NA
bsdb:250/3/1,Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 3,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,engraftment,hematopoietic stem cell transplantation 100 days after the transplant,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,2345678,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,10 January 2021,Shaimaa Elsafoury,WikiWorks,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis",2|1224|1236|135625|712|724|729;2|1239|91061|1385|539738|1378|84135,Complete,NA
bsdb:250/4/1,Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 4,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,engraftment,hematopoietic stem cell transplantation 100 days after the transplant,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,3456789,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,10 January 2021,Shaimaa Elsafoury,WikiWorks,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,2|201174|1760|85006|1268|32207|43675,Complete,NA
bsdb:251/1/1,Study 251,laboratory experiment,30643289,10.1038/s41591-018-0324-z,NA,"Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R , Nagler CR",Healthy infants harbor intestinal bacteria that protect against food allergy,Nature medicine,2019,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy Infants-colonised mice,cow’s milk allergic (CMA) infants-colonized mice,Germ-free mice colonised with human feces from cow’s milk allergic (CMA) infant donors,8,9,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,mode of birth,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 2e,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees,Joan Chuks",LEfSe analysis of genera that are differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|526524|526525|2810280|100883;2|1239|91061|186826|81852|1350;2|1239|186801|186802;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263;2|976|200643|171549|2005519;2|1239|186801|186802;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:251/1/2,Study 251,laboratory experiment,30643289,10.1038/s41591-018-0324-z,NA,"Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R , Nagler CR",Healthy infants harbor intestinal bacteria that protect against food allergy,Nature medicine,2019,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy Infants-colonised mice,cow’s milk allergic (CMA) infants-colonized mice,Germ-free mice colonised with human feces from cow’s milk allergic (CMA) infant donors,8,9,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,mode of birth,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 2e,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees,Joan Chuks",LEfSe analysis of genera that are differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|1236|91347|543;2|1224|1236|91347|543|590;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543;2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:252/1/1,Study 252,case-control,31211854,10.1111/sji.12799,NA,"Huang S, Mao J, Zhou L, Xiong X , Deng Y",The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients,Scandinavian journal of immunology,2019,"cytokines, gut microbiota, pemphigus vulgaris",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pemphigus vulgaris,EFO:0004719,healthy control,Pemphigus vulgaris (PV)  Patients,Patients with pemphigus vulgaris,14,18,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2b,10 January 2021,Lucy Mellor,"Chloe,WikiWorks",Bacterial taxa difference between pemphigus vulgaris (PV) patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827;2|1239|91061;2|1239|91061|186826|186828;2|1239|526524|526525|2810280|100883;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|186802|216572|946234;2|1224|1236;2|1239|91061|186826|186828|117563;2|1239|91061|186826;2|1239|91061|186826|1300;2|1224|1236|91347|543|1940338,Complete,Chloe
bsdb:252/1/2,Study 252,case-control,31211854,10.1111/sji.12799,NA,"Huang S, Mao J, Zhou L, Xiong X , Deng Y",The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients,Scandinavian journal of immunology,2019,"cytokines, gut microbiota, pemphigus vulgaris",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pemphigus vulgaris,EFO:0004719,healthy control,Pemphigus vulgaris (PV)  Patients,Patients with pemphigus vulgaris,14,18,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2b,10 January 2021,Lucy Mellor,"WikiWorks,Merit",Bacterial taxa difference between pemphigus vulgaris (PV) patients and healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1224|28211;2|1224|28216;2|1224|28216|80840;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042,Complete,Chloe
bsdb:253/1/1,Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 1,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma,asthma,31,31,3 months,16S,123,Roche454,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|91061|1385|90964|1279;2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:253/1/2,Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 1,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma,asthma,31,31,3 months,16S,123,Roche454,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma and healthy controls,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,Folakunmi
bsdb:253/2/1,Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 2,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma remission,asthma remission,31,30,3 months,16S,123,Roche454,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma remission and healthy controls,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|543311,Complete,Folakunmi
bsdb:253/2/2,Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 2,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma remission,asthma remission,31,30,3 months,16S,123,Roche454,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma remission and healthy controls,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,Folakunmi
bsdb:254/1/1,Study 254,"cross-sectional observational, not case-control",27115405,10.1007/s00240-016-0882-9,NA,"Stern JM, Moazami S, Qiu Y, Kurland I, Chen Z, Agalliu I, Burk R , Davies KP",Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers,Urolithiasis,2016,"Gut microbiome, Kidney stones, Nephrolithiasis, Urolithiasis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"Nephrolithiasis,Urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone patient,patients with kidney stones,6,23,2 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,10 January 2021,Rimsha Azhar,"WikiWorks,Claregrieve1",Differential abundance of the microbiota between kidney stone formers and non-stone forming controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288,Complete,Claregrieve1
bsdb:254/1/2,Study 254,"cross-sectional observational, not case-control",27115405,10.1007/s00240-016-0882-9,NA,"Stern JM, Moazami S, Qiu Y, Kurland I, Chen Z, Agalliu I, Burk R , Davies KP",Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers,Urolithiasis,2016,"Gut microbiome, Kidney stones, Nephrolithiasis, Urolithiasis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"Nephrolithiasis,Urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone patient,patients with kidney stones,6,23,2 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2b,10 January 2021,Rimsha Azhar,"WikiWorks,Claregrieve1",The composition of the microbiota between kidney stone formers and non-stone forming controls,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171552|838;2|201174|1760|2037|2049|184869,Complete,Claregrieve1
bsdb:255/1/1,Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 1,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,23,45,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between unmatched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1224|1236|72274|135621|351;2|1239|91061|1385|90964|1279;2|1224|1236|72274;2|544448;2|544448|31969|2085;2|1239|91061|1385|90964,Complete,Fatima Zohra
bsdb:255/1/2,Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 1,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,23,45,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between unmatched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",2|1224|1236;2|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
bsdb:255/2/1,Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 2,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,4,4,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,figure 6b,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales",2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|543311;2|544448;2|544448|31969;2|544448|31969|2085,Complete,Fatima Zohra
bsdb:255/2/2,Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 2,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,4,4,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,figure 6b,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578|147802;2|1239|91061;2|1239|91061|186826;2|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
bsdb:255/3/1,Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 3,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,HIV infection,EFO:0000764,HIV-,HIV+,HIV+ comfirmed by Standard Diagnostics HIV-1/2 3.0 detection kit,95,39,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,figure 6c,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",LEfSe linear discriminant analysis (LDA) scores.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|201174|1760|2037|2049;2|201174|1760|2037;2|1239|91061|186826|186827|1375;2|1224|28211;2|1239;2|201174|1760|85004|31953;2|1239|91061|186826|186828;2|1239|186801;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724|727;2|544448|31969;2|1239|186801|3085636|186803|437755;2|544448|31969|2085|2092;2|544448|31969|2085;2|544448;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1239|186801|3082720|186804|1257|1261;2|1224|28211|356|82115;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1328,Complete,Fatima Zohra
bsdb:255/3/2,Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 3,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,HIV infection,EFO:0000764,HIV-,HIV+,HIV+ comfirmed by Standard Diagnostics HIV-1/2 3.0 detection kit,95,39,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,figure 6c,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|2037|2049|28263;2|544448|2790996|2790998|2129;2|1239|91061|186826|33958|2742598|1598;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953|1678,Complete,Fatima Zohra
bsdb:256/1/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,peritumoral tissues,gastric cancer,230,247,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between peritumoral tissues and normal tissues,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Aquabacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|74201|203494|48461|1647988|239934|239935;2|1224|28211|356|335928|45402;2|976|200643|171549|815|816|817;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1224|28211|356|119045|407;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1224;2|1239|909932|909929|1843491|970;2|1224|1236|135622|267890|22;2|1224|1236|135622|267890;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:256/1/2,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,peritumoral tissues,gastric cancer,230,247,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between peritumoral tissues and normal tissues,decreased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|57723;2|1239|91061|1385|186817;2|1239;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817|1386|1396;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976;2|200795;2|201174|1760|85007|1653|1716;2|1224|1236|91347|543;2|1239|186801|186802|216572|216851;2|32066;2|32066|203490|203491|203492|848;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|201174|1760|85009|31957|1743;2|1224|1236|72274|135621|286;2|976|200643|171549|171552|2974251|165179;2|1224|28211|204457|41297;2|1224|28211|204457|41297|13687,Complete,Claregrieve1
bsdb:256/2/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumoral tissues,tumoral tissues,gastric cancer,247,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,increased,NA,unchanged,Signature 1,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and peritumoral tissues,increased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|57723;2|1224|1236|72274|135621|351;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817|1386|1396;2|200795;2|1224|1236|91347|543;2|1239|186801|3085636|186803;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552;2|201174|1760|85009|31957|1743;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301|1328,Complete,Claregrieve1
bsdb:256/2/2,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumoral tissues,tumoral tissues,gastric cancer,247,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,increased,NA,unchanged,Signature 2,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and peritumoral tissues,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1239|186801|186802|216572|216851;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|29547|3031852|213849|72293|209|210;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551;2|1224;2|1224|1236|135622|267890|22;2|1224|1236|135622|267890;2|976|117747|200666|84566;2|1224|28211|204457|41297|13687,Complete,Claregrieve1
bsdb:256/3/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,tumoral tissues,gastric cancer,230,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and normal tissues,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174;2|74201|203494|48461|1647988|239934|239935;2|1239;2|1239|91061|1385|186817|1386;2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216|1747;2|32066;2|32066|203490|203491|203492|848;2|1224|1236|135619|28256|2745;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804;2|976|200643|171549|171552|838|28132;2|201174|1760|85009|31957|1743;2|1239|909932|909929|1843491|970;2|1224|1236|135622|267890|22;2|1224|1236|135622|267890;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1328;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:256/3/2,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,tumoral tissues,gastric cancer,230,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and normal tissues,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|1236|72274|135621|351;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|815|816|820;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293|209|210;2|29547|3031852|213849|72293;2|1224;2|1224|1236|72274|135621|286;2|976|200643|171549|171552|2974251|165179;2|1224|28211|204457|41297|13687,Complete,Claregrieve1
bsdb:256/4/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 4,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,early stage normal,early stage tumor,gastric cancer,112,116,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Early-stage gastric microbiota between normal and tumor samples,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|1300|1301|1328,Complete,Claregrieve1
bsdb:256/4/2,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 4,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,early stage normal,early stage tumor,gastric cancer,112,116,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,decreased,unchanged,NA,NA,Signature 2,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Early-stage gastric microbiota between normal and tumor samples,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae",2|976|200643|171549|171552|2974251|165179;2|1224|28211|204457|41297|13687|172044,Complete,Claregrieve1
bsdb:256/5/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 5,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,early stage normal,early stage peritumor,gastric cancer,112,118,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Early-stage gastric microbiota in normal and peritumor samples,decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae,2|1224|28211|204457|41297|13687|172044,Complete,Claregrieve1
bsdb:256/6/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 6,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,late stage normal,late stage tumor,gastric cancer,118,113,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Late-stage gastric microbiota in normal and tumor samples,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|1300|1301|1328,Complete,Claregrieve1
bsdb:256/8/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 8,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,late stage normal,late stage peritumor,gastric cancer,118,129,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",late-stage gastric microbiota in normal vs peritumor samples,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,2|976|200643|171549|171552|2974251|165179,Complete,Claregrieve1
bsdb:256/9/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 9,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal HP-,normal HP+,normal samples that are H. Pylori positive,64,166,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 5l, Supp FigS9",10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota",2|1224|28216|80840;2|1224|28216|80840|75682|149698;2|1224|28216|80840|75682;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|1224|28211|356|119045|407;2|1224|28211|356|119045;2|1239|186801|3085636|186803;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1224|28211|204457|41297;2|1224|28211;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|29547|3031852|213849|72293;2|29547|3031852|213849|72293|209;2|29547|3031852|213849;2|29547;2|1224,Complete,Claregrieve1
bsdb:256/9/2,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 9,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal HP-,normal HP+,normal samples that are H. Pylori positive,64,166,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,"Figure 5, Supp FigS9",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|909932|1843488|909930;2|1224|1236|135622;2|1224|28216;2|1239|186801|3085636|186803|572511;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|186802|204475;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|1224|1236|135619;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|1236|135622|267890|22;2|1224|1236|135622|267890;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:256/10/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 10,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor HP-,peritumor HP+,peritumor samples that are H. Pylori positive,65,182,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure S10,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis",2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061|1385|186817|1386;2|29547|3031852|213849;2|29547;2|1239|91061|1385|539738|1378;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1224;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|1385|539003,Complete,Claregrieve1
bsdb:256/10/2,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 10,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor HP-,peritumor HP+,peritumor samples that are H. Pylori positive,65,182,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure S10,10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|186801;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930;2|1239|186801|186802;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|216851;2|976|200643|171549|171550|239759;2|976|200643|171549|171550;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|541000;2|1239|186801|186802|204475;2|1239|909932|909929|1843491|158846;2|1239|91061|1385|186817|1386;2|1239|91061|186826;2|976|200643|171549|2005525|375288,Complete,Claregrieve1
bsdb:256/11/1,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 11,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,tumor HP-,tumor HP+,tumor samples that are H. Pylori positive,77,152,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S11,10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota",2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|28211|204458;2|1224|28211|204458|76892;2|1224|28211|204458|76892|41275;2|1224|28211|356;2|1224|28211;2|1239|186801|3085636|186803|572511;2|1224|28216|80840;2|1224|28216|80840|75682|149698;2|1224|28211|204457;2|976|117747|200666|84566;2|1224|28211|204457|41297|165696;2|29547|3031852|213849|72293;2|29547|3031852|213849|72293|209;2|29547|3031852|213849;2|29547,Complete,Claregrieve1
bsdb:256/11/2,Study 256,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 11,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,tumor HP-,tumor HP+,tumor samples that are H. Pylori positive,77,152,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure S11,10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468;2|1239|186801|186802|216572|1263;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351;2|1224|1236|72274;2|1224|28216;2|1224|28211|356|118882;2|1224|28211|204457|41297|13687;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|1224,Complete,Claregrieve1
bsdb:257/1/1,Study 257,case-control,29687353,10.1007/s00430-018-0542-5,NA,"Allali I, Boukhatem N, Bouguenouch L, Hardi H, Boudouaya HA, Cadenas MB, Ouldim K, Amzazi S, Azcarate-Peril MA , Ghazal H",Gut microbiome of Moroccan colorectal cancer patients,Medical microbiology and immunology,2018,"16S rRNA sequencing, Bacterial community, Colorectal cancer, Gut microbiome composition, Moroccan population",Experiment 1,Morocco,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control,colorectal cancer,untreated colorectal cancer patients,12,11,3 months,16S,12,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region","body mass index,family history of cancer,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,Table 2 and text,10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial taxa between controls and CRC patients,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|74201|203494|48461|1647988|239934;2|200940|3031449|213115|194924|35832;2|976|200643|171549|1853231|574697;2|1239|186801|3082768|990719|990721;2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186807|51514;2|200940|3031449|213115|194924;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|1224|28216|80840|75682|846;2|976|200643|171549|2005525|375288;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1239|186801|186802|216572|1263;2|1239|909932|909929|1843491|970;2|1239|186801|3085636|186803;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730,Complete,Claregrieve1
bsdb:257/1/2,Study 257,case-control,29687353,10.1007/s00430-018-0542-5,NA,"Allali I, Boukhatem N, Bouguenouch L, Hardi H, Boudouaya HA, Cadenas MB, Ouldim K, Amzazi S, Azcarate-Peril MA , Ghazal H",Gut microbiome of Moroccan colorectal cancer patients,Medical microbiology and immunology,2018,"16S rRNA sequencing, Bacterial community, Colorectal cancer, Gut microbiome composition, Moroccan population",Experiment 1,Morocco,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control,colorectal cancer,untreated colorectal cancer patients,12,11,3 months,16S,12,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region","body mass index,family history of cancer,sex",NA,NA,NA,NA,NA,unchanged,Signature 2,Table 2 and text,10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial taxa between controls and CRC patients,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",2|1239|909932|909929|1843491|158846;2|1224|28211|356|41294;2|1239|909932|909929|1843491|52225,Complete,Claregrieve1
bsdb:258/1/1,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 1,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 2 and text,10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy",LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1224|1236|91347|543;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803;2|976|200643|171549|171551|836;2|1239|186801|186802|31979|1485;2|976|200643|171549|171551,Complete,Peace Sandy
bsdb:258/1/2,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 1,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 2 and text,10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy",LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|815|816;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|91061|1385|90964|1279;2|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:258/2/1,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Adenoma,Patients with colonic adenoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,19 January 2024,Peace Sandy,Peace Sandy,LeFSe analysis for healthy vs. adenoma clinical groups. LDA values are represented for OTUs enriched in healthy and adenoma clinical groups.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1239|186801|186802|31979|1485;2|976|200643|171549|171551;2|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:258/2/2,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Adenoma,Patients with colonic adenoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 1,19 January 2024,Peace Sandy,Peace Sandy,LeFSe analysis for healthy vs. adenoma clinical groups. LDA values are represented for OTUs enriched in healthy and adenoma clinical groups.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803;2|976|200643|171549|1853231|283168,Complete,Peace Sandy
bsdb:258/3/1,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 3,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colonic lesions,Combination of the clinical and microbiome data from adenoma and carcinoma subjects to create a combined colonic lesion group.,30,60,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 3,19 January 2024,Peace Sandy,Peace Sandy,LeFSe analysis for healthy vs. colonic lesion clinical groups.  Adenoma and carcinoma clinical groups were combined into one clinical group (colonic lesion clinical group).  LDA values are represented for OTUs enriched in healthy and combined colonic lesions clinical groups.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|976|200643|171549|171551;2|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:258/3/2,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 3,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colonic lesions,Combination of the clinical and microbiome data from adenoma and carcinoma subjects to create a combined colonic lesion group.,30,60,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 3.,19 January 2024,Peace Sandy,Peace Sandy,LeFSe analysis for healthy vs. colonic lesion clinical groups. Adenoma and carcinoma clinical groups were combined into one clinical group (colonic lesion clinical group). LDA values are represented for OTUs enriched in healthy and combined colonic lesions clinical groups.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|815|816;2|1239|186801|3085636|186803;2|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:258/4/1,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 4,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 4.,19 January 2024,Peace Sandy,Peace Sandy,LeFSe analysis for adenoma vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in adenoma and carcinoma clinical groups.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|32066|203490|203491|203492|848;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551|836,Complete,Peace Sandy
bsdb:258/4/2,Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 4,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 4,19 January 2024,Peace Sandy,Peace Sandy,LeFSe analysis for adenoma vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in adenoma and carcinoma clinical groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|1263;2|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:259/1/1,Study 259,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M, Jo JH, Kennedy EA, Polley EC, Segre JA, Simpson EL , Kong HH",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Skin of cheek,UBERON:0008803,Atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,during study,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in cheek sample,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:259/2/1,Study 259,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M, Jo JH, Kennedy EA, Polley EC, Segre JA, Simpson EL , Kong HH",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Skin of forearm,UBERON:0003403,Atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,during study,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in dorsal forearm sample,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:259/2/2,Study 259,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M, Jo JH, Kennedy EA, Polley EC, Segre JA, Simpson EL , Kong HH",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Skin of forearm,UBERON:0003403,Atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,during study,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in volar forearm sample,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:260/1/1,Study 260,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B, Naaber P, Sepp E , Mikelsaar M",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 1,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Nonallergic  Estonian children.,Allergic Estonian children.,2-year-old children with confirmed diagnosis of allergy,16,13,NIL,NA,NA,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1,10 January 2021,Lucy Mellor,"WikiWorks,Peace Sandy","Intestinal microflora of 13 allergic (grey) and 16 nonallergic
(white) Estonian children. The results are presented as colonization
rate (%, columns) and counts (log CFU/g, range and median, lines
and filled symbols).",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,Peace Sandy
bsdb:260/1/2,Study 260,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B, Naaber P, Sepp E , Mikelsaar M",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 1,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Nonallergic  Estonian children.,Allergic Estonian children.,2-year-old children with confirmed diagnosis of allergy,16,13,NIL,NA,NA,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1.,10 January 2021,Lucy Mellor,"WikiWorks,Peace Sandy","Intestinal microflora of 13 allergic (grey) and 16 nonallergic (white) Estonian children. The results are presented as colonization rate (%, columns) and counts (log CFU/g, range and median, lines and filled symbols).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:260/2/1,Study 260,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B, Naaber P, Sepp E , Mikelsaar M",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 2,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Non-allergic Swedish children.,Allergic Swedish children,2-year-old children with confirmed diagnosis of allergy,19,14,NIL,NA,NA,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2,29 February 2024,Peace Sandy,Peace Sandy,"Intestinal microflora of 14 allergic (grey) and 19 nonallergic
(white) Swedish children. The results are presented as colonization
rate (%, columns) and counts (log CFU/g, range and median, lines
and filled symbols).",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,Peace Sandy
bsdb:260/2/2,Study 260,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B, Naaber P, Sepp E , Mikelsaar M",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 2,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Non-allergic Swedish children.,Allergic Swedish children,2-year-old children with confirmed diagnosis of allergy,19,14,NIL,NA,NA,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2.,29 February 2024,Peace Sandy,Peace Sandy,"Intestinal microflora of 14 allergic (grey) and 19 nonallergic(white) Swedish children. The results are presented as colonization rate (%, columns) and counts (log CFU/g, range and median, lines and filled symbols).",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:261/1/1,Study 261,"cross-sectional observational, not case-control",29434076,10.1620/tjem.244.113,NA,"Hamada S, Masamune A, Nabeshima T , Shimosegawa T",Differences in Gut Microbiota Profiles between Autoimmune Pancreatitis and Chronic Pancreatitis,The Tohoku journal of experimental medicine,2018,"16S sequence, microbiome, next generation sequencing, pancreatic cancer, pancreatitis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic pancreatitis,EFO:0000342,chronic pancreatitis,autoimmune pancreatitis type 1,autoimmune pancreatitis type 1,8,12,NA,16S,45,Illumina,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",10 January 2021,Rimsha Azhar,"Claregrieve1,Atrayees,WikiWorks",Differential microbial abundance between patients with type 1 autoimmune pancreatitis (AIP) and chronic pancreatitis (CP),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium lacusfryxellense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans",2|976|200643|171549|815|816|28116;2|1239|186801|186802|31979|1485|205328;2|1239|186801|3085636|186803|2719313|460384;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1302;2|1239|186801|3085636|3118652|2039240|160404,Complete,Claregrieve1
bsdb:262/1/1,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 1,United States of America,Homo sapiens,"Bronchus,Nose","UBERON:0000004,UBERON:0002185",Atopic asthma,EFO:0010638,bronchial brush specimens,nasal brush speciments,nasal brush specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and nasal brush (NB) specimen types,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|186826|186828|1651;2|201174|1760|85007|1653|1716;2|1224|1236|2887326|468|475;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:262/1/2,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 1,United States of America,Homo sapiens,"Bronchus,Nose","UBERON:0000004,UBERON:0002185",Atopic asthma,EFO:0010638,bronchial brush specimens,nasal brush speciments,nasal brush specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and nasal brush (NB) specimen types,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:262/2/1,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 2,United States of America,Homo sapiens,"Bronchus,Mouth","UBERON:0000165,UBERON:0002185",Atopic asthma,EFO:0010638,bronchial brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and oral wash (OW) specimen types,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:262/2/2,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 2,United States of America,Homo sapiens,"Bronchus,Mouth","UBERON:0000165,UBERON:0002185",Atopic asthma,EFO:0010638,bronchial brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and oral wash (OW) specimen types,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|1224|1236|2887326|468|475;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:262/3/1,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 3,United States of America,Homo sapiens,"Nose,Sputum","UBERON:0000004,UBERON:0007311",Atopic asthma,EFO:0010638,nasal brush specimens,induced sputum specimens,induced sputum specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,OdigiriGreat",Differential microbial abundance between paired Nasal brush (NB) and induced sputum (IS) specimen types,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:262/3/2,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 3,United States of America,Homo sapiens,"Nose,Sputum","UBERON:0000004,UBERON:0007311",Atopic asthma,EFO:0010638,nasal brush specimens,induced sputum specimens,induced sputum specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,OdigiriGreat",Differential microbial abundance between paired Nasal brush (NB) and induced sputum (IS) specimen types,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|186826|186828|1651;2|201174|1760|85007|1653|1716;2|1224|1236|2887326|468|475;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:262/4/1,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 4,United States of America,Homo sapiens,"Nose,Mouth","UBERON:0000004,UBERON:0000165",Atopic asthma,EFO:0010638,nasal brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired nasal brush (NB) and oral wash (OW) specimen types,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:262/4/2,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 4,United States of America,Homo sapiens,"Nose,Mouth","UBERON:0000004,UBERON:0000165",Atopic asthma,EFO:0010638,nasal brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired nasal brush (NB) and oral wash (OW) specimen types,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|186826|186828|1651;2|201174|1760|85007|1653|1716;2|1224|1236|2887326|468|475;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:262/5/1,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 5,United States of America,Homo sapiens,"Sputum,Mouth","UBERON:0000165,UBERON:0007311",Atopic asthma,EFO:0010638,induced sputum specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,2|201174|1760|2037|2049|1654,Complete,Claregrieve1
bsdb:262/5/2,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 5,United States of America,Homo sapiens,"Sputum,Mouth","UBERON:0000165,UBERON:0007311",Atopic asthma,EFO:0010638,induced sputum specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:262/6/1,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 6,United States of America,Homo sapiens,"Bronchus,Sputum","UBERON:0002185,UBERON:0007311",Atopic asthma,EFO:0010638,bronchial brush specimens,induced sputum specimens,induced sputum specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and induced sputum (IS) specimen types,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|32066|203490|203491|1129771|32067;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:262/7/1,Study 262,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 7,United States of America,Homo sapiens,Nose,UBERON:0000004,Atopic asthma,EFO:0010638,healthy controls,atopic asthma subjects,subjects with atopic asthma,11,22,3 months,16S,4,Illumina,Zero-Inflated Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6B,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,Chloe",Asthmatic subjects showed significant enrichment in a number of specific Staphylococcus taxa in NB samples compared to HCs.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae",2|1239|91061|1385|90964|1279;2|1224|28216|206351|481;2|201174|1760|85007|1653|1716;2|1224|28216|80840|80864|47420;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|186818,Complete,Claregrieve1
bsdb:263/1/1,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,crohn's disease,patients with immune-mediated inflammatory disease (IMID),23,20,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|201174|1760|2037|2049|1654;2|1239;2|1239|186801|3085636|186803|572511;2|1239|91061|186826|186828;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|128827|1573536;2|1239|91061|1385|539738|1378;2|1239|186801|3082720|186804|1505657;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803,Complete,Fatima
bsdb:263/1/2,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,crohn's disease,patients with immune-mediated inflammatory disease (IMID),23,20,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,ChiomaBlessing",Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC),decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174|84998|1643822|1643826|553372;2|1239|186801;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572|459786;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|216572,Complete,Fatima
bsdb:263/2/1,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Ulcerative colitis patients microbiota relative to healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|201174|1760|2037|2049|1654;2|1239|186801|186802|186806|264995;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|128827|1573536;2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803,Complete,Fatima
bsdb:263/2/2,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Abundant taxa in Ulcerative colitis patients microbiota relative to healthy controls (HC),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|1239|186801|186802|204475;2|201174|84998|1643822|1643826|644652;2|1239|186801|3085636|186803|28050;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748,Complete,Fatima
bsdb:263/3/1,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sceloris,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Multiple sclerosis patients microbiota relative to healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|1760|2037|2049|1654;2|1239|186801|186802|186806|264995;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|128827|1573536;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303,Complete,Fatima
bsdb:263/3/2,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sceloris,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Abundant taxa in Multiple sclerosis patients microbiota relative to healthy controls (HC),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|186802|3085642|580596;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|100132;2|1239|186801|186802|216572|292632,Complete,Fatima
bsdb:263/4/1,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,arthiritis,patients with immune-mediated inflammatory disease (IMID),23,21,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Rheumatoid arthritis patients microbiota relative to healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|201174|1760|2037|2049|1654;2|1239;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|128827|1573536;2|1239|91061|1385|539738|1378;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803,Complete,Fatima
bsdb:263/4/2,Study 263,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,arthiritis,patients with immune-mediated inflammatory disease (IMID),23,21,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Abundant taxa in Rheumatoid arthritis patients microbiota relative to healthy controls (HC),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|186802|186806|264995;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|28050;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|44748;2|1239|186801|186802|216572|292632,Complete,Fatima
bsdb:264/1/1,Study 264,"cross-sectional observational, not case-control",26062721,10.1017/S0950268815000965,NA,"Dareng EO, Ma B, Famooto AO, Adebamowo SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H, Gajer P, Brotman RM, Ravel J , Adebamowo CA",Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women,Epidemiology and infection,2016,"HIV/AIDS, human papilloma virus (HPV), public health",Experiment 1,Nigeria,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-/HIV-,HPV+/HIV-,HR-HPV+ confirmed by medical records and HPV genotyping test,99,12,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4b,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees",Identified phylotype biomarkers ranked by effect size in HIV–women,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium|s__Arcanobacterium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus asaccharolyticus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sp.",2|1239|1737404|1737405|1570339|165779|1872515;2|201174|1760|2037|2049|28263;2|201174|1760|2037|2049|28263|72409;2|976|200643|171549;2|976|200643;2|976;2|1239|186801|186802|31979;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|309120;2|32066|203490|203491;2|32066;2|32066|203490|203491|1129771;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906|2023260;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|162289|1258;2|1239|1737404|1737405|1570339|162289|1971214;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1239|186801|3082720|186804|1257|1261;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|2776143,Complete,Fatima Zohra
bsdb:264/1/2,Study 264,"cross-sectional observational, not case-control",26062721,10.1017/S0950268815000965,NA,"Dareng EO, Ma B, Famooto AO, Adebamowo SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H, Gajer P, Brotman RM, Ravel J , Adebamowo CA",Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women,Epidemiology and infection,2016,"HIV/AIDS, human papilloma virus (HPV), public health",Experiment 1,Nigeria,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-/HIV-,HPV+/HIV-,HR-HPV+ confirmed by medical records and HPV genotyping test,99,12,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4b,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees,Merit",Identified phylotype biomarkers ranked by effect size in HIV–women,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum|s__Halorubrum sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|1224|28211;2157|28890|183963|2235|1644056|56688;2157|28890|183963|2235|1644056|56688|1879286;2|1224|28211|356;2|1239|91061|186826|33958|1578|147802;2|1224|1236|135614;2|1239|91061|186826|33958|1578;2|1239|91061|186826,Complete,Fatima Zohra
bsdb:265/1/1,Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 1,Finland,Homo sapiens,Mouth,UBERON:0000165,"Human papilloma virus infection,Age","EFO:0001668,EFO:0000246",at birth,two months,infants with HPV infection at 2 months of age,13,22,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,"Figure 2D, text",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between samples at birth and after 2 months,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|976|117743|200644|2762318;2|1224|1236|135625|712|724;2|1239|1737404|1737405|1570339|165779|1872515;2|1239|1737404|1737405|1570339|150022,Complete,Claregrieve1
bsdb:265/1/2,Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 1,Finland,Homo sapiens,Mouth,UBERON:0000165,"Human papilloma virus infection,Age","EFO:0001668,EFO:0000246",at birth,two months,infants with HPV infection at 2 months of age,13,22,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,"Figure 2D, text",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between samples at birth and after 2 months,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",2|1224|28211|356|82115|357;2|976|200643|171549|815|816;2|1224|28216|80840|80864|80865;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|201174|1760|85009|31957|1743;2|1224|1236|72274|135621|286;2|1239|91061|1385|90964|1279;2|1239|1737404|1737405|1737406,Complete,Claregrieve1
bsdb:265/2/1,Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 2,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,infants that were positive for HPV infection,21,14,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 5F,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HPV+ and HPV- infants,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",2|1239|91061|1385|186817|400634;2|544448|2790996|2790998|2129,Complete,Claregrieve1
bsdb:265/2/2,Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 2,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,infants that were positive for HPV infection,21,14,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 5F,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HPV+ and HPV- infants,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:265/3/1,Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 3,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV- at two months,HPV+ at two months,HPV+ infants at two months,17,5,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,decreased,Signature 1,text,10 January 2021,Fatima Zohra,WikiWorks,effect of age on infant oral HPV infection and bacterial microbiota,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:266/1/1,Study 266,case-control,27381339,10.4014/jmb.1603.03057,NA,"Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J , Nitisinprasert S","Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk",Journal of microbiology and biotechnology,2016,"Enterobacteriaceae, Fecal microbiota, Prevotella, core gut microbiota, pathogen risk, pyrosequencing",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Healthy non-vegetarian,Healthy vegetarian,"The vegetarian volunteers consisted of ovo-lacto vegetarians, lacto-vegetarians, an ovo-vegetarian, and vegans. They had all been vegetarians for at least 3 years before participating in this study.",36,36,1 month,16S,678,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Fig. 3 , Table1 and Table 3",10 January 2021,Valentina Pineda,"WikiWorks,Peace Sandy","Abundance of gut microbiota at the family, genus and species levels detected in both vegetarian and non-vegetarian groups.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis",2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|1224|1236|91347|543|570;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|570|573;2|976|200643|171549|171552|838|28128,Complete,Peace Sandy
bsdb:266/1/2,Study 266,case-control,27381339,10.4014/jmb.1603.03057,NA,"Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J , Nitisinprasert S","Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk",Journal of microbiology and biotechnology,2016,"Enterobacteriaceae, Fecal microbiota, Prevotella, core gut microbiota, pathogen risk, pyrosequencing",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Healthy non-vegetarian,Healthy vegetarian,"The vegetarian volunteers consisted of ovo-lacto vegetarians, lacto-vegetarians, an ovo-vegetarian, and vegans. They had all been vegetarians for at least 3 years before participating in this study.",36,36,1 month,16S,678,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Fig. 3 , Table3 and Table 1",10 January 2021,Valentina Pineda,"WikiWorks,Peace Sandy","Abundance of gut microbiota at the family, genus and species levels detected in both vegetarian and non-vegetarian groups.",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171550;2|1224|1236|91347|543|590,Complete,Peace Sandy
bsdb:267/1/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 1,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,Patients who have atopic asthma,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, Supplemental Table S4",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differentially abundant microbial taxa in atopic asthmatic (AA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|1283313|76122;2|1239|186801|3082720|3030910|109326;2|29547|3031852|213849|72294|194;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28216|206351|481|32257;2|1239|91061|186826|33958|1578|147802;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|28449;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179;2|1224|28211|204457|41297|165697;2|1224|28211|204457|41297|165697|117207;2|203691|203692|136|2845253|157;2|203691|203692|136|2845253|157|59892;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:267/1/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 1,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,Patients who have atopic asthma,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, Supplemental Table S4",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic asthmatic (AA) subjects compared with healthy controls (HC),decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1224|1236|135625|712|713;2|201174|1760|85006|1268|57493|71999;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067;2|1224|28211|356|119045|407;2|1239|186801|3082720|186804|1257,Complete,Claregrieve1
bsdb:267/2/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 2,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic nonasthmatic subjects,21,21,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Supplemental Table S5",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|739;2|201174|1760|85007|1653|1716;2|29547|3031852|213849|72293|2353;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|727;2|1224|1236|2887326|468|475;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|2974257|425941;2|1239|909932|909929|1843491|970;2|1239|526524|526525|2810280|519427;2|1224|28211|204457|41297|165697;2|1224|28211|204457|41297|165697|117207;2|203691|203692|136|2845253|157|59892;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:267/2/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 2,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic nonasthmatic subjects,21,21,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Supplemental Table S5",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|29547|3031852|213849|72293|209;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:267/3/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 3,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Supplemental Table S6",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA) subjects,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1239|909932|1843489|31977|39948;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067;2|544448|31969|2085|2092|2093;2|1224|28216|206351|481|482|28449;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28131;2|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:267/3/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 3,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Supplemental Table S6",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA) subjects,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium columnare,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|739;2|1239|526524|526525|128827|174708;2|976|200643|171549|815|816|817;2|976|117743|200644|49546|1016|1018;2|201174|1760|85007|1653|1716;2|976|117743|200644|49546|237|996;2|29547|3031852|213849|72293|2353;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|186826|33958|1578;2|976|200643|171549|171551|836;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552|2974257|425941;2|1239|526524|526525|2810280|519427;2|1224|28211|204457|41297|165697;2|1224|28211|204457|41297|165697|117207;2|1239|91061|186826|1300|1301;2|203691|203692|136|2845253|157|59892;2|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:267/4/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 4,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,nonresponder,inhaled corticosteroid responder,inhaled corticosteroid (ICS) responder,10,15,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,Merit",Differential relative taxon abundance in inhaled corticosteroid (ICS) responders versus nonresponders among those with atopic asthma,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826|1300;2|1239|526524|526525|128827;2|32066|203490|203491|203492;2|1239|186801|3085636|186803;2|1224|1236|2887326|468;2|1224|28216|206351|481;2|1239|186801|3082720|186804;2|1224|28211|204457|41297;2|1239|909932|1843489|31977;2|1239|186801|3082720|3030910|86331;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:267/4/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 4,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,nonresponder,inhaled corticosteroid responder,inhaled corticosteroid (ICS) responder,10,15,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential relative taxon abundance in inhaled corticosteroid (ICS) responders versus nonresponders among those with atopic asthma,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|201174|1760|2037|2049;2|1239|91061|186826|186827;2|1224|1236|72274|135621|351;2|976|117743|200644|49546;2|1239|91061|186826|33958;2|201174|1760|85006|85023;2|544448|31969|2085|2092;2|1224|1236|135625|712;2|976|200643|171549|171551;2|976|200643|171549|171552;2|203691|203692|136|137;2|976|117743|200644|2762318;2|1239|91061|1385|539738|1378,Complete,Claregrieve1
bsdb:267/5/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 5,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (corticosteroid treatment group),post inhaled corticosteroid treatment,asthma patients after inhaled corticosteroid treatment,8,8,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae",2|201174|1760|85006|85023;2|1224|28216|206351|481|482;2|1224|1236|2887326|468|475;2|203691|203692|136|137;2|201174|1760|2037|2049;2|544448|31969|2085|2092,Complete,Claregrieve1
bsdb:267/5/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 5,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (corticosteroid treatment group),post inhaled corticosteroid treatment,asthma patients after inhaled corticosteroid treatment,8,8,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment,decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|544448|31969|186329|2146;2|1239|91061|186826|33958;2|976|200643|171549|171552;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|39948,Complete,Claregrieve1
bsdb:267/6/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 6,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (placebo group),post placebo treatment,placebo treatment,8,8,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects after placebo treatment,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae",2|1224|28216|206351|481|538;2|203691|203692|136|137;2|544448|31969|2085|2092,Complete,Claregrieve1
bsdb:267/6/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 6,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (placebo group),post placebo treatment,placebo treatment,8,8,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects after placebo treatment,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1224|1236|2887326|468|469;2|201174|1760|2037|2049;2|976|200643|171549|171552;2|1239|186801|3082720|186804,Complete,Claregrieve1
bsdb:267/7/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 7,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4a,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota",2|201174;2|976;2|32066;2|1224;2|203691,Complete,Claregrieve1
bsdb:267/7/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 7,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4a,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Claregrieve1
bsdb:267/8/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 8,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4b,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|201174;2|1239;2|1224,Complete,Claregrieve1
bsdb:267/8/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 8,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4b,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Spirochaetota",2|976;2|32066;2|203691,Complete,Claregrieve1
bsdb:267/9/1,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 9,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4c,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota",2|976;2|32066,Complete,Claregrieve1
bsdb:267/9/2,Study 267,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 9,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4c,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota",2|201174;2|1239;2|1224;2|203691,Complete,Claregrieve1
bsdb:268/1/1,Study 268,time series / longitudinal observational,29563617,10.1038/s41598-018-23389-0,NA,"Zhang H, Lu J, Lu Y, Cai Q, Liu H , Xu C",Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in china,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,after loop electrosurgical excision procedure,before,Cervical intraepithelial neoplasia 2/3 patients who underwent Loop electrosurgical excision procedure(LEEP),26,26,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,increased,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"Atrayees,WikiWorks",Histogram of the LDA scores was used to features differentially abundant between LEEP and no LEEP state.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis",2|201174|1760;2|201174|1760|85004|31953;2|201174|1760|85004;2|1224|28216|80840|119060;2|1239|186801;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|186801|186802;2|201174|1760|85004|31953|2701|2702;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|1578|33959;2|32066|203490|203491|1129771;2|201174|1760|85007;2|1239|186801|186802|541000;2|1239|186801|3082720|186804;2|976|200643|171549|171552|838|419005;2|32066|203490|203491|1129771|168808;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|168808|187101,Complete,Fatima Zohra
bsdb:268/1/2,Study 268,time series / longitudinal observational,29563617,10.1038/s41598-018-23389-0,NA,"Zhang H, Lu J, Lu Y, Cai Q, Liu H , Xu C",Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in china,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,after loop electrosurgical excision procedure,before,Cervical intraepithelial neoplasia 2/3 patients who underwent Loop electrosurgical excision procedure(LEEP),26,26,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,increased,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Histogram of the LDA scores was used to features differentially abundant between LEEP and no LEEP state.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|1385|90964|1279;2|1224|1236|2887326|468;2|1239|526524|526525;2|1239|526524;2|1239|526524|526525|128827;2|1224|28216|80840|119060|48736;2|201174|84998|84999;2|201174|84998|84999|84107;2|1239;2|1239|91061,Complete,Fatima Zohra
bsdb:269/1/1,Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients pre-chemotherapy and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",2|976|200643|171549|815|816;2|976|200643|171549|815|816|820;2|976|200643|171549|815|816|817,Complete,NA
bsdb:269/1/2,Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients pre-chemotherapy and healthy controls,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|29547|3031852|213849|72294|194;2|1239|909932|1843489|31977;2|201174|1760|85007|1653|1716;2|201174|1760|85004|31953|1678;2|201174|84998|84999|1643824|1380;2|1239|1737404|1737405|1570339|162289;2|1239|91061|1385|90964|1279;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|171551|836,Complete,NA
bsdb:269/1/3,Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 3b,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients post-chemotherapy and healthy controls,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
bsdb:269/1/4,Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 3b,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients post-chemotherapy and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|32066|203490|203491|203492|848;2|201174|1760|85007|1653|1716,Complete,NA
bsdb:270/1/1,Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 1,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+  determined through HR-HC2 assay,17,55,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|32066|203490|203491|1129771|168808;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1253;2|201174|1760|85006|85019|1696;2|1224|1236|72274|135621|286,Complete,Fatima Zohra
bsdb:270/1/2,Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 1,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+  determined through HR-HC2 assay,17,55,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges",2|1224|1236|135614|32033|83618;2|201174|1760|2037|2049|1654;2|1798710|3118680|2211217|213484;2|1224|1236|2887326|468|222991,Complete,Fatima Zohra
bsdb:270/2/1,Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 2,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV+ (clearance),HPV+ (persistance),HR-HPV+ persistence confirmed by HPV genotyping after 1 year,27,28,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,figure 6b,10 January 2021,Cynthia Anderson,WikiWorks,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ (clearance) and HPV+ (persistence),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|201174|84998|84999|1643824|1380;2|1239|186801|186802|216572|216851,Complete,Fatima Zohra
bsdb:270/2/2,Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 2,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV+ (clearance),HPV+ (persistance),HR-HPV+ persistence confirmed by HPV genotyping after 1 year,27,28,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 6b,10 January 2021,Cynthia Anderson,"Atrayees,WikiWorks",Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ (clearance) and HPV+ (persistence),decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Rhodoferax,2|1224|28216|80840|80864|28065,Complete,Fatima Zohra
bsdb:271/1/1,Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 1a,10 January 2021,William Lam,WikiWorks,Linear discriminant analysis (LDA) effect size analysis of microbiota differentially associated with MRD status with subclass of autologous stem cell transplantation (ASCT),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|186802|216572|253238|253239;2|1239|186801|186802|216572|253238;2|1239|186801|186802|216572|44748|44749;2|1239|186801|186802|216572|44748,Complete,Atrayees
bsdb:271/1/2,Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 1a,10 January 2021,William Lam,WikiWorks,Linear discriminant analysis (LDA) effect size analysis of microbiota differentially associated with MRD status with subclass of autologous stem cell transplantation (ASCT),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus",2|201174|1760|2037|2049|1654|1659;2|201174|1760|2037|2049|1654|1655;2|201174|1760|85006;2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1239|186801|3085636|186803|1506577|29361;2|1239|91061|186826|1300|1301|1335,Complete,Atrayees
bsdb:271/2/1,Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1b,10 January 2021,William Lam,"WikiWorks,Atrayees",Relative abundance of genera Eubacterium and Faecalibacterium by MRD status,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:271/3/1,Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,Atrayees
bsdb:271/4/1,Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,female,males,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,Atrayees
bsdb:271/5/1,Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,2|1239|186801|3085636|186803|2569097|39488,Complete,Atrayees
bsdb:271/6/1,Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Age greater than 65 years old,Age less than 65 years old,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,2|1239|186801|3085636|186803|2569097|39488,Complete,Atrayees
bsdb:272/1/1,Study 272,case-control,30153231,10.1097/INF.0000000000002174,NA,"Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, Goldfarb DM, Pernica JM, Arscott-Mills T, Boiditswe S, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Feemster KA , Seed PC",Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana,The Pediatric infectious disease journal,2018,NA,Experiment 1,Botswana,Homo sapiens,Nasopharynx,UBERON:0001728,Pneumonia,EFO:0003106,negative,S.pneumoniae positive,clinical pneumonnia,74,96,NA,16S,3,Illumina,Logistic Regression,0.05,FALSE,NA,"date,primary care clinic",age,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Relative abundance of highly abundant genera by S. pneumoniae colonization,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|2887326|468|475;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:272/1/2,Study 272,case-control,30153231,10.1097/INF.0000000000002174,NA,"Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, Goldfarb DM, Pernica JM, Arscott-Mills T, Boiditswe S, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Feemster KA , Seed PC",Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana,The Pediatric infectious disease journal,2018,NA,Experiment 1,Botswana,Homo sapiens,Nasopharynx,UBERON:0001728,Pneumonia,EFO:0003106,negative,S.pneumoniae positive,clinical pneumonnia,74,96,NA,16S,3,Illumina,Logistic Regression,0.05,FALSE,NA,"date,primary care clinic",age,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Relative abundance of highly abundant genera by S. pneumoniae colonization,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:273/1/1,Study 273,prospective cohort,30838178,10.3389/fcimb.2019.00028,NA,"Nearing JT, Connors J, Whitehouse S, Van Limbergen J, Macdonald T, Kulkarni K , Langille MGI",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,"cancer, clinical, genomics, infection, leukemia, metagenomics, microbiome",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,"Prophylactic Septra which was prescribed ubiquitously to patients throughout the study, as per standard of care.",WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,"Figure 3, Supp. Figure 10-12",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients who experienced infectious complications and those who did not,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|815;2|201174|1760|85004|31953;2|1239|186801|186802|186806;2157|28890;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|541000;2|976|200643|171549|171552;2|976|200643|171549|171550;2|976;2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:273/1/2,Study 273,prospective cohort,30838178,10.3389/fcimb.2019.00028,NA,"Nearing JT, Connors J, Whitehouse S, Van Limbergen J, Macdonald T, Kulkarni K , Langille MGI",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,"cancer, clinical, genomics, infection, leukemia, metagenomics, microbiome",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,"Prophylactic Septra which was prescribed ubiquitously to patients throughout the study, as per standard of care.",WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3a,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients who experienced infectious complications and those who did not,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium tumefaciens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota",2|1224|28216|80840|506|222|134375;2|1224|28211|356|82115|357;2|1224|28211|356|82115|357|358;2|1224|28216|80840|506|507;2|1224|28211|204458|76892|41275|293;2|1224|28211|204458|76892|41275;2|1224|28216|80840|506|517;2|1224|28211|204458|76892;2|1224|28211|356|82115;2|1224|28216|80840|506;2|1224|28216|80840|119060;2|1224,Complete,Claregrieve1
bsdb:274/1/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control prior to adjusting,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens",2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:274/1/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|165779|33032;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|1686313|938288;2|32066|203490|203491|203492|848|851;2|201174|1760|85004|31953|2701;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1596;2|201174|1760|2037|2049|2050|2052;2|1239|1737404|1737405|1570339|162289|1465756;2|1239|91061|186826|1300|1301|1328,Complete,Fatima Zohra
bsdb:274/2/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the low grade dysplasia  group when compared to HPV-negative control prior to adjusting,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens",2|201174|84998|84999|1643824|2767327|82135;2|1239|91061|1385|539738|3076174|502393;2|201174|1760|2037|2049|2050|2052;2|1239|1737404|1737405|1570339|543311;2|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:274/2/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the low grade dysplasia group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|1239|1737404|1737405|1570339|165779|1287640;2|1224|1236|91347|1903410|71655;2|29547|3031852|213849|72294|194|827;2|1224|1236|91347|543|561;2|1239|1737404|1737405|1570339|150022|1260;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|2981628|755172;2|1239|1737404|1737405|1570339|162289|507750;2|1239|1737404|1737405|1570339|162289|1465756;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1328,Complete,Fatima Zohra
bsdb:274/3/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control prior to adjusting,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",2|201174|84998|84999|1643824|1380;2|1239|186801|186802|31979|1485;2|201174|84998|84999|1643824|2767327|82135;2|201174|1760|85004|31953|2701;2|976|200643|171549|171552|2974257|28127;2|1239|909932|1843489|31977|906;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838|419005;2|1239|186801|3085636|186803|177971;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|40543;2|1239|91061|186826|1300|1301|1311,Complete,Fatima Zohra
bsdb:274/3/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",2|1239|1737404|1737405|1570339|165779|33032;2|1239|1737404|1737405|1570339|165779|1287640;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|308994;2|1239|186801|186802|1686313|938288;2|1239|1737404|1737405|1570339|150022|1260;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1596;2|1239|1737404|1737405|1570339|2981628|755172;2|1239|1737404|1737405|1570339|162289|507750;2|1239|1737404|1737405|1570339|162289|1465756;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|28128;2|976|200643|171549|171552|838|28130;2|1239|91061|186826|1300|1301;2|544448|2790996|2790998|2129,Complete,Fatima Zohra
bsdb:274/4/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the invasive cervical carcinoma group when compared to HPV-negative control prior to adjusting,increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,2|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:274/4/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the invasive cervical carcinoma group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii|s__Winkia neuii subsp. anitrata",2|1239|1737404|1737405|1570339|165779|33032;2|201174|1760|85004|31953|1678;2|1224|1236|91347|1903410|71655;2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|308994;2|1224|1236|91347|543|561;2|1239|186801|186802|1686313|938288;2|32066|203490|203491|203492|848|851;2|1239|186801|186802|404402;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|1239|1737404|1737405|1570339|2981628|755172;2|1239|1737404|1737405|1570339|162289|507750;2|1239|1737404|1737405|1570339|162289|1465756;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|28128;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1328;2|544448|2790996|2790998|2129;2|201174|1760|2037|2049|2692118|33007|29318,Complete,Fatima Zohra
bsdb:274/5/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella",2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|201174|84998|84999|1643824|133925;2|1239|186801|3082720|186804|1257|1261;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|177971,Complete,Fatima Zohra
bsdb:274/5/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",2|1239|91061|186826|186827|1375;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|1287640;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|2701;2|976|200643|171549|171552|2974257|386414;2|1239|1737404|1737405|1570339|162289|1465756;2|976|200643|171549|171552|838|28125,Complete,Fatima Zohra
bsdb:274/6/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the low grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii|s__Winkia neuii subsp. anitrata",2|1239|1737404|1737405|1570339|165779|33032;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1239|91061|1385|539738|3076174|502393;2|976|200643|171549|171552|2974257|28127;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1578|147802;2|201174|1760|2037|2049|2050|2052;2|1239|186801|3082720|186804|1257|1261;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|419005;2|976|200643|171549|171552|838|28130;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|40543;2|201174|1760|2037|2049|2692118|33007|29318,Complete,Fatima Zohra
bsdb:274/6/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the low grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|1737404|1737405|1570339|2981628|755172,Complete,Fatima Zohra
bsdb:274/7/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 7,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens",2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|2701;2|1239|91061|186826|33958|1578|147802;2|1239|909932|1843489|31977|906;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838|419005;2|1239|186801|3085636|186803|177971;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:274/7/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 7,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"Fatima,WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium coyleae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella coagulans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",2|201174|1760|2037|2049|1653174|59505;2|1239|91061|186826|186827|1375;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|33032;2|1239|1737404|1737405|1570339|165779|1287640;2|201174|1760|85004|31953|1678;2|29547|3031852|213849|72294|194|827;2|201174|1760|85007|1653|1716|53374;2|1239|909932|1843489|31977|39948;2|1239|1737404|1582879|46507;2|1239|186801|186802|1686313|938288;2|1239|1737404|1737405|1570339|162290;2|201174|1760|85004|31953|2701;2|1239|186801|186802|404402;2|976|200643|171549|171552|2974257|28127;2|976|200643|171549|171552|2974257|386414;2|1239|1737404|1737405|1570339|2981628|755172;2|1239|1737404|1737405|1570339|162289|507750;2|1239|1737404|1737405|1570339|162289|1465756;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|28125,Complete,Fatima Zohra
bsdb:274/8/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 8,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"Cynthia Anderson,Lwaldron,WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the invasive cervical carcinoma group when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",2|1239|1737404|1737405|1570339|165779;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|2701;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|186801|3085636|186803|437755;2|1239|1737404|1737405|1570339|162289|1465756;2|976|200643|171549|171552|838|28125,Complete,Fatima
bsdb:274/9/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 9,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Human papilloma virus infection,Cervical cancer","EFO:0001668,MONDO:0002974",abnormal pH,normal pH,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",20,74,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|32066|203490|203491|203492|848|851;2|201174|1760|85004|31953|2701;2|1239|91061|1385|539738|1378;2|1239|909932|1843489|31977|906;2|544448|2790996|2895623|2895509|2098;2|201174|1760|2037|2049|2050|2052;2|1239|186801|3085636|186803|437755;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|419005;2|976|200643|171549|171552|838|28130;2|1239|186801|3085636|186803|177971;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|40543;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1311;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|187328,Complete,Fatima Zohra
bsdb:274/9/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 9,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Human papilloma virus infection,Cervical cancer","EFO:0001668,MONDO:0002974",abnormal pH,normal pH,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",20,74,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1224|1236|91347|1903410|71655;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543|561;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1596;2|1224|1236|91347|543|620,Complete,Fatima Zohra
bsdb:274/10/1,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 10,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,non-Hispanic,Hispanic,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",53,47,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in Hispanic vs. non-Hispanic group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",2|1239|91061|186826|186827|1375;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|81852|1350;2|201174|84998|84999|1643824|2767327|82135;2|201174|1760|85004|31953|2701;2|1239|909932|1843489|31977|906;2|201174|1760|2037|2049|2050|2052;2|1239|186801|3085636|186803|437755;2|976|200643|171549|171551|836;2|1239|186801|3085636|186803|177971;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|40543;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1328;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|187328,Complete,Fatima Zohra
bsdb:274/10/2,Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 10,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,non-Hispanic,Hispanic,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",53,47,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in Hispanic vs. non-Hispanic group,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|1239|1737404|1737405|1570339|165779|33037;2|976|200643|171549|171552|2974257|28127;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1596,Complete,Fatima Zohra
bsdb:275/1/1,Study 275,case-control,27527070,10.1186/s12864-016-2965-y,NA,"Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L , Nelson KE",Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis,BMC genomics,2016,"16S rRNA gene sequencing, Gastrointestinal microbiota, Pediatric leukemia, Ribosomal RNA, rRNA",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,healthy sibling control,adolescent ALL patient,Patients with pediatric and adolescent Acute Lymphoblastic Leukemia at time of disease diagnosis,23,28,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Mean microbial taxon abundances in Acute Lymphoblastic Leukemia Patient and Control groups (prior to chemotherapy treatment-  visit 1),increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:275/1/2,Study 275,case-control,27527070,10.1186/s12864-016-2965-y,NA,"Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L , Nelson KE",Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis,BMC genomics,2016,"16S rRNA gene sequencing, Gastrointestinal microbiota, Pediatric leukemia, Ribosomal RNA, rRNA",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,healthy sibling control,adolescent ALL patient,Patients with pediatric and adolescent Acute Lymphoblastic Leukemia at time of disease diagnosis,23,28,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Mean microbial taxon abundances in Acute Lymphoblastic Leukemia  Patient and Control groups (prior to chemotherapy treatment-  visit 1),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:276/1/1,Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Table 6 & text,10 January 2021,William Lam,"WikiWorks,Atrayees",Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Atrayees
bsdb:276/1/2,Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Table 6 & text,10 January 2021,William Lam,"WikiWorks,Atrayees",Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level,decreased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Atrayees
bsdb:276/2/1,Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,LEfSe,2,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,William Lam,WikiWorks,Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224;2|1239|526524|526525|2810281|191303;2|1224|1236|91347|543|413496;2|1224|1236|91347|543|413496|28141,Complete,Atrayees
bsdb:276/2/2,Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,LEfSe,2,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,William Lam,WikiWorks,Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|186802|186806|1730;2|201174|84998;2|201174|84998|84999;2|201174|84998|84999|84107;2|1239|186801|3085636|186803|207244;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|2810280|135858;2|1224|28211|204441|41295;2|1224|28211;2|1224|28211|204441;2|1239|909932|1843488|909930|904,Complete,Atrayees
bsdb:276/3/1,Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 7 and text,10 January 2021,William Lam,"WikiWorks,Atrayees","Genus with significant difference between Multiple Myeloma group and healthy control group was selected, followed by ordering according to the abundance in the intestinal tract of MM patients",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Solanales|f__Solanaceae|s__Nicotianoideae|g__Nicotiana|s__Nicotiana otophora,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977|29465;2|1239|909932|1843488|909930|904;2|1239|526524|526525|128827|1472649;2|1239|186801|3085636|186803|830;2759|33090|35493|3398|4069|4070|424554|4085|4091;2|1239|526524|526525|128827|174708,Complete,Atrayees
bsdb:276/3/2,Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 7 & text,4 July 2023,Atrayees,Atrayees,"Genus with significant difference between Multiple Myeloma group and healthy control group was selected, followed by ordering according to the abundance in the intestinal tract of MM patients",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,2|1239|186801|3082720|3120161|1481960,Complete,Atrayees
bsdb:276/4/1,Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy relatives control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",21,21,3 months,16S,34,RT-qPCR,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 8 and text,10 January 2021,William Lam,"WikiWorks,Atrayees",Intestinal Microbial detection in Multiple Myeloma patients and their family members using Quantitative Reverse Transcription Polymerase Chain Reaction,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",2|1224|1236|72274|135621|286|287;2|1239|186801|186802|216572|1535,Complete,Atrayees
bsdb:277/1/1,Study 277,case-control,30581271,10.3748/wjg.v24.i46.5223,NA,"Rojas-Feria M, Romero-García T, Fernández Caballero-Rico JÁ, Pastor Ramírez H, Avilés-Recio M, Castro-Fernandez M, Chueca Porcuna N, Romero-Gόmez M, García F, Grande L , Del Campo JA",Modulation of faecal metagenome in Crohn's disease: Role of microRNAs as biomarkers,World journal of gastroenterology,2018,"Bacteroidetes, Crohn’s disease, Dysbiosis, Firmicutes, microRNAs",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy control,crohn's disease,new-onset adult crohn's disease (CD) patients,16,13,10 weeks,16S,123,Illumina,Chi-Square,0.05,FALSE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"figure 2, 3, 4",10 January 2021,Fatima Zohra,WikiWorks,Significant difference between control group and crohn's disease,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Mesoplasma,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfonauticaceae|g__Desulfonauticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",2|1239|186801;2|1239|186801|186802|541000;2|1239|186801|3085636|186803;2|1239|186801|186802|186806;2|976|200643|171549|171550;2|544448|31969|186328|33925;2|200940|3031449|213115|213117;2|201174|1760|85007|1653;2|544448|31969|2085|2092;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|186806|1730;2|544448|31969|186328|33925|46239;2|200940|3031449|213115|2956789|206664;2|976|200643|171549|171551|836;2|976|200643|171549|171550|28138;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|830,Complete,Fatima
bsdb:278/1/1,Study 278,"cross-sectional observational, not case-control",29362454,10.1038/s41598-018-19753-9,NA,"Da Silva HE, Teterina A, Comelli EM, Taibi A, Arendt BM, Fischer SE, Lou W , Allard JP",Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance,Scientific reports,2018,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy control,NAFLD- [non alcoholic fatty liver disease],Adults with biopsy-proven steatosis and non-alcoholic fatty liver disease,28,39,6 Months,PCR,NA,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,table 2,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy",Taxa identified as differentially abundant in patients with nonalocholic fatty liver disease (NAFLD) compared to HC,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061,Complete,Peace Sandy
bsdb:278/1/2,Study 278,"cross-sectional observational, not case-control",29362454,10.1038/s41598-018-19753-9,NA,"Da Silva HE, Teterina A, Comelli EM, Taibi A, Arendt BM, Fischer SE, Lou W , Allard JP",Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance,Scientific reports,2018,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy control,NAFLD- [non alcoholic fatty liver disease],Adults with biopsy-proven steatosis and non-alcoholic fatty liver disease,28,39,6 Months,PCR,NA,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy",Taxa identified as differentially abundant in patients with nonalocholic fatty liver disease (NAFLD) compared to HC,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1239;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|976|200643|171549|171551;2|976|200643|171549|171550;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|841;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803;2|1239|186801;2|976|200643|171549,Complete,Peace Sandy
bsdb:279/1/2,Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Acute myeloid leukemia,EFO:0000222,Low Intensity Chemotherapy,High Intensity Chemotherapy,Acute Myeloid Leukemia patients receiving low-intensity remission induction chemotherapy at a later timepoint T6,11,28,None,ITS / ITS2,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 4,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi,ChiomaBlessing",Significantly enriched taxa in patients who received high-intensity chemotherapies compared to those who received low-intensity chemotherapy,decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,2759|4751|5204|1538075|162474|742845|55193,Complete,ChiomaBlessing
bsdb:279/2/1,Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Acute myeloid leukemia,EFO:0000222,Patients without bacterial infections at T3,Patients with bacterial infections at T3,Acute Myeloid Leukemia patients that experienced microbiologically defined bacterial infections during remission induction chemotherapy at midpoint timepoint T3,30,9,None,ITS / ITS2,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2 + Figure 6,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi,ChiomaBlessing",Differential abundance among acute leukemia patients who had infections during induction chemotherapy compared to those who did not experience infections at midpoint time point (T3),increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes",2759|4751|4890|3239874|2916678|766764|1535326;2759|4751|4890|3239874|2916678|766764;2759|4751|4890|4891|4892;2759|4751|4890|4891,Complete,ChiomaBlessing
bsdb:279/3/1,Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Acute myeloid leukemia,EFO:0000222,Patients with no bacterial infections at T6,Patients with bacterial infections at T6,Acute Myeloid Leukemia patients that experience microbiologically defined bacterial infections during remission induction chemotherapy at endpoint timepoint T6,30,9,None,ITS / ITS2,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6 + Figure S3,1 December 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differential abundance among acute leukemia patients who had infections during induction chemotherapy compared to those who did not experience infections at a later time point (T6),decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales,k__Eukaryota|k__Fungi",2759|4751|4890|147550|5125|110618|5506;2759|4751|4890|147550|5125|110618;2759|4751|4890|147550;2759|4751|4890|147550|5125;2759|4751,Complete,ChiomaBlessing
bsdb:279/4/1,Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 4,United States of America,Homo sapiens,Mouth,UBERON:0000165,Antimicrobial agent,CHEBI:33281,Patients who did not receive Amphotericin B,Patients who received Amphotericin B,Acute Myeloid Leukemia patients who received amphotericin B.,66,6,None,ITS / ITS2,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,1 December 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Effect of amphotericin B on the composition of the oral fungal community at T6 in those who received amphotericin B compared to those who did not,increased,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,2759|4751|4890|147550|5125|110618|5506,Complete,ChiomaBlessing
bsdb:280/1/1,Study 280,"cross-sectional observational, not case-control",26574055,10.1038/srep16865,NA,"Mitra A, MacIntyre DA, Lee YS, Smith A, Marchesi JR, Lehne B, Bhatia R, Lyons D, Paraskevaidis E, Li JV, Holmes E, Nicholson JK, Bennett PR , Kyrgiou M",Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity,Scientific reports,2015,NA,Experiment 1,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,low grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion confirmed by histology or cytology,52,92,14 days,16S,12,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,figure 5,10 January 2021,Cynthia Anderson,WikiWorks,Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|1239|186801|3082720|186804|1257|1261;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|33036;2|32066|203490|203491|1129771|168808;2|32066|203490|203491;2|32066|203490|203491|1129771|168808|40543;2|32066;2|32066|203490|203491|1129771,Complete,Fatima Zohra
bsdb:280/1/2,Study 280,"cross-sectional observational, not case-control",26574055,10.1038/srep16865,NA,"Mitra A, MacIntyre DA, Lee YS, Smith A, Marchesi JR, Lehne B, Bhatia R, Lyons D, Paraskevaidis E, Li JV, Holmes E, Nicholson JK, Bennett PR , Kyrgiou M",Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity,Scientific reports,2015,NA,Experiment 1,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,low grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion confirmed by histology or cytology,52,92,14 days,16S,12,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,figure 5,10 January 2021,Cynthia Anderson,WikiWorks,Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus coleohominis",2|1239|91061|186826|33958|1578|109790;2|1239|91061|186826|33958|2742598|181675,Complete,Fatima Zohra
bsdb:281/1/1,Study 281,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y , Gyarmati P",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition in small intestines of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4a, 4b and text",10 January 2021,William Lam,"WikiWorks,Peace Sandy",Relative abundances (a) and the ratio of relative abundances (b) of the bacterial microbiota between the fecal compositions in the small intestine of control and leukemic mice,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|74201|203494|48461|1647988|239934;2|544448|31969|186332|186333|2086;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|830;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186807|51514|51515;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263,Complete,Peace Sandy
bsdb:281/1/2,Study 281,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y , Gyarmati P",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition in small intestines of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4a, 4b and text",10 January 2021,William Lam,"WikiWorks,Peace Sandy",Relative abundances (a) and the ratio of relative abundances (b) of the bacterial microbiota between the fecal compositions in the small intestine of control and leukemic mice,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|84998|1643822|1643826|447020;2|1239|91061|186826|33958|1578;2|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:281/2/1,Study 281,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y , Gyarmati P",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,text (subset of Figure 2),7 March 2024,Lwaldron,Lwaldron,Increased relative abundance in leukemic mice compared to control mice,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1224|28216|80840|119060|48736;2|1239|91061|186826|1300|1357,Complete,NA
bsdb:281/2/2,Study 281,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y , Gyarmati P",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,7 March 2024,Lwaldron,Lwaldron,Decreased relative abundance in leukemic mice compared to control mice. I skipped the middle part of Figure 2 where the two groups look almost the same.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|1239|91061|186826|33958|1578;2|201174|1760|85011|2062|1883;2|1239|186801|186802|31979;2|32066|203490|203491|203492|848;2|1239|526524|526525|2810281|191303;2|74201|203494|48461|1647988|239934,Complete,NA
bsdb:282/1/1,Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,Grades 0-I (non-acute graft-host disease),Grades II-IV (acute graft-host-disease),patients diagnoised with acute graft-versus-host disease (aGVHD),49,32,NA,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,"Figure 3a, b and text",10 January 2021,William Lam,WikiWorks,Differences of intestinal microbiota at engraftment between acute graft-verse-house disease (aGVHD) and non-acute graft-versus host disease (non-aGVHD) patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota",2|976|200643|171549|171551;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236;2|1224,Complete,Atrayees
bsdb:282/1/2,Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,Grades 0-I (non-acute graft-host disease),Grades II-IV (acute graft-host-disease),patients diagnoised with acute graft-versus-host disease (aGVHD),49,32,NA,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,"Figure 3a, b and text",10 January 2021,William Lam,WikiWorks,Differences of intestinal microbiota at engraftment between acute graft-verse-house disease (aGVHD) and non-acute graft-versus host disease (non-aGVHD) patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|186806;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804;2|1239|186801|186802|541000;2|1239|186801|186802;2|1239|186801;2|1239|526524|526525|128827;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:282/2/1,Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,standard conditioning,intensified conditioning,patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning,19,13,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,"Figure 5a, b, c, d",10 January 2021,William Lam,WikiWorks,Differences in the intestinal microbiota (diversity and composition) are associated with conditioning intensity in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803;2|1239|186801|186802|541000,Complete,Atrayees
bsdb:282/3/1,Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,no b-lactum antibiotics,b-lactum antibiotics,"patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning treated with b-lactum (include carbapenem, cephalosporin, and b-lactam-b-lactamase combinations.)",48,31,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 4 a, b, d",10 January 2021,William Lam,WikiWorks,Differences in the intestinal microbiota (diversity and composition) are associated with Beta-Lactum antibiotic in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:282/4/1,Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,no vancomycin antibiotics,vancomycin antibiotics,patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning treated with vancomycin,59,20,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 4 a, b, d",10 January 2021,William Lam,WikiWorks,Differences in the intestinal microbiota (diversity and composition) are associated with Vancomycin antibiotic in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Atrayees
bsdb:283/1/1,Study 283,"cross-sectional observational, not case-control",31749298,10.1111/1471-0528.15981,NA,"Borgogna JC, Shardell MD, Santori EK, Nelson TM, Rath JM, Glover ED, Ravel J, Gravitt PE, Yeoman CJ , Brotman RM",The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis,BJOG : an international journal of obstetrics and gynaecology,2020,"16S rRNA gene amplicon sequencing, human papillomavirus, vaginal metabolome, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed using Roche Linear Array HPV Genotyping Test,13,26,30 days,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplemental figure 3,10 January 2021,Cynthia Anderson,WikiWorks,The association between vaginal taxa and detection status as identified by LEfSE,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus asaccharolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",2|201174|1760|85004|31953|2701|2702;2|201174|84998|1643822|1643826|84111;2|1239|91061|1385|539738|1378;2|201174|84998|84999|1643824|1380|1872650;2|1239|909932|1843489|31977;2|1239|91061|186826|186827|1375|87541;2|1239|1737404|1737405|1570339|162289|1258;2|1239|91061|186826|33958|2742598|1633,Complete,Fatima Zohra
bsdb:283/1/2,Study 283,"cross-sectional observational, not case-control",31749298,10.1111/1471-0528.15981,NA,"Borgogna JC, Shardell MD, Santori EK, Nelson TM, Rath JM, Glover ED, Ravel J, Gravitt PE, Yeoman CJ , Brotman RM",The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis,BJOG : an international journal of obstetrics and gynaecology,2020,"16S rRNA gene amplicon sequencing, human papillomavirus, vaginal metabolome, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed using Roche Linear Array HPV Genotyping Test,13,26,30 days,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supplemental figure 3,10 January 2021,Cynthia Anderson,WikiWorks,The association between vaginal taxa and detection status as identified by LEfSE,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus",2|201174|1760|85004|31953;2|201174|84998|84999|1643824|2767327|82135;2|1239|91061|186826|33958|1578|109790;2|1239|91061|186826|33958|1578|47770,Complete,Fatima Zohra
bsdb:284/1/1,Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,34,Illumina,Metastats,0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between CKD patients and healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|2037|2049|1654;2|976|117743|200644|2762318|59735;2|201174|1760|85007|1653|1716;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:284/1/2,Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,34,Illumina,Metastats,0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between CKD patients and healthy controls,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:284/2/1,Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 2,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,345,Illumina,LEfSe,0.05,FALSE,2,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,Atrayees,WikiWorks",Differential microbial abundance between CKD patients and healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum",2|201174|1760|2037|2049|1654|1655;2|29547|3031852|213849|72294|194|200;2|976|117743|200644|49546|1016|44737;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|1300|1301|1310;2|1239|186801|186802|543314|56774,Complete,Claregrieve1
bsdb:284/2/2,Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 2,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,345,Illumina,LEfSe,0.05,FALSE,2,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4,15 July 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between CKD patients and healthy controls,decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|s__Acholeplasmatales bacterium canine oral taxon 172,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. GHG17,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. CM12,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella genomosp. P6,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral clone GU027,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii",2|544448|31969|186329|1151604;2|976|117743|200644|49546|1016|45243;2|1224|1236|135625|712|724|726;2|1239|186801|3085636|186803|43994|43995;2|1224|28216|206351|481|482|742463;2|1239|186801|3085636|186803|265975|936567;2|976|200643|171549|171552|838|239138;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|2974257|425941;2|976|200643|171549|171552|838|242668;2|32066|203490|203491|1129771|2755140|157692,Complete,Claregrieve1
bsdb:284/4/1,Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 4,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,3456,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of Streptococcus mutans in supragingival plaque measured by quantitative real-time PCR between kidney disease patients and healthy controls,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,2|1239|91061|186826|1300|1301|1309,Complete,Claregrieve1
bsdb:285/1/1,Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,pediatric multiple sclerosis,early pediatric multiple sclerosis,17,18,2 months,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex","age,breast feeding,ethnic group,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,"Figure 3a, 3b",10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls in the gut microbial communities,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|200940|3031449|213115|194924|35832;2|201174|1760|85004|31953|1678;2|1239|186801|186802;2|200940|3031449|213115|194924|872;2|201174|84998|84999|84107;2|976|200643|171549|171552|2974251|165179;2|1239|526524|526525|2810280|135858;2|1239|186801|3082768|990719;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024,Complete,Atrayees
bsdb:285/1/2,Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,pediatric multiple sclerosis,early pediatric multiple sclerosis,17,18,2 months,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex","age,breast feeding,ethnic group,sex",NA,NA,NA,NA,NA,unchanged,Signature 2,"Figure 3a, 3b",10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls in the gut microbial communities,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",2|1239|186801|3085636|186803|28050;2|1239|186801|186802|541000;2|976|200643|171549|171552|577309;2|1239|186801|186802;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|815|816;2|1239|186801|186802|216572|119852;2|1239|186801|3082720|186804|1257|1261,Complete,Atrayees
bsdb:285/2/1,Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,IMD naive cases,IMD exposure multiple sclerosis cases,Sclerosis cases influenced by the immunomodulatory drug [IMD] exposure status.,9,9,2 months,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2b,10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases,increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Atrayees
bsdb:285/2/2,Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,IMD naive cases,IMD exposure multiple sclerosis cases,Sclerosis cases influenced by the immunomodulatory drug [IMD] exposure status.,9,9,2 months,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2b,10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases,decreased,"k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Cyanobacteriota",2|544448;2|1117,Complete,Atrayees
bsdb:285/3/1,Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,IMD naive cases multiple sclerosis,NA,16,9,2 months,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Supplementary Table 7a, Supp Table 7b",10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Taxa enriched and depleted in the IMD naive cases vs. controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1239|909932|1843488|909930|904;2|74201|203494|48461|1647988|239934|239935;2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|28116;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511|33035;2|1239|526524|526525|2810280|135858;2|1239|186801|3082768|990719;2|1224|28216|80840|80864;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|189330;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851|853;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288|823;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552|2974265|363265;2|1239|186801|186802|186806|113286;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|3085636|186803|2316020|33038,Complete,Atrayees
bsdb:285/3/2,Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,IMD naive cases multiple sclerosis,NA,16,9,2 months,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Supplementary Table 7a, Supp Table 7b",10 January 2021,Rimsha Azhar,WikiWorks,Taxa enriched and depleted in the IMD naive cases vs. controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1239|186801|186802|541000;2|976|200643|171549|171552|2974251|165179;2|1239|91061|186826|33958|2767887|1623;2|976|200643|171549|171552|577309;2|1239|186801|3085636|186803;2|976|200643|171549|171550;2|976|200643|171549|815|816;2|1239|186801|186802|216572|1263;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|574697;2|1239|909932|909929|1843491|52225|52226;2|1239|186801|3085636|186803|33042;2|1239|186801|3082720|186804|1257|1261;2|1239|186801|3085636|186803|207244;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|28111;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|815|816|817;2|1239|526524|526525|2810280|135858;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815|909656|387090;2|976|200643|171549|815|816|28116;2|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:286/1/1,Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy controls,graves orbitopathy,"The diagnosis of GO was established according to the EUGOGO Guidelines. The active GO was defined by a clinical activity score (CAS)≥3/7, and the severe GO was defined by NOSPECS score≥IV. CT or MRI was used to exclude any orbital space-occupying disease such as tumor or extraocular myositis.",32,33,4 weeks,16S,4,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,"Figure 4a, 4b, 4c",10 January 2021,Rimsha Azhar,"Rimsha,Fatima,LGeistlinger,WikiWorks","Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls",increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552,Complete,Fatima
bsdb:286/1/2,Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy controls,graves orbitopathy,"The diagnosis of GO was established according to the EUGOGO Guidelines. The active GO was defined by a clinical activity score (CAS)≥3/7, and the severe GO was defined by NOSPECS score≥IV. CT or MRI was used to exclude any orbital space-occupying disease such as tumor or extraocular myositis.",32,33,4 weeks,16S,4,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,"Figure 4a, 4b, 4c",10 January 2021,Rimsha Azhar,"Rimsha,Fatima,WikiWorks","Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|976|200643|171549|1853231|574697;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186806|1730|39496;2|1239;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|216572|1930587|1852369;2|976|200643|171549|815|909656|204516;2|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:286/2/1,Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,healthy controls,graves orbitopathy,severe and active graves' orbitopathy,32,33,4 weeks,16S,4,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 5b,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549;2|976;2|976|200643;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552;2|976|200643|171549|171552,Complete,Fatima
bsdb:286/2/2,Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,healthy controls,graves orbitopathy,severe and active graves' orbitopathy,32,33,4 weeks,16S,4,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 5b,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|186802;2|1239;2|1239|186801|3085636|186803,Complete,Fatima
bsdb:287/1/1,Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 1,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 1 HPV (progression),HPV progression to CIN2+ lesion diagnosis,70,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",Bacteria associated with progression to CIN2+ identified using LEfSe,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter canadensis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus|s__Methylobacillus flagellatus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus|s__Methylobacillus glycogenes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus indolicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema pallidum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",2|1239|91061|186826|186827|1375|87541;2|1239|1737404|1737405|1570339|165779|33034;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|3085636|186803|572511|1322;2|29547|3031852|213849|72294|194|449520;2|29547|3031852|213849|72294|194|827;2|201174|1760|85007|1653|1716|191610;2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171552|52228|242750;2|1224|28216|32003|32011|404|405;2|1224|28216|32003|32011|404|406;2|1224|28216|206351|481|482|485;2|1239|1737404|1737405|1570339|162289|54005;2|1239|1737404|1737405|1570339|162289|33030;2|976|200643|171549|171551|836|501496;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|28137;2|201174|1760|2037|2049|2529408|52773;2|201174|1760|2037|2049|2529408|1660;2|1224|28211|204457|41297|13687|68569;2|203691|203692|136|2845253|157|160;2|1239|909932|1843489|31977|29465|187328,Complete,Fatima Zohra
bsdb:287/1/2,Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 1,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 1 HPV (progression),HPV progression to CIN2+ lesion diagnosis,70,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Bacteria associated with progression to CIN2+ identified using LEfSe,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella paludivivens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|976|200643|171549|171552|2974251|185294;2|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
bsdb:287/2/1,Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 2,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 2 HPV (progression),HPV progression to CIN2+ lesion diagnosis,69,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Bacteria associated with progression to CIN2+ identified using LEfSe,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas circumdentaria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella bergeri,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gleum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",2|976|200643|171549|171552|838|419005;2|976|200643|171549|171551|836|29524;2|1239|1737404|1737405|1570339|543311|33033;2|1239|909932|1843489|31977|39948|487173;2|1239|1737404|1737405|1570339|165779|33034;2|1239|1737404|1737405|1570339|162289|54005;2|1239|186801|3082720|186804|1870884|1496;2|1239|91061|1385|539738|1378|84136;2|976|117743|200644|2762318|59732|250;2|1239|186801|3085636|186803|33042|33043,Complete,Fatima Zohra
bsdb:287/2/2,Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 2,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 2 HPV (progression),HPV progression to CIN2+ lesion diagnosis,69,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees",Bacteria associated with progression to CIN2+ identified using LEfSe,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium minutum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio clariflavus",2|201174|1760|2037|2049|1654|544581;2|201174|84998|84999|1643824|1380|1381;2|1239|186801|186802|216572|35829|288965,Complete,Fatima Zohra
bsdb:288/1/1,Study 288,case-control,29502926,10.1016/j.numecd.2018.01.004,NA,"Verduci E, Moretti F, Bassanini G, Banderali G, Rovelli V, Casiraghi MC, Morace G, Borgo F , Borghi E",Phenylketonuric diet negatively impacts on butyrate production,"Nutrition, metabolism, and cardiovascular diseases : NMCD",2018,"Butyrate, Faecalibacterium prausnitzii, Phenylketonuria, Short chain fatty acids",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Phenylketonuria,MONDO:0009861,mild hyperphenylalaninemic with unrestricted diet,phenylketonuric with Phe-restricted diet,phenylketonuric patients with restricted (phenylalanine-free) diets,21,21,3 months,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Aboud Ezzeddine,WikiWorks,"Microbial quantification, in phenylketonuric (PKU) and mild hyperphenylalaninemia (MHP) children, of Faecalibacterium prausnitzii, and Roseburia spp",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|841;2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:289/1/1,Study 289,case-control,31808612,10.1111/jcmm.14880,NA,"Sun Q, Xu X, Zhang J, Sun M, Tian Q, Li Q, Cao W, Zhang X, Wang H, Liu J, Zhang J, Meng X, Wu L, Song M, Liu H, Wang W , Wang Y",Association of suboptimal health status with intestinal microbiota in Chinese youths,Journal of cellular and molecular medicine,2020,"16S rRNA, LEfSe analysis, intestinal microbiota, random forest tree, suboptimal health status",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Health trait,EFO:0007652,healthy controls,suboptimal health status,subjects with SHSQ-25 (SHS score >= 35),50,50,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",LDA score of LEfSe analysis between suboptimal health status (SHS) and control group,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",2|976|117743|200644|2762318|59732;2|1117;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|1239|186801|186802|186807;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|74201;2|1239|186801|186802|1898207;2|32066|203490|203491|203492,Complete,Claregrieve1
bsdb:289/1/2,Study 289,case-control,31808612,10.1111/jcmm.14880,NA,"Sun Q, Xu X, Zhang J, Sun M, Tian Q, Li Q, Cao W, Zhang X, Wang H, Liu J, Zhang J, Meng X, Wu L, Song M, Liu H, Wang W , Wang Y",Association of suboptimal health status with intestinal microbiota in Chinese youths,Journal of cellular and molecular medicine,2020,"16S rRNA, LEfSe analysis, intestinal microbiota, random forest tree, suboptimal health status",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Health trait,EFO:0007652,healthy controls,suboptimal health status,subjects with SHSQ-25 (SHS score >= 35),50,50,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,LDA score of LEfSe analysis between suboptimal health status (SHS) and control group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|1236|91347|1903414|581;2|1224|28216|80840|119060|48736;2|1224|28216;2|1224|28216|80840|506;2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:290/1/1,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 1,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,no ulcerative oral mucositis,ulcerative oral mucositis,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,William Lam,WikiWorks,Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1301;2|1239|91061|1385|90964|1279;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:290/1/2,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 1,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,no ulcerative oral mucositis,ulcerative oral mucositis,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,William Lam,WikiWorks,Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654,Complete,Atrayees
bsdb:290/2/1,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 2,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|2037|2049|1654|29317;2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|29465|1926307,Complete,Atrayees
bsdb:290/2/2,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 2,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2742598|1613;2|201174|1760|85004|31953|196081|230143,Complete,Atrayees
bsdb:290/3/1,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 3,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis",2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|55565;2|1239|91061|1385|539738|1378|1379;2|1239|91061|1385|539738|1378|29391;2|1239|91061|1385|539738|1378|84135,Complete,Atrayees
bsdb:290/3/2,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 3,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis",2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|29380;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1292;2|201174|1760|85004|31953|196081|230143;2|1239|91061|186826|81852|1350|1351,Complete,Atrayees
bsdb:290/4/1,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 4,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,low or no fungi load,0.1% or higher fungi load,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953|196081;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:290/4/2,Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 4,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,low or no fungi load,0.1% or higher fungi load,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:291/1/1,Study 291,case-control,30263008,10.7150/ijbs.24151,NA,"Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P , Xu J",Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients,International journal of biological sciences,2018,"DGGE, GD, Gut microbiota, High-throughput sequencing, Hyperthyroidism, Ophthalmopathy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,healthy controls,graves disease,graves' disease patients,11,27,2 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,"Fig 5, Fig6, Table 6,7 and text",10 January 2021,Rimsha Azhar,WikiWorks,Gut microbial composition differences between Graves' disease and control at different levels,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii",2|976|200643|171549|171552;2|1224|1236|135625|712;2|976|200643|171549|171552|838;2|1224|1236|135625|712|724;2|29547|3031852|213849|72294|194|204;2|1239|909932|1843489|31977|29465|1926307;2|1224|1236|91347|1903414|581|582,Complete,Folakunmi
bsdb:291/1/2,Study 291,case-control,30263008,10.7150/ijbs.24151,NA,"Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P , Xu J",Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients,International journal of biological sciences,2018,"DGGE, GD, Gut microbiota, High-throughput sequencing, Hyperthyroidism, Ophthalmopathy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,healthy controls,graves disease,graves' disease patients,11,27,2 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Fig 5, Fig6, Table 6,7 and text",10 January 2021,Rimsha Azhar,"WikiWorks,Folakunmi",Gut microbial composition differences between Graves' disease and control at different levels,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|1872444;2|1224|1236|91347|543;2|1239|186801|186802|216572|216851;2|1239|91061|186826|33958|1578|1596;2|976|200643|171549|171550;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|39948,Complete,Folakunmi
bsdb:292/1/2,Study 292,case-control,32150591,10.1371/journal.ppat.1008348,NA,"Oku S, Takeshita T, Futatsuki T, Kageyama S, Asakawa M, Mori Y, Miyamoto T, Hata J, Ninomiya T, Kashiwazaki H , Yamashita Y",Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation,PLoS pathogens,2020,NA,Experiment 1,Japan,Homo sapiens,Tongue,UBERON:0001723,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,community-dwelling controls,allogeneic-hematopoietic stem cell transplant,patient ages 36-69 years old undergoing allogeneic- hematopoietic stem cell transplantation,164,45,NA,16S,12,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 2,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential abundances of predominant bacterial genera in the tongue microbiota of community-dwelling adults and allogeneic-hematopoietic stem cell transplantation patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|1283313;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:293/1/1,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,Baseline HPV-,Baseline HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,increased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",2|544448|31969;2|544448;2|544448|31969|2085;2|544448|31969|2085|2092;2|544448|2790996|2790998|2129,Complete,Fatima Zohra
bsdb:293/1/2,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,Baseline HPV-,Baseline HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,unchanged,Signature 2,figure 3,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacteria|p__Deinococcota|c__Deinococci,k__Bacteria|p__Deinococcota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",2|1224|1236|118969|118968;2|1297|188787;2|1297;2|1224|1236|135613|72276;2|1239|1737404|1582879;2|1239|186801|186802|216572|216851;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1239|91061|1385|186820;2|1224|1236|118969|118968|873565;2|32066|203490|203491,Complete,Fatima Zohra
bsdb:293/2/1,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 2,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no new acquisition of HPV within a year,new acquisition of HPV within a year,New HPV-type acquisition confirmed by HPV assay and genotyping,109,24,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,2|201174|1760|2037|2049|1654,Complete,Fatima Zohra
bsdb:293/3/1,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 3,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,with at least one HPV type cleared in a year,without any HPV type cleared,No HPV-type cleared confirmed by HPV assay and genotyping,75,15,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales",2|1224|28211|204455|31989;2|1224|28211|204455,Complete,Fatima Zohra
bsdb:293/4/1,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,2|544448|2790996|2790998|2129|134821,Complete,Fatima Zohra
bsdb:293/4/2,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|1737404|1582879|1852374;2|1224|1236|72274|135621|286|287,Complete,Fatima Zohra
bsdb:293/5/1,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 5,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no new acquisition of HPV within a year,new acquisition of HPV within a year,New HPV-type acquisition confirmed by HPV assay and genotyping,109,24,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus",2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|171552|838|28133;2|976|200643|171549|171552|2974251|28136;2|1239|909932|1843489|31977|39948|218538,Complete,Fatima Zohra
bsdb:293/6/1,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 6,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,with any HPV type cleared in a year,without any HPV type cleared,No HPV-type cleared confirmed by HPV assay and genotyping,75,15,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Myxococcota|o__Polyangiales|f__Labilitrichaceae|g__Labilithrix|s__Labilithrix luteola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea glycerini",2|1239|91061|1385|539738|3076174|502393;2|976|200643|171549|171552|838|419005;2|2818505|3031712|1524216|1524217|1391654;2|1239|186801|3085636|186803|1763508|1763509,Complete,Fatima Zohra
bsdb:293/7/1,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 7,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV type persisted,at least one HPV type persisted,Any HPV-type persisted confirmed by HPV assay and genotyping,64,29,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga|s__Microvirga lupini,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus radiopugnans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium|s__Anaerobacterium chartisolvens",2|976|200643|171549|171552|2974257|386414;2|1224|28211|356|119045|186650|420324;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|3085636|186803|33042|410072;2|1297|188787|118964|183710|1298|1182571;2|1239|186801|186802|216572|1486725|1297424,Complete,Fatima Zohra
bsdb:293/7/2,Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 7,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV type persisted,at least one HPV type persisted,Any HPV-type persisted confirmed by HPV assay and genotyping,64,29,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,2|1239|91061|186826|33958|1578|1584,Complete,Fatima Zohra
bsdb:294/1/1,Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-induction therapy,6 weeks of remission induction therapy,112,87,NA,16S,123,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"antibiotic exposure,demographics",NA,decreased,decreased,decreased,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239;2|1239|186801|186802|31979;2|1239|91061|186826|1300;2|1239|91061|186826|81852;2|1239|91061|186826|33958,Complete,Atrayees
bsdb:294/1/2,Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-induction therapy,6 weeks of remission induction therapy,112,87,NA,16S,123,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"antibiotic exposure,demographics",NA,decreased,decreased,decreased,NA,NA,Signature 2,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota",2|1239|186801|186802|216572|216851|1971605;2|201174;2|74201,Complete,Atrayees
bsdb:294/2/1,Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-consolidation therapy,8 weeks of consolidation,112,107,NA,16S,123,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239;2|1239|91061|186826|33958,Complete,Atrayees
bsdb:294/2/2,Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-consolidation therapy,8 weeks of consolidation,112,107,NA,16S,123,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table 1, Figure 1 and  2, Supplemental Table S3",10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota",2|976;2|201174;2|74201,Complete,Atrayees
bsdb:294/3/1,Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post re-induction therapy,120 weeks of continuation phase with the last 17-20 weeks of reinduction II therapy,112,90,NA,16S,123,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,decreased,unchanged,decreased,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239;2|1239|186801|186802|31979;2|1239|91061|186826|81852;2|1239|91061|186826|33958,Complete,Atrayees
bsdb:294/3/2,Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post re-induction therapy,120 weeks of continuation phase with the last 17-20 weeks of reinduction II therapy,112,90,NA,16S,123,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,decreased,unchanged,decreased,NA,NA,Signature 2,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|1971605;2|201174;2|74201,Complete,Atrayees
bsdb:294/4/1,Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,non-febrile neutropenia,febrile neutropenia,fever as an oral temperature more than 38.0°C persisting for more than 1 hour; neutropenia as an absolute neutrophil count less than or equal to 500 cells per microliter after baseline first sampled,47,65,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplemental Table S6, Figure 5a",10 January 2021,William Lam,WikiWorks,Comparison of baseline diversity and composition between acute lymphoblastic leukemia children with and without febrile neutropenia occurring throughout therapy,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Atrayees
bsdb:295/1/1,Study 295,"cross-sectional observational, not case-control",31555603,10.3389/fcimb.2019.00294,NA,"Zhou Y, Wang L, Pei F, Ji M, Zhang F, Sun Y, Zhao Q, Hong Y, Wang X, Tian J , Wang Y",Patients With LR-HPV Infection Have a Distinct Vaginal Microbiota in Comparison With Healthy Controls,Frontiers in cellular and infection microbiology,2019,"16S RNA sequencing, condyloma acuminatum, low-risk HPV, sexually transmitted infections, vaginal microbiome",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,negative control,low risk HPV,LR-HPV+ according to results of screening,20,42,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 4B,10 January 2021,Cynthia Anderson,"Lwaldron,WikiWorks,Merit",Comparisons of vaginal bacteria between the NC and HPV-LR groups,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|976|200643|171549|171550|239759;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1224|28216|80840|119060;2|976|200643|171549|1853231|574697;2|1239|186801;2|1239|186801|186802|31979|1485;2|1224|28216|80840|80864;2|976|200643|171549|2005519|1348911;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802;2|1239|186801|3085636|186803|1407607;2|32066|203490|203491;2|32066|203490;2|32066;2|1239|186801|186802|204475;2|1224|2008785|119069|206349;2|1224|2008785|119069;2|1224|2008785|119069|206349|70774;2|1239|186801|3085636|186803;2|32066|203490|203491|1129771;2|1239|909932|1843489|31977|906;2|544448|31969;2|544448;2|1239|186801|186802|541000;2|1224|1236|135625|712|745;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1200657;2|32066|203490|203491|1129771|168808;2|1224|28216|80840|995019|40544;2|1224|28216|80840|995019,Complete,Fatima
bsdb:295/1/2,Study 295,"cross-sectional observational, not case-control",31555603,10.3389/fcimb.2019.00294,NA,"Zhou Y, Wang L, Pei F, Ji M, Zhang F, Sun Y, Zhao Q, Hong Y, Wang X, Tian J , Wang Y",Patients With LR-HPV Infection Have a Distinct Vaginal Microbiota in Comparison With Healthy Controls,Frontiers in cellular and infection microbiology,2019,"16S RNA sequencing, condyloma acuminatum, low-risk HPV, sexually transmitted infections, vaginal microbiome",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,negative control,low risk HPV,LR-HPV+ according to results of screening,20,42,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 4B,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",Comparisons of vaginal bacteria between the NC and HPV-LR groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Nitrososphaera,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales,k__Archaea|p__Nitrososphaerota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1224|1236|135624;2|1224|1236|72274|135621|351;2|1224|1236;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1224|1236|135614|32033|68;2157|651137|1643678|1033996|1033997|497726;2157|651137|1643678|1033996|1033997;2157|651137|1643678|1033996;2157|651137;2|1224|1236|72274;2|1224|1236|135624|83763;2|1224|1236|72274|135621,Complete,Fatima Zohra
bsdb:296/1/1,Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,16S,12,RT-qPCR,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental table S2,10 January 2021,William Lam,WikiWorks,The differential species and subspecies identified by DESeq2 (abs(log2(fold change)) > 1 and adjusted P < 0.05) enriched in multiple myeloma patients and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|244366;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1302;2|1224|1236|91347|543|547|550;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85004|31953|1678|1689;2|1224|1236|91347|543|544|546;2|201174|84998|84999|84107|102106|74426;2|1239|91061|186826|1300|1301|28037;2|1224|1236|91347|543|570|548;2|976|200643|171549|171552|558436|839;2|976|200643|171549|171552|838|589436;2|1239|91061|186826|1300|1301|1328;2|976|200643|171549|171552|838|28132;2|1239|186801|186802|1392389|1297617;2|1239|91061|186826|1300|1301|1313;2|1224|1236|91347|543|160674|54291;2|201174|1760|85004|31953|1678|1680;2|1224|1236|135625|712|416916|732;2|1224|1236|91347|543|547|61645;2|1239|909932|1843489|31977|906|907;2|1239|186801|186802|216572|459786|351091,Complete,Claregrieve1
bsdb:296/1/2,Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,16S,12,RT-qPCR,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental table S2,10 January 2021,William Lam,WikiWorks,The differential species and subspecies identified by DESeq2 (abs(log2(Fold Change)) > 1 and adjusted P < 0.05) enriched in multiple myeloma patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium baratii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saccharobutylicum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio hungatei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saccharoperbutylacetonicum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium beijerinckii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium|s__Paraclostridium sordellii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium",2|1239|91061|186826|1300|1301|197614;2|1239|186801|3085636|186803|1506553|66219;2|1239|186801|186802|31979|1485|1561;2|1239|186801|186802|31979|1485|169679;2|1239|186801|3085636|186803|830|43305;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3085636|186803|830|185008;2|976|200643|171549|815|816|246787;2|1239|186801|186802|31979|1485|36745;2|976|200643|171549|2005525|375288|1869337;2|976|200643|171549|815|816|28116;2|1239|186801|3085636|186803|1663717|1679721;2|976|200643|171549|815|816|818;2|976|200643|171549|2005525|375288|823;2|1239|186801|3085636|186803|28050|39485;2|976|200643|171549|815|816|47678;2|201174|1760|85004|31953|1678|1686;2|1239|186801|186802|31979|1485|1520;2|1239|186801|3082720|186804|1849822|1505;2|1239|186801|186802|31979|1485|1491;2|1239|186801|3085636|186803|207244|649756;2|1239|909932|909929|1843491|158846|158847;2|1239|186801|186802|31979|1485|1492;2|201174|1760|85004|31953|1678|1686|630129;2|201174|1760|85004|31953|1678|28026;2|32066|203490|203491|203492|848|856,Complete,Claregrieve1
bsdb:296/2/1,Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy controls,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 2b, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Nitrogen- recycling bacteria species with differential abundance in multiple myeloma patients and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|244366;2|1224|1236|91347|543|160674|54291;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|28037,Complete,Claregrieve1
bsdb:296/2/2,Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy controls,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 2b, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Nitrogen- recycling bacteria species with differential abundance in multiple myeloma patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum",2|1239|186801|3085636|186803|207244|649756;2|1239|186801|3085636|186803|2719231|84030;2|1239|186801|186802|31979|1485|1492,Complete,Claregrieve1
bsdb:297/1/1,Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,non pregnant no HPV,non pregnant high risk HPV,non pregnant high risk HPV confirmed using HPV genotyping kit,30,19,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|201174|1760|85004|31953|1678;2|976;2|1239|91061|1385;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386,Complete,Fatima Zohra
bsdb:297/1/2,Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,non pregnant no HPV,non pregnant high risk HPV,non pregnant high risk HPV confirmed using HPV genotyping kit,30,19,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826,Complete,Fatima Zohra
bsdb:297/2/1,Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,pregnant no HPV,pregnant high risk HPV,pregnant high risk HPV confirmed using HPV genotyping kit,48,38,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax",2|1224;2|1224|28216;2|1224|28216|80840|80864;2|1224|28216|80840;2|1224|28216|80840|80864|12916,Complete,Fatima Zohra
bsdb:297/2/2,Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,pregnant no HPV,pregnant high risk HPV,pregnant high risk HPV confirmed using HPV genotyping kit,48,38,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061;2|1239|186801|3085636|186803;2|1239|186801;2|1239|186801|186802;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Fatima Zohra
bsdb:298/2/1,Study 298,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP , Shelburne SA",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,"Antibiotics, Chemotherapy, Leukemia, Microbiome, Temporal variability",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5e,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients who experienced infection and patients who did not,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,2|1224|1236|135614|32033|40323,Complete,Claregrieve1
bsdb:298/2/2,Study 298,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP , Shelburne SA",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,"Antibiotics, Chemotherapy, Leukemia, Microbiome, Temporal variability",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5e,28 July 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between patients who experienced infection and patients who did not,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:298/3/1,Study 298,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP , Shelburne SA",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,"Antibiotics, Chemotherapy, Leukemia, Microbiome, Temporal variability",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5e,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance in stool samples between patients with infection and patients with no infection,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,2|1224|1236|135614|32033|40323,Complete,Claregrieve1
bsdb:299/1/1,Study 299,time series / longitudinal observational,32115690,10.1002/ijc.32942,NA,"De Pietri S, Ingham AC, Frandsen TL, Rathe M, Krych L, Castro-Mejía JL, Nielsen DS, Nersting J, Wehner PS, Schmiegelow K, Hasle H, Pamp SJ , Müller K",Gastrointestinal toxicity during induction treatment for childhood acute lymphoblastic leukemia: The impact of the gut microbiota,International journal of cancer,2020,"C-reactive protein, acute lymphoblastic leukemia, citrulline, gastrointestinal toxicity, microbiota, mucositis",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,induction chemotherapy,children (ages 1-18 years old) newly diagnosed with Acute Lymphoblastic Leukemia and undergoing induction chemotherapy according to the Nordic Society of Paediatric Haematology and Oncology (NOPHO) post initiation of induction chemotherapy,32,51,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and Day 15 of induction chemotherapy,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,2|1239|91061|186826|81852|1350|35783,Complete,Claregrieve1
bsdb:300/1/1,Study 300,laboratory experiment,28714953,10.1038/nn.4606,NA,"Shen S, Lim G, You Z, Ding W, Huang P, Ran C, Doheny J, Caravan P, Tate S, Hu K, Kim H, McCabe M, Huang B, Xie Z, Kwon D, Chen L , Mao J",Gut microbiota is critical for the induction of chemotherapy-induced pain,Nature neuroscience,2017,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,H2O mice,Exposed abx mice,Mice fed with antibiotic water,10,10,None,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1C,22 February 2024,ChiomaBlessing,ChiomaBlessing,Phylum analysis of altered microbiota in mice after antibiotic water feeding compared to mice fed with regular water,increased,"k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota",2|1117;2|1224;2|1239,Complete,ChiomaBlessing
bsdb:300/1/2,Study 300,laboratory experiment,28714953,10.1038/nn.4606,NA,"Shen S, Lim G, You Z, Ding W, Huang P, Ran C, Doheny J, Caravan P, Tate S, Hu K, Kim H, McCabe M, Huang B, Xie Z, Kwon D, Chen L , Mao J",Gut microbiota is critical for the induction of chemotherapy-induced pain,Nature neuroscience,2017,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,H2O mice,Exposed abx mice,Mice fed with antibiotic water,10,10,None,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1C,22 February 2024,ChiomaBlessing,"ChiomaBlessing,Scholastica,Joan Chuks",Phylum analysis of altered microbiota in mice after antibiotic water feeding compared to mice fed with regular water,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Candidatus Saccharibacteria",2|201174;2|976;2|32066|203490;2|544448;2|74201|203494;2|95818,Complete,ChiomaBlessing
bsdb:301/1/1,Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection through PCR confirmation,9,9,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 3,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees,Merit",A comparison of the vaginal microbiota among nine HPV infection-discordant twin pairs,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1239|909932|1843489|31977|39948;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066;2|1239|909932|1843489|31977|906;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|2776143;2|32066|203490|203491|203492|848,Complete,Fatima Zohra
bsdb:301/1/2,Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection through PCR confirmation,9,9,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 3,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",A comparison of the vaginal microbiota among nine HPV infection-discordant twin pairs,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|91061|186826|33958|1578;2|1239|91061|186826;2|1239|91061|186826|33958,Complete,Fatima Zohra
bsdb:301/2/1,Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 2,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ through PCR confirmation,26,19,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1b,10 January 2021,Cynthia Anderson,WikiWorks,Comparison of the vaginal microbiotas of the HIV+ and HIV- women without CIN,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",2|32066|203490|203491|1129771|168808;2|32066|203490|203491|203492;2|32066|203490|203491,Complete,Fatima Zohra
bsdb:301/3/1,Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 3,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HR-HPV+,"HR-HPV+ through PCR confirmation, HPV genotype 16, 18, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 66",26,13,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1c,10 January 2021,Cynthia Anderson,WikiWorks,Comparison of the vaginal microbiotas of HIV- and women infected with high risk high risk HPV types,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",2|32066|203490|203491|1129771|168808;2|32066|203490|203491|203492;2|32066|203490|203491,Complete,Fatima Zohra
bsdb:301/3/2,Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 3,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HR-HPV+,"HR-HPV+ through PCR confirmation, HPV genotype 16, 18, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 66",26,13,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 1c,10 January 2021,Cynthia Anderson,WikiWorks,Comparison of the vaginal microbiotas of HIV- and women infected with high risk high risk HPV types,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,2|1239|91061|186826,Complete,Fatima Zohra
bsdb:302/1/1,Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,21,20,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Distinct bacterial composition in subjects with exacerbated asthma and healthy controls (phylum level),increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota",2|976;2|1224,Complete,Atrayees
bsdb:302/2/1,Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,non-exacerbated asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care.",21,31,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Distinct bacterial composition in subjects with non-exacerbated asthma and healthy controls (phyum level),increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota",2|976;2|1224,Complete,Atrayees
bsdb:302/3/1,Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,non-exacerbated asthma,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,31,20,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Victoria Goulbourne,WikiWorks,Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|976|200643|171549|171552|838;2|1224|1236|2887326|468|222991;2|201174|1760|85004|31953|2701,Complete,Lucy Mellor
bsdb:302/3/2,Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,non-exacerbated asthma,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,31,20,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Victoria Goulbourne,WikiWorks,Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,2|1239|909932|1843489|31977|39948,Complete,Lucy Mellor
bsdb:302/4/1,Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care or with an encounter diagnosis of asthma exacerbation",21,51,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, text",10 January 2021,Lucy Mellor,WikiWorks,Species differentially abundant between asthmatics and health controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges|s__Alkanindiges hongkongensis",2|976|200643|171549|171552|2974257|28127;2|1239|909932|1843489|31977|39948|218538;2|201174|1760|85004|31953|2701|2702;2|1224|1236|2887326|468|222991|208968,Complete,Atrayees
bsdb:302/5/1,Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care or with an encounter diagnosis of asthma exacerbation",21,51,NA,16S,34,RT-qPCR,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 January 2021,Victoria Goulbourne,WikiWorks,Difference in fold change between asthmatics and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",2|976|200643|171549|171552|2974257|28127;2|201174|1760|85004|31953|2701|2702,Complete,Lucy Mellor
bsdb:303/1/1,Study 303,prospective cohort,26147207,10.1111/apt.13302,NA,"Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E , Knights D",Chemotherapy-driven dysbiosis in the intestinal microbiome,Alimentary pharmacology & therapeutics,2015,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"non-Hodgkin's lymphoma patients post myeloablative conditiong regimen (chemotherapy) fecal sampling for 5 consecutive days of high-dose Carmustine, Etoposide, Aracytine and Melphalan and with no antibiotics treatment after starting regimen",28,15,1 month,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Supplemental Table S1a-c, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial taxa abundance for non-Hodgkins Lymphoma patients from the fecal samples collected before and after chemotherapy,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|1239|91061|186826|186827;2|1239|91061|186826|186828;2|1224|1236|91347|543|544;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1224;2|201174|84998|84999|1643824|1380;2|1224|1236|91347|543|570,Complete,Claregrieve1
bsdb:303/1/2,Study 303,prospective cohort,26147207,10.1111/apt.13302,NA,"Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E , Knights D",Chemotherapy-driven dysbiosis in the intestinal microbiome,Alimentary pharmacology & therapeutics,2015,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"non-Hodgkin's lymphoma patients post myeloablative conditiong regimen (chemotherapy) fecal sampling for 5 consecutive days of high-dose Carmustine, Etoposide, Aracytine and Melphalan and with no antibiotics treatment after starting regimen",28,15,1 month,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Supplemental Table S1a-c, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial taxa abundance for non-Hodgkins Lymphoma patients from the fecal samples collected before and after chemotherapy,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|201174;2|201174|84998|1643822|1643826|447020;2|1239|1737404|1737405|1570339|165779;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|543;2|1239;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:304/1/1,Study 304,randomized controlled trial,27411009,10.1016/j.cmet.2016.06.016,NA,"Reijnders D, Goossens GH, Hermes GD, Neis EP, van der Beek CM, Most J, Holst JJ, Lenaerts K, Kootte RS, Nieuwdorp M, Groen AK, Olde Damink SW, Boekschoten MV, Smidt H, Zoetendal EG, Dejong CH , Blaak EE",Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial,Cell metabolism,2016,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,or placebo (microcrystalline cellulose),oral intake of vancomycin (directed against Gram-positive bacteria),"low-active (<3 hr organized sports activities per week), weight-stable (<2 kg body weight change 3 months prior to inclusion) overweight/obese (BMI 25–35 kg/m2) Caucasian men, between 35 and 70 years with impaired glucose metabolism (either fasting glucose >5.6 mmol/l, and/or 2 hr glucose between 7.8–11 mmol/l) and insulin resistant (homeostasis model assessment for insulin resistance; HOMA-IR > 2.2).",37,38,3 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table S1,10 January 2021,Mst Afroza Parvin,"Lwaldron,WikiWorks",Significantly different microbial taxa after 7 days intervention with vancomycin and placebo in feces using linear mixed models,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax|s__Anaerovorax odorimutans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi",2|1239|186801|3085636|186803|207244|105841;2|1239|186801|3082720|3030910|109326|109327;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511|40520;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042|33043;2|1239|186801|3085636|186803|189330|39486;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|140625|140626;2|1239|186801|3085636|186803|28050|28052;2|1239|186801|3085636|186803|2719231|29370;2|1239|91061|186826|33958|2767842|1590;2|1239|186801|186802|216572|100175|100176;2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|186802|216572|29343,Complete,Rimsha Azhar
bsdb:305/1/1,Study 305,case-control,32237205,10.1002/cam4.3027,NA,"Tsementzi D, Pena-Gonzalez A, Bai J, Hu YJ, Patel P, Shelton J, Dolan M, Arluck J, Khanna N, Conrad L, Scott I, Eng TY, Konstantinidis KT , Bruner DW",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Genital neoplasm, female",EFO:1001331,healthy controls,women with gynecological cancer,postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer treated with radiotherapy with or without surgery and/or chemotherapy,69,65,course of the study,16S,4,Illumina,LEfSe,0.05,TRUE,3,NA,NA,unchanged,increased,increased,NA,NA,increased,Signature 1,"Figure 3, Supplemental Figure 2",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant bacterial operational taxonomic units between endometrial and cervical cancer and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|39948;2|1239|1737404|1582879;2|32066|203490|203491|203492|848;2|201174|1760|2037|2049|2050;2|1239|186801|3085636|186803|437755;2|544448|31969|2085|2092|2093;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771,Complete,Claregrieve1
bsdb:305/1/2,Study 305,case-control,32237205,10.1002/cam4.3027,NA,"Tsementzi D, Pena-Gonzalez A, Bai J, Hu YJ, Patel P, Shelton J, Dolan M, Arluck J, Khanna N, Conrad L, Scott I, Eng TY, Konstantinidis KT , Bruner DW",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Genital neoplasm, female",EFO:1001331,healthy controls,women with gynecological cancer,postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer treated with radiotherapy with or without surgery and/or chemotherapy,69,65,course of the study,16S,4,Illumina,LEfSe,0.05,TRUE,3,NA,NA,unchanged,increased,increased,NA,NA,increased,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant bacterial operational taxonomic units between endometrial and cervical cancer and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|177971,Complete,Claregrieve1
bsdb:306/1/NA,Study 306,prospective cohort,31951695,10.21101/cejph.a5393,NA,"Parco S, Benericetti G, Vascotto F , Palmisciano G",Microbiome and diversity indices during blood stem cells transplantation - new perspectives?,Central European journal of public health,2019,"blood stem cells transplantation, graft versus host disease, oral and gut microbiome",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,pre- allogeneic hematopoietic stem cell transplant,post- allogeneic hematopoietic stem cell transplant,children between 3 and 10 years of age that have undergone allogeneic hematopoeitic stem cell transplantation and hospitalized at Institute for Maternal and Child Health of Trieste,5,5,None,16S,123,Ion Torrent,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:307/1/1,Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),moxifloxacin treated group (MXF),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Archaea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2157;2|1239|186801|3085636|186803|572511,Complete,NA
bsdb:307/1/2,Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),moxifloxacin treated group (MXF),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,"Lwaldron,WikiWorks",A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|328814;2|976|200643|171549;2|976|200643|171549|2005519|397864|487174;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|28026;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|1955243;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|574697|544645;2|1239|526524|526525|2810280|135858;2|976|117743|200644|2762318|501783|1913682;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1506;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239;2|1224|1236|135625|712|724|729;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|1945593;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288|823;2|1224|28216|80840|995019|577310|487175;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40519;2|1239|91061|186826|1300|1301|1318,Complete,NA
bsdb:307/2/1,Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,moxifloxacin treated group (MXF),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,14,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis",2|976|200643|171549|2005525|375288|823;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|841|360807;2|976|200643|171549|1853231|283168|28118;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|186802|31979|1485|1506;2|1239;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263|40519;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|216851;2|1224|28216|80840|995019|577310|487175;2|976|117743|200644|2762318|501783|1913682;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|171550|239759|328813;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|1945593;2|1239|526524|526525|2810280|100883;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|1853231|574697|544645;2|1239|186801|186802|541000;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|1853231|574697;2|976|200643|171549|2005519|397864|487174;2|1239|186801|3085636|186803|28050|39485;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|189330|39486;2|1224|1236|135625|712|724|729;2|976|200643|171549|171550|239759|1288121,Complete,NA
bsdb:307/2/2,Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,moxifloxacin treated group (MXF),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,14,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,2|1239|186801|3085636|186803|572511,Complete,NA
bsdb:307/3/1,Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239;2|1239|186801|3085636|186803,Complete,NA
bsdb:307/3/2,Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",2|200940|3031449|213115|194924|35832|35833;2|201174|1760|85004|31953|1678|1680;2|1239|186801|3082720|186804|1505657|261299;2|201174|1760|85004|31953|1678|28026;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|216572|946234|292800,Complete,NA
bsdb:308/1/1,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure S3,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826;2|976|200643|171549|815;2|976|200643|171549,Complete,ChiomaBlessing
bsdb:308/1/2,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure S3,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks",Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae",2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1239|91061|186826|186827,Complete,ChiomaBlessing
bsdb:308/2/1,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure S6,10 January 2021,Zyaijah Bailey,"Atrayees,WikiWorks,Merit",Individual abundance histograms of bacterial lineages changing particularly in the fecal samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium",2|976|200643|171549;2|1239|186801|3085636|186803;2759|4751|5204|155619|139380|1124673;2|1239|186801|3085636|186803|28050;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|2030927;2|976|200643|171549|815|2212467,Complete,ChiomaBlessing
bsdb:308/2/2,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure S6,10 January 2021,Zyaijah Bailey,WikiWorks,Individual abundance histograms of bacterial lineages changing particularly in the fecal samples,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|976|200643|171549|815|816;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578;2|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:308/3/1,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 3,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Figure S4,10 January 2021,Zyaijah Bailey,"WikiWorks,Rukky",Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium",2|976|200643|171549|2030927;2|976|200643|171549|171550|2049048,Complete,Rukky
bsdb:308/3/2,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 3,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Figure S4,10 January 2021,WikiWorks,"Atrayees,WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|976|200643|171549|815;2|976|200643|171549|815|2212467;2|976|200643|171549;2|976|200643|171549|2030927;2|976|200643|171549|815|816;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:308/4/1,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 4,United States of America,Mus musculus,Stomach,UBERON:0000945,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Figure S2,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks",Histograms of relative abundance of selected statistically differentially abundant genera in the stomach,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|1239|91061|186826|33958;2|976|200643|171549,Complete,ChiomaBlessing
bsdb:308/4/2,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 4,United States of America,Mus musculus,Stomach,UBERON:0000945,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Figure S2,10 January 2021,Zyaijah Bailey,WikiWorks,Histograms of relative abundance of selected statistically differentially abundant genera in the stomach,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:308/5/1,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 5,United States of America,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 1,Figure S5,10 January 2021,Zyaijah Bailey,"WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the colon,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|1869337;2|976|200643|171549|2005525|375288,Complete,ChiomaBlessing
bsdb:308/5/2,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 5,United States of America,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 2,Figure S5,10 January 2021,Zyaijah Bailey,"WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the colon,decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|544448|31969|186332|186333|2086;2|1239|186801|186802|31979|1485;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979;2|1239|186801;2|1239|186801|186802|1898207;2|1239|186801;2|1239|186801|186802|31979,Complete,ChiomaBlessing
bsdb:308/6/1,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 6,United States of America,Mus musculus,"Feces,Stomach,Caecum,Small intestine,Colon","UBERON:0001988,UBERON:0001153,UBERON:0001155,UBERON:0000945,UBERON:0002108",Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,10 January 2021,Zyaijah Bailey,"Atrayees,WikiWorks",LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1239|91061,Complete,Atrayees
bsdb:308/6/2,Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 6,United States of America,Mus musculus,"Feces,Stomach,Caecum,Small intestine,Colon","UBERON:0001988,UBERON:0001153,UBERON:0001155,UBERON:0000945,UBERON:0002108",Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,10 January 2021,Zyaijah Bailey,"Atrayees,WikiWorks",LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|1239|91061|186826|33958;2|976|200643|171549|171550;2|976|200643|171549,Complete,Atrayees
bsdb:309/1/1,Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2, supplemental table 1",10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oleovorans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella",2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|815|816|28111;2|976|200643|171549|1853231|574697;2|1224|1236|118969|118968;2|1239|186801|186802|31984;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1224|1236|118969|444;2|1239|91061|186826|33958|2742598|1598;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1224|1236|72274|135621|286|330;2|1224|1236|118969|118968|59195,Complete,Fatima Zohra
bsdb:309/1/2,Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2, supplemental table 1",10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|186802;2|1239|186801|186802|541000,Complete,Fatima Zohra
bsdb:309/2/1,Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,<=38.8% 8-OHdG-positive cervical cells,>38.8% 8-OHdG-positive cervical cells,patients with >38.8% of 8-OHdG-positive cervical cells,NA,NA,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental Figure 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in >38.8% 8-OHdG-positive cervical cells group VS  <=38.8% 8-OHdG-positive cervical cells group,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae",2|1224|28211|356|82115|357;2|1224|1236|72274|135621|351;2|1224|28216;2|1224|28216|80840;2|1224|28216|80840|80864;2|1224|28211|356;2|1224|28216|80840|80864|665874;2|1224|28216|80840|75682;2|1224|28211|204458|76892|20;2|1224|1236|72274|135621|286;2|1224|28211|356|82115,Complete,Fatima Zohra
bsdb:309/2/2,Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,<=38.8% 8-OHdG-positive cervical cells,>38.8% 8-OHdG-positive cervical cells,patients with >38.8% of 8-OHdG-positive cervical cells,NA,NA,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental Figure 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in >38.8% 8-OHdG-positive cervical cells group VS <=38.8% 8-OHdG-positive cervical cells group,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,Fatima Zohra
bsdb:309/3/1,Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental Table 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",2|74201|203494|48461|1647988|239934|239935;2|1239|91061|186826|33958|2742598|1598,Complete,Fatima Zohra
bsdb:309/3/2,Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental Table 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|186803|572511|33035;2|1239|186801|186802|31979|1485|1502;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|2974251|165179;2|1239|91061|186826|1300|1301|1311,Complete,Fatima Zohra
bsdb:310/1/1,Study 310,prospective cohort,24402367,10.1007/s00248-013-0355-4,NA,"Montassier E, Batard E, Massart S, Gastinne T, Carton T, Caillon J, Le Fresne S, Caroff N, Hardouin JB, Moreau P, Potel G, Le Vacon F , de La Cochetière MF",16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation,Microbial ecology,2014,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan",8,8,all antibiotics after starting chemotherapy,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 4, 5, text",10 January 2021,William Lam,"WikiWorks,Aiyshaaaa,Atrayees","Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota",2|976|200643|171549|815|816;2|976;2|1224|1236|91347|543|561;2|1224,Complete,Atrayees
bsdb:310/1/2,Study 310,prospective cohort,24402367,10.1007/s00248-013-0355-4,NA,"Montassier E, Batard E, Massart S, Gastinne T, Carton T, Caillon J, Le Fresne S, Caroff N, Hardouin JB, Moreau P, Potel G, Le Vacon F , de La Cochetière MF",16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation,Microbial ecology,2014,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan",8,8,all antibiotics after starting chemotherapy,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 4, 5, text",10 January 2021,William Lam,"WikiWorks,Atrayees","Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239;2|201174;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:311/1/1,Study 311,time series / longitudinal observational,25893458,10.1038/bmt.2015.16,NA,"Biagi E, Zama D, Nastasi C, Consolandi C, Fiori J, Rampelli S, Turroni S, Centanni M, Severgnini M, Peano C, de Bellis G, Basaglia G, Gotti R, Masetti R, Pession A, Brigidi P , Candela M",Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT,Bone marrow transplantation,2015,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-GvHD (Graft-versus-host disease),aGvHD (acute Graft-versus-host disease),pre-HSCT (hematopoietic stem cell transplant) samples of subjects who underwent HSCT who developed acute graft-versus-host disease,5,5,None.,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results (Text): Page 4, 3rd paragraph under sub-heading ""aGvHD-associated gut microbiota signatures.""",10 January 2021,William Lam,"WikiWorks,Chloe,ChiomaBlessing",Gut microbiota signatures in pre-HSCT samples of subjects who developed aGvHD compared to subjects who did not develop aGvHD (non-aGvHD),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia,2|976|200643,Complete,ChiomaBlessing
bsdb:311/1/2,Study 311,time series / longitudinal observational,25893458,10.1038/bmt.2015.16,NA,"Biagi E, Zama D, Nastasi C, Consolandi C, Fiori J, Rampelli S, Turroni S, Centanni M, Severgnini M, Peano C, de Bellis G, Basaglia G, Gotti R, Masetti R, Pession A, Brigidi P , Candela M",Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT,Bone marrow transplantation,2015,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-GvHD (Graft-versus-host disease),aGvHD (acute Graft-versus-host disease),pre-HSCT (hematopoietic stem cell transplant) samples of subjects who underwent HSCT who developed acute graft-versus-host disease,5,5,None.,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results (Text): Page 4, 3rd paragraph under sub-heading ""aGvHD-associated gut microbiota signatures.""",1 February 2024,ChiomaBlessing,ChiomaBlessing,Gut microbiota signatures in pre-HSCT samples of subjects who developed aGvHD compared to subjects who did not develop aGvHD (non-aGvHD),increased,k__Bacteria|p__Bacillota,2|1239,Complete,ChiomaBlessing
bsdb:312/1/1,Study 312,prospective cohort,26971496,10.1007/s00253-016-7410-2,NA,"Aloisio I, Quagliariello A, De Fanti S, Luiselli D, De Filippo C, Albanese D, Corvaglia LT, Faldella G , Di Gioia D",Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions,Applied microbiology and biotechnology,2016,"16S rDNA hypervariable regions, Gut microbiota, Intrapartum antibiotic prophylaxis, Newborns, Next generation sequencing technology",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants born by mothers negative to GBS,Infants born by mothers positive to GBS and received IAP,Infants of Mothers positive to Streptococcus (GBS) and received intrapartum antibiotic prophylaxis (IAP),10,10,perinatal antibiotics,16S,23456789,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table S3, Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Evaluation of microbial genus composition between Control and IAP groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|201174|1760|85004|31953;2|976|200643|171549|815,Complete,Atrayees
bsdb:312/2/1,Study 312,prospective cohort,26971496,10.1007/s00253-016-7410-2,NA,"Aloisio I, Quagliariello A, De Fanti S, Luiselli D, De Filippo C, Albanese D, Corvaglia LT, Faldella G , Di Gioia D",Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions,Applied microbiology and biotechnology,2016,"16S rDNA hypervariable regions, Gut microbiota, Intrapartum antibiotic prophylaxis, Newborns, Next generation sequencing technology",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants born by mothers negative to GBS,Infants born by mothers positive to GBS and received IAP,Infants of Mothers positive to Streptococcus (GBS) and received intrapartum antibiotic prophylaxis (IAP),10,10,perinatal antibiotics,16S,23456789,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table S3, Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Evaluation of microbial genus composition between Control and IAP groups,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:313/1/1,Study 313,prospective cohort,27121964,10.1186/s13073-016-0301-4,NA,"Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, de la Cochetiere MF, Batard E , Knights D",Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection,Genome medicine,2016,"Bloodstream infection, Chemotherapy, Intestinal microbiome, Prediction",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,non-bloodstream infection,bloodstream infection,"participants had blood stream infection, diagnosis with non-Hodgkins lymphoma (NHL), undergone hematopoeitic stem cell transplant and chemotherapy that did not had a history of inflammatory bowel disease, no exposure to probiotics, prebiotics or broad-soectrium antibiotics, no administered nasal-tube feeding or parenteral nutrition in a month prior to initiation of the study",17,11,NA,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2, 3, aditional file 5a and b, 7",10 January 2021,William Lam,"WikiWorks,Aiyshaaaa",Relative abundance of the differentiated taxa in samples collected prior to treatment in patients who developed subsequent Blood Stream Infections and patients who did not develop Blood Stream Infections,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827,Complete,NA
bsdb:313/1/2,Study 313,prospective cohort,27121964,10.1186/s13073-016-0301-4,NA,"Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, de la Cochetiere MF, Batard E , Knights D",Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection,Genome medicine,2016,"Bloodstream infection, Chemotherapy, Intestinal microbiome, Prediction",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,non-bloodstream infection,bloodstream infection,"participants had blood stream infection, diagnosis with non-Hodgkins lymphoma (NHL), undergone hematopoeitic stem cell transplant and chemotherapy that did not had a history of inflammatory bowel disease, no exposure to probiotics, prebiotics or broad-soectrium antibiotics, no administered nasal-tube feeding or parenteral nutrition in a month prior to initiation of the study",17,11,NA,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 2, 3, aditional file 5a and b, 7",10 January 2021,William Lam,"WikiWorks,Merit",Relative abundance of the differentiated taxa in samples collected prior to treatment in patients who developed subsequent Blood Stream Infections and patients who did not develop Blood Stream Infections,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|28216|80840|506;2|976|200643|171549|2005519;2|976|200643|171549|1853231|574697;2|1239|186801|186802|186807|51514;2|200795|301297|1202465|1202464;2|200940|3031449|213115|194924;2|1239|186801|186802|216572|216851;2|976|200643|171549|1853231;2|1239|186801|186802|216572|119852;2|1224|28216|80840|75682;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:314/1/1,Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe analysis identified baseline vaginal microbiota biomarkers associated with clinical outcomes at 12 months follow-up,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Actinomycetota|c__Actinomycetes",2|976|200643|171549|171552|2974257|386414;2|1239|909932;2|1239|909932|909929;2|201174|84998|84999;2|1239|186801|186802;2|201174|84998|84999|1643824|1380;2|201174|84998|84999|1643824|2767327|82135;2|201174|84998|84999|84107;2|32066;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|906;2|32066|203490;2|32066|203490|203491;2|1239|1737404|1737405|1570339|543311;2|1239|186801;2|1239|186801|3085636|186803;2|976|200643|171549|171552|838;2|976;2|976|200643;2|976|200643|171549|171552;2|976|200643|171549;2|201174|1760,Complete,Fatima Zohra
bsdb:314/1/2,Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe analysis identified baseline vaginal microbiota biomarkers associated with clinical outcomes at 12 months follow-up,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota",2|1239|91061|186826;2|1239|91061;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239,Complete,Fatima Zohra
bsdb:314/2/1,Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Outcomes at 12-month follow-up according to baseline VMB composition at baseline,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",2|976|200643|171549|171552|2974257|386414;2|201174|1760|85004|31953|2701|2702,Complete,Fatima Zohra
bsdb:314/3/1,Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 24 months",63,24,NA,16S,12,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Supplementary Figure 2,10 January 2021,Cynthia Anderson,WikiWorks,Outcomes at 24 month follow-up according to baseline VMB composition at baseline,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis",2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171552|2974257|386414,Complete,Fatima Zohra
bsdb:314/4/1,Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 4,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 24 months among women with no regression after 12 months",21,14,NA,16S,12,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Supplementary Figure 3. Outcomes at 24 months according to VMB composition at 12 months in a subgroup of 35 women with ongoing disease,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,2|1239|91061|186826|186827|1375|87541,Complete,Fatima Zohra
bsdb:315/1/1,Study 315,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Infants to mothers didn't receive IAP,Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,22,18,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S1,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,"Levels (relative frequencies; %) of the bacterial families showing differences, in at least one time point analyzed, between infants from mothers receiving IAP and those whose mothers did not receive it.",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|29547|3031852|213849|72294;2|1239|186801|186802|31979;2|29547|3031852|213849|72293;2|976|200643|171549|171552;2|976|200643|171549|171550,Complete,Atrayees
bsdb:315/1/2,Study 315,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Infants to mothers didn't receive IAP,Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,22,18,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S1,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,"Levels (relative frequencies; %) of the bacterial families showing differences, in at least one time point analyzed, between infants from mothers receiving IAP and those whose mothers did not receive it.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota",2|201174|1760|85004|31953;2|201174,Complete,Atrayees
bsdb:315/2/1,Study 315,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,breast-fed Infants to mothers didn't receive IAP,Breast-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,18,11,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Verrucomicrobiota",2|1239;2|74201,Complete,Atrayees
bsdb:315/2/2,Study 315,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,breast-fed Infants to mothers didn't receive IAP,Breast-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,18,11,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota",2|201174;2|976,Complete,Atrayees
bsdb:315/3/1,Study 315,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Formula-fed Infants to mothers didn't receive IAP,Formula-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,4,7,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Atrayees
bsdb:315/3/2,Study 315,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Formula-fed Infants to mothers didn't receive IAP,Formula-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,4,7,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,decreased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Atrayees
bsdb:316/1/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,2-day old Full-term infants(born after uncomplicated pregnancy),2-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" Line 7 to 15",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|201174|1760|85004|31953;2|1224|28216|80840|80864;2|201174|1760|85009|31957;2|1239|91061|186826|1300;2|201174;2|1239|91061;2|1239|91061|186826,Complete,ChiomaBlessing
bsdb:316/1/2,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,2-day old Full-term infants(born after uncomplicated pregnancy),2-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (Line 7 to 15)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549|815;2|1239|186801|186802|31979;2|201174|1760|85006|1268;2|1224|1236|135625|712;2|976|200643|171549|171551,Complete,ChiomaBlessing
bsdb:316/2/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,10-day old Full-term infants(born after uncomplicated pregnancy),10-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 15 to 22)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",2|1224|1236|91347|543;2|1224|1236;2|201174|1760|85006|1268,Complete,ChiomaBlessing
bsdb:316/2/2,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,10-day old Full-term infants(born after uncomplicated pregnancy),10-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 15 to 22)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota",2|1239|909932|1843489|31977;2|976|200643|171549|815;2|201174|1760|85004|31953;2|1239|186801|186802|31979;2|201174|84998|84999|84107;2|1239|91061|186826|81850;2|1224|1236|135625|712;2|976|200643|171549|171551;2|201174,Complete,ChiomaBlessing
bsdb:316/3/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,30 and 90-day old Full-term infants,30 and 90-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 23 to 26)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Lwaldron
bsdb:316/3/2,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,30 and 90-day old Full-term infants,30 and 90-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 23 to 26)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,2|976|200643|171549|815,Complete,Lwaldron
bsdb:316/4/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,10-day old cesarean-delivered pre-term neontes,10-day old vaginally-delivered pre-term neonates,10-day old pre-term infants who were delivered vaginally.,20,7,NA,PCR,NA,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the sub-heading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (Line 6-8)",20 November 2023,Folakunmi,Folakunmi,"Impact of Delivery method on the Intestinal Microbiota between 10-day old vaginally-delivered pre-term neonates and cesarean-delivered pre-term neonates, as observed by qPCR.",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,ChiomaBlessing
bsdb:316/5/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,2-day old full-term neonates not exposed to antibiotics (IAP/postnatal),2-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 11)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 2-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 2-day old pre-term neonates exposed to antibiotics (IAP),decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,Atrayees
bsdb:316/6/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,10-day old full-term neonates not exposed to antibiotics (IAP/postnatal),10-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 11)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 10-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 10-day old pre-tem neonates exposed to antibiotics (IAP),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",2|201174|1760|85006|1268;2|201174|1760|85009|31957,Complete,Atrayees
bsdb:316/7/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 18)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP),decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli",2|1224|28216|80840|80864;2|1239|91061|1385|90964;2|1239|91061,Complete,Atrayees
bsdb:316/8/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,90-day old full-term neonates not exposed to antibiotics (IAP/postnatal),90-day old pre-term neonates with mothers exposed to antibiotics (IAP),90-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 31)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 90-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 90-day old pre-term neonates with mothers exposed to antibiotics (IAP),decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,Atrayees
bsdb:316/9/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates with mothers exposed to antibiotics (IAP),30-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.,5,14,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 24)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates with mothers exposed to antibiotics (IAP),increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:316/9/2,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates with mothers exposed to antibiotics (IAP),30-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.,5,14,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 20)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates with mothers exposed to antibiotics (IAP),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Actinomycetota",2|201174|1760|85004|31953;2|1239|91061|186826|1300;2|1239|91061|186826;2|201174,Complete,ChiomaBlessing
bsdb:316/10/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,PCR,NA,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results for qtPCR within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"", 5th paragraph)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP/postnatal),decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,2|1239|91061|1385|90964,Complete,ChiomaBlessing
bsdb:316/10/2,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,PCR,NA,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results for qtPCR within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"", 5th paragraph)",20 November 2023,ChiomaBlessing,ChiomaBlessing,Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP/postnatal),increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:316/11/1,Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 11,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,90-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),90-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,PCR,NA,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results for qtPCR within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (5th paragraph)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 90-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 90-day old pre-term neonates exposed to antibiotics (IAP/postnatal),decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:317/1/1,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0 (Baseline),"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",33,32,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,decreased,unchanged,unchanged,decreased,Signature 1,Figure 3A,24 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Merit,Claregrieve1",Differential microbial abundance in stool samples between controls and OCD patients at the T0 timepoint,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|976|200643|171549|2005519;2|976|200643|171549|2005519|1348911;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|216572|459786;2|976|200643|171549|171550;2|544448|31969;2|1239|186801|186802|216572|2485925,Complete,Claregrieve1
bsdb:317/1/2,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0 (Baseline),"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",33,32,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,decreased,unchanged,unchanged,decreased,Signature 2,Figure 3A,24 March 2023,Kahvecirem,"Kahvecirem,Merit,Claregrieve1",Differential microbial abundance in stool samples between controls and OCD patients at the T0 timepoint,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|3085636|186803|1766253;2|1239|186801|186802|3085642|580596;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|404402;2|1239|186801|3085636|186803|28050;2|1239|909932;2|976|200643|171549|171552|577309;2|976|200643|171549|171552;2|1239|186801|3082720|186804|1501226;2|1239|909932|909929;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:317/2/1,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 2,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0,"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",32,32,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 4A,24 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Merit,Claregrieve1",Differential microbial abundance in oropharyngeal samples between controls and T0 OCD patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.",2|1239|186801|3085636|186803|265975;2|201174|1760|2037|2049|1654;2|201174|1760|2037;2|201174|84998|84999|1643824;2|201174|84998|84999|1643824|1380;2|201174|84998|84999;2|201174|84998;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|265975|1969407,Complete,Claregrieve1
bsdb:317/2/2,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 2,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0,"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",32,32,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 4A,24 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Merit,Claregrieve1",Differential microbial abundance in oropharyngeal samples between controls and T0 OCD patients,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium",2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|1239|186801|3082720|186804|1904861,Complete,Claregrieve1
bsdb:317/3/1,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",33,31,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure S4,29 March 2023,Kahvecirem,"Kahvecirem,Atrayees,Merit,Claregrieve1",Differential microbial abundance in stool samples between controls and OCD patients at the T3 timepoint,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|244127;2|976|200643|171549|2005519;2|200940|3031449|213115|194924|35832;2|976|200643|171549|2005519|1348911;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802|216572|946234;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1929305;2|976|200643|171549|171550;2|1239|186801|186802|216572|1508657,Complete,Claregrieve1
bsdb:317/3/2,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",33,31,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure S4,29 March 2023,Kahvecirem,"Kahvecirem,Merit,Claregrieve1",Differential microbial abundance in stool samples between controls and OCD patients at the T3 timepoint,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|33042;2|1239|186801|3082720|186804|1505657;2|1239|186801|3085636|186803|28050|2049031;2|976|200643|171549|171552|577309;2|1239|186801|3082720|186804;2|976|200643|171549|171552;2|1239|186801|3082720|186804|1501226;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:317/4/1,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 4,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",32,31,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure S6,29 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Claregrieve1",Differential microbial abundance in oropharyngeal samples between controls and T3 OCD patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|84998|84999|1643824;2|201174|84998|84999|1643824|1380;2|1239|186801|3085636|186803|43996;2|201174|84998|84999;2|201174|84998;2|1239|186801|3085636|186803;2|1239|186801|3082720|3030910|86331,Complete,Claregrieve1
bsdb:317/4/2,Study 317,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P , Rabionet R",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 4,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",32,31,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure S6,29 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Claregrieve1",Differential microbial abundance in oropharyngeal samples between controls and T3 OCD patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella",2|1239|186801|3085636|186803|830;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|186801|3085636|186803|43994,Complete,Claregrieve1
bsdb:318/1/1,Study 318,prospective cohort,28733895,10.1007/s00277-017-3069-8,NA,"Doki N, Suyama M, Sasajima S, Ota J, Igarashi A, Mimura I, Morita H, Fujioka Y, Sugiyama D, Nishikawa H, Shimazu Y, Suda W, Takeshita K, Atarashi K, Hattori M, Sato E, Watakabe-Inamoto K, Yoshioka K, Najima Y, Kobayashi T, Kakihana K, Takahashi N, Sakamaki H, Honda K , Ohashi K",Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation,Annals of hematology,2017,"Acute gastrointestinal graft-versus-host disease (GVHD), Allogeneic hematopoietic stem cell transplantation (allo-HSCT), Intestinal microbiota, Microbial diversity",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-acute graft-versus-host disease,acute graft-versus-host disease,"participants that developed acute graft-versus-host disease after allogeneic hematopoeitic transplant and graded accordinly to pattern of organ involvement and clinical performance status using a system introduced by Glucksberg et al. (Severity Index), which includes late-onset of acute graft-versus-host disease (more than 100 days after transplantation)",NA,107,NA,16S,12,Roche454,T-Test,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,William Lam,WikiWorks,pre-transplant relative abundance of phylum-level gut microbial diversity on the non-acute graft-versus-host disease compared to acute graft-versus-host disease in outcomes of allogeneic hematopoietic stem cell transplantation,increased,k__Bacteria|p__Bacillota,2|1239,Complete,Atrayees
bsdb:318/2/1,Study 318,prospective cohort,28733895,10.1007/s00277-017-3069-8,NA,"Doki N, Suyama M, Sasajima S, Ota J, Igarashi A, Mimura I, Morita H, Fujioka Y, Sugiyama D, Nishikawa H, Shimazu Y, Suda W, Takeshita K, Atarashi K, Hattori M, Sato E, Watakabe-Inamoto K, Yoshioka K, Najima Y, Kobayashi T, Kakihana K, Takahashi N, Sakamaki H, Honda K , Ohashi K",Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation,Annals of hematology,2017,"Acute gastrointestinal graft-versus-host disease (GVHD), Allogeneic hematopoietic stem cell transplantation (allo-HSCT), Intestinal microbiota, Microbial diversity",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-acute graft-versus-host disease,acute graft-versus-host disease,"participants that developed acute graft-versus-host disease after allogeneic hematopoeitic transplant and graded accordinly to pattern of organ involvement and clinical performance status using a system introduced by Glucksberg et al. (Severity Index), which includes late-onset of acute graft-versus-host disease (more than 100 days after transplantation)",NA,107,NA,16S,12,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,William Lam,WikiWorks,pre-transplant genus-level gut microbial diversity on the non-acute graft-versus-host disease compared to acute graft-versus-host disease in outcomes of allogeneic hematopoietic stem cell transplantation,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186806|1730,Complete,Atrayees
bsdb:319/1/1,Study 319,laboratory experiment,29665823,10.1186/s12989-018-0252-6,NA,"Wang W, Zhou J, Chen M, Huang X, Xie X, Li W, Cao Q, Kan H, Xu Y , Ying Z",Exposure to concentrated ambient PM<sub>2.5</sub> alters the composition of gut microbiota in a murine model,Particle and fibre toxicology,2018,"Diabetes, Glucose homeostatic, Gut microbiota, PM2.5",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,mice exposed to PM 2.5 (CAP),mice exposed to filtered air (FA),male C57Bl/6 J mice exposed to PM2.5 (CAP),10,10,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,unchanged,Signature 1,Figure 4 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",The differential taxa between FA- and CAP-exposed mice,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma sualvi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella|s__Rikenella microfusus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium DW52",2|1239|186801|3085636|186803|248744;2|544448|31969|2085|2092|2093;2|544448|31969|2085|2092;2|544448|31969|2085;2|976|200643|171549|171550;2|976|200643|171549|171550|239759|214856;2|544448|2790996|2895623|2895509|2125;2|976|200643|171549|171550|28138|28139;2|1239|186801|3085636|186803|1837329,Complete,Claregrieve1
bsdb:319/1/2,Study 319,laboratory experiment,29665823,10.1186/s12989-018-0252-6,NA,"Wang W, Zhou J, Chen M, Huang X, Xie X, Li W, Cao Q, Kan H, Xu Y , Ying Z",Exposure to concentrated ambient PM<sub>2.5</sub> alters the composition of gut microbiota in a murine model,Particle and fibre toxicology,2018,"Diabetes, Glucose homeostatic, Gut microbiota, PM2.5",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,mice exposed to PM 2.5 (CAP),mice exposed to filtered air (FA),male C57Bl/6 J mice exposed to PM2.5 (CAP),10,10,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,unchanged,Signature 2,Figure 4 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",The differential taxa between FA- and CAP-exposed mice,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 001,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Culture Jar-56,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter hepaticus",2|29547|3031852|213849;2|29547;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|31979|1485|1970093;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|1235800;2|1239|186801|186802|31979|1485|1003360;2|1239|186801|186802|216572|100175;2|1239|526524|526525|128827|174708;2|1239|526524|526525|2810281|191303;2|29547|3031852|213849|72293|209|32025,Complete,Claregrieve1
bsdb:320/1/1,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  intrapartum antibiotic,infants(6-weeks) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Table S1, Figure S2 & Text",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|186801|186802|216572|119852;2|1239|186801|186802|186806|113286;2|201174|1760|2037|2049|184869;2|1239|909932|1843489|31977|29465|39778,Complete,Atrayees
bsdb:320/1/2,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  intrapartum antibiotic,infants(6-weeks) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Table S1, Figure S2 & Text",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263,Complete,Atrayees
bsdb:320/2/1,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  intrapartum antibiotic,infants(1-year) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S1,10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|186801|186802|216572|119852;2|1239|186801|186802|186806|113286;2|201174|1760|2037|2049|184869;2|1239|909932|1843489|31977|29465|39778,Complete,Atrayees
bsdb:320/2/2,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  intrapartum antibiotic,infants(1-year) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S1,10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:320/3/1,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  antibiotic,infants(6-weeks) to mothers exposed to  antibiotic penicillin,vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"text, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|976|200643|171549|815|816;2|976|200643|171549|815|816|28116;2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:320/4/1,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  antibiotic,infants(1-year) to mothers exposed to the penicillin group,vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Table S1, Figure S2 & Text, Figure 1, Figure 3",10 January 2021,Mst Afroza Parvin,WikiWorks,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|2316020|33038,Complete,Atrayees
bsdb:320/4/2,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  antibiotic,infants(1-year) to mothers exposed to the penicillin group,vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Text, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|815|816;2|976|200643|171549|815|816|817;2|1239|186801|186802|31979|1485;2|1239|909932|909929|1843491|158846;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:320/5/1,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  antibiotic,infants(6-weeks) to mothers exposed to multi-class antibiotics,vaginally delivered at full-term (>37 weeks of gestation),179,12,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,"Text, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,2|1239|909932|1843489|31977|29465|39778,Complete,Atrayees
bsdb:320/6/1,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants to mothers unexposed to intrapartum antibiotic,infants to mothers exposed to cephalosporins,NA,179,14,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"text, figure 3",10 August 2023,Atrayees,Atrayees,Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:320/6/2,Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants to mothers unexposed to intrapartum antibiotic,infants to mothers exposed to cephalosporins,NA,179,14,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 3",10 August 2023,Atrayees,Atrayees,Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,2|976|200643|171549|815|816|817,Complete,Atrayees
bsdb:321/1/1,Study 321,time series / longitudinal observational,24819377,10.1038/pr.2014.69,NA,"Dardas M, Gill SR, Grier A, Pryhuber GS, Gill AL, Lee YH , Guillet R",The impact of postnatal antibiotics on the preterm intestinal microbiome,Pediatric research,2014,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,10 d old 2 day treatment infants,10 d old 7-10 day treatment infants,Infants who received antibiotics for 7-10 days,15,12,None.,16S,123,Roche454,Kruskall-Wallis,0.05,TRUE,NA,NA,delivery procedure,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Results within text- Page 4, 3rd paragraph, under subheading ""Discussion""",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Genus level differential abundance of breast milk–fed infants at age 10 d with 7days of antibiotic treatment,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|976|200643|171549|815|816;2|1239|91061|186826|1300|1357,Complete,ChiomaBlessing
bsdb:321/2/NA,Study 321,time series / longitudinal observational,24819377,10.1038/pr.2014.69,NA,"Dardas M, Gill SR, Grier A, Pryhuber GS, Gill AL, Lee YH , Guillet R",The impact of postnatal antibiotics on the preterm intestinal microbiome,Pediatric research,2014,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30 d old minimal antibiotics exposure (2 day treatment infants),30 d old prolonged antibiotics exposure (>=7 day treatment infants),prolonged antibiotics exposure (greater than or equal to 7 day treatment infants),8,11,None.,16S,123,Roche454,Kruskall-Wallis,0.05,TRUE,NA,NA,delivery procedure,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:322/1/1,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 1,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,reference,patients with newly diagnosed malignancies,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden),38,37,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1a, Supplemental Table S2",10 January 2021,William Lam,WikiWorks,Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Derxia",2|1239|91061|186826|186827|46123;2|1239|91061|186826|1300|1357;2|1224|28216|80840|506|203697,Complete,Rimsha
bsdb:322/1/2,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 1,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,reference,patients with newly diagnosed malignancies,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden),38,37,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 1a, Supplemental Table S2",10 January 2021,William Lam,WikiWorks,Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",2|201174|1760|85004|31953;2|201174|1760|85007|1653|1716;2|201174|84998|84999|84107;2|976|200643|171549|2005523|346096;2|976|117747;2|1239|91061|1385|539738|1378;2|1239|186801|3085636|186803;2|32066|203490|203491|203492|848;2|1224|1236|135622|267890|22;2|1224|1236|135619|28256|2745;2|1224|1236|135625|712|713,Complete,Claregrieve1
bsdb:322/2/1,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 2,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,no oral mucositis,oral mucositis,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization),12,25,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Comparison of the oral bacterial community at the time of malignancy diagnosis (before chemotherapy) in patients who later developed oral mucositis and those who did not develop oral mucositis,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|976|117743|200644|49546|1016;2|32066;2|1239|91061|186826|1300|1357;2|203691|203692|136|137|146;2|1239|186801|3082720|186804,Complete,Claregrieve1
bsdb:322/3/1,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 3,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment,12,12,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:322/3/2,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 3,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment,12,12,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Derxia,k__Bacteria|p__Pseudomonadota",2|1224|28216|80840|506|203697;2|1224,Complete,Claregrieve1
bsdb:322/4/1,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 4,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that did not develop oral mucositis (graded by the World Health Organization) during chemotherapy treatment,10,10,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who do not have oral mucositis,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,2|1224|1236|135614|32033|338,Complete,Claregrieve1
bsdb:322/5/1,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 5,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,all samples,mucositis lesions,samples from mucositis lesions,97,27,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplemental Table S4, Figure S1, S2",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Archaea|p__candidate phylum NAG2,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",2|1239|91061|186826|186827|46123;2|201174|1760|2037|2049|1654;2|1239|91061|1385|186817|1386;2|1239|526524|526525|128827;2|1239|91061|186826|1300|1357;2|976|200643|171549|171550;2|201174|1760|85004|31953|196081;2|1239|91061|1385|90964|1279;2157|1448937;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804|1257;2|1224|1236|135614|32033|40323;2|544448;2|544448|31969|2085|2092|2093,Complete,Claregrieve1
bsdb:322/5/2,Study 322,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T , Pütsep K",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 5,Sweden,Homo sapiens,"Buccal mucosa,Lower lip","UBERON:0006956,UBERON:0001835",Oral mucositis,EFO:1001904,all samples,mucositis lesions,samples from mucositis lesions,97,27,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Supplemental Table S4, Figure S1, S2",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:323/1/1,Study 323,"cross-sectional observational, not case-control",30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J, Shilts MH, Tovchigrechko A, Wang C, Brucker RM, Moore DJ, Fonnesbeck C, Meng S, Correa H, Lovvorn HN, Tang YW, Hooper L, Bordenstein SR, Das SR , Weitkamp JH",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Mucosa of small intestine,UBERON:0001204,Necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age with NEC,14,10,NA,16S,123,Roche454,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 5,10 January 2021,Fatima Zohra,WikiWorks,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|186801|186802|31979|1485;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:323/1/2,Study 323,"cross-sectional observational, not case-control",30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J, Shilts MH, Tovchigrechko A, Wang C, Brucker RM, Moore DJ, Fonnesbeck C, Meng S, Correa H, Lovvorn HN, Tang YW, Hooper L, Bordenstein SR, Das SR , Weitkamp JH",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Mucosa of small intestine,UBERON:0001204,Necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age with NEC,14,10,NA,16S,123,Roche454,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 5,23 December 2022,Claregrieve1,Claregrieve1,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC),decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|29547|3031852|213849|2808963|28196;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|186823|29330;2|201174|1760|2037|2049|1654;2|1224|1236|72274|135621|286;2|976|117743|200644|2762318|59732;2|1224|28216|80840|80864|283;2|201174|1760|2037;2|976|1853228|1853229|563835;2|976;2|1239|91061|186826|1300|1301;2;2|201174|1760|85007|1653|1716,Complete,Claregrieve1
bsdb:323/3/1,Study 323,"cross-sectional observational, not case-control",30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J, Shilts MH, Tovchigrechko A, Wang C, Brucker RM, Moore DJ, Fonnesbeck C, Meng S, Correa H, Lovvorn HN, Tang YW, Hooper L, Bordenstein SR, Das SR , Weitkamp JH",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age with NEC,14,10,NA,16S,1234,Roche454,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Fatima Zohra,WikiWorks,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC) after adjusting,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:324/1/1,Study 324,case-control,30565661,10.1002/ijc.32007,NA,"Feng J, Zhao F, Sun J, Lin B, Zhao L, Liu Y, Jin Y, Li S, Li A , Wei Y",Alterations in the gut microbiota and metabolite profiles of thyroid carcinoma patients,International journal of cancer,2019,"clinical parameter, gut microbiota, metabolite, predictive model, thyroid carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Thyroid carcinoma,EFO:0002892,healthy controls,patients with thyroid carcinoma,at least one solid lesion identified by thyroid ultrasonagraphy,35,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 2a,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and thyroid carcinoma patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Archaea|p__Candidatus Bathyarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 001,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium ND3006,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2157|928852;2|1239|186801|3082768|990719;2|1239|186801|3085636|186803|33042;2|1224|1236|91347|543;2|1239|526524|526525|128827;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|42322;2|1239;2|1239|186801|3082720|186804|1505657;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804;2|1224;2|976|200643|171549|171550;2|1224|1236|91347|543|620;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979|1485|1970093;2|1239|91061|186826|1300|1357;2|1239|186801|3085636|186803|1410629;2|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:324/1/2,Study 324,case-control,30565661,10.1002/ijc.32007,NA,"Feng J, Zhao F, Sun J, Lin B, Zhao L, Liu Y, Jin Y, Li S, Li A , Wei Y",Alterations in the gut microbiota and metabolite profiles of thyroid carcinoma patients,International journal of cancer,2019,"clinical parameter, gut microbiota, metabolite, predictive model, thyroid carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Thyroid carcinoma,EFO:0002892,healthy controls,patients with thyroid carcinoma,at least one solid lesion identified by thyroid ultrasonagraphy,35,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 2a,10 January 2021,Rimsha Azhar,"Lwaldron,Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and thyroid carcinoma patients,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|909932|1843488|909930;2|976|200643|171549|171552|1283313;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976;2|1239|186801|3085636|186803|1506553;2|1239|909932|909929|1843491|158846;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:325/1/1,Study 325,case-control,31141234,10.1111/1346-8138.14933,NA,"Shapiro J, Cohen NA, Shalev V, Uzan A, Koren O , Maharshak N",Psoriatic patients have a distinct structural and functional fecal microbiota compared with controls,The Journal of dermatology,2019,"bacteria, inflammation, metabolome, microbiota, psoriasis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,healthy controls,psoriasis,patients with active psoriatic disease diagnosed by a senior dermatologist,22,24,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,comorbidity,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of genera signatures between psoriatic patients and the control participants,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|33042;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|189330;2|1239|186801|3082768|990719|990721;2|201174|1760|2037|2049|1654;2|201174|84998|84999|84107|102106,Complete,NA
bsdb:325/1/2,Study 325,case-control,31141234,10.1111/1346-8138.14933,NA,"Shapiro J, Cohen NA, Shalev V, Uzan A, Koren O , Maharshak N",Psoriatic patients have a distinct structural and functional fecal microbiota compared with controls,The Journal of dermatology,2019,"bacteria, inflammation, metabolome, microbiota, psoriasis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,healthy controls,psoriasis,patients with active psoriatic disease diagnosed by a senior dermatologist,22,24,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,comorbidity,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of genera signatures between psoriatic patients and the control participants,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|976|200643|171549|1853231|574697;2|200940|3031449|213115|194924|35832;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|28050;2|976|200643|171549|171552|577309,Complete,NA
bsdb:326/1/1,Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Non-Responders (progression or death),Responders (partial response or stable disease),"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",36,42,NA,WMS,NA,Mass spectrometry,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,10 January 2021,William Lam,"WikiWorks,Folakunmi",Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|626932;2|976|200643|171549|815|816;2|976|200643|171549|815|816|29523;2|508458|649775|649776|649777|508459|1197717;2|1239|91061|186826|81852|1350|1352;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730|142586;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803;2|976|200643|171549|171552|838;2|1239,Complete,Folakunmi
bsdb:326/1/2,Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Non-Responders (progression or death),Responders (partial response or stable disease),"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",36,42,NA,WMS,NA,Mass spectrometry,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2b,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi",Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,decreased,"k__Bacteria|p__Bacillota|s__Bacillota bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|1879010;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|291645;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485|1506;2|1239|186801|3085636|186803|2719313|208479;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171552|838;2|1224;2|1239|186801|186802,Complete,Folakunmi
bsdb:326/2/1,Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Progressive- Free- Survival more less than 30 days,Progressive -Free- Survival more than 30 days,"non-small cell lung carcinoma or renal carcinoma patients (excluding ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease that are Progressive- Free- Survival greater than 3 months",100,100,none,WMS,NA,Mass spectrometry,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi",Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|s__Bacillota bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759;2|1239;2|1239|1879010;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|816|371601;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802;2|1239|186801|186802|186806|1730|142586;2|1239|1263000;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|41978;2|1239;2|1239|186801|186802,Complete,Folakunmi
bsdb:326/2/2,Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Progressive- Free- Survival more less than 30 days,Progressive -Free- Survival more than 30 days,"non-small cell lung carcinoma or renal carcinoma patients (excluding ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease that are Progressive- Free- Survival greater than 3 months",100,100,none,WMS,NA,Mass spectrometry,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi",Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacillota|s__Bacillota bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|186802|216572|244127|169435;2|1239|1879010;2|1239|526524|526525|128827;2|1239|186801|186802;2|1239|186801|3085636|186803;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802,Complete,Folakunmi
bsdb:326/3/1,Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Non-Responders,Responders,"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",16,16,none,WMS,NA,Mass spectrometry,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2g,10 January 2021,William Lam,WikiWorks,"Culturomics-based analyses of fecal samples in 16 Responders and 16 Non-Responders Non-Small Cell Lung Carcinoma patients (defined as the best clinical outcome) before PD-1 blockage immunotherapy, each commensal colony having been identified by mass spectrometry",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum",2|1239|91061|1385|90964|1279|1283;2|201174|1760|85007|1653|1716|169292,Complete,Folakunmi
bsdb:327/1/1,Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control (no treatment) - week 1,infants who received short-term or long-term antibiotic treatment - week 1,infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received short-term antibiotics (<3 days) or longterm antibiotics (>5 days),28,35,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:327/1/2,Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control (no treatment) - week 1,infants who received short-term or long-term antibiotic treatment - week 1,infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received short-term antibiotics (<3 days) or longterm antibiotics (>5 days),28,35,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|91347|543|561;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:327/2/1,Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control(no treatment) - week 2,infants received long-term(>5days) antibiotic treatment - week 2,"infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received >5 days antibiotics, week 2 timepoint",28,13,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"WikiWorks,Claregrieve1","Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:327/3/1,Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants received short-term (<3days) antibiotic treatment - week 1,infants received long-term (>5days) antibiotic treatment - week 1,"infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received longterm (>5 days) antibiotics, first post-natal week timepoint",22,13,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,24 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between infants who received short-term and long-term antibiotics,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,2|1239|186801|186802|31979|1485|1506,Complete,Claregrieve1
bsdb:327/3/2,Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants received short-term (<3days) antibiotic treatment - week 1,infants received long-term (>5days) antibiotic treatment - week 1,"infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received longterm (>5 days) antibiotics, first post-natal week timepoint",22,13,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Text,24 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between infants who received short-term and long-term antibiotics,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:328/1/1,Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,healthy controls,psoriatic arthiritis,patients fulfilling the criteria of the Classification of Psoriatic arthritis (CASPAR),17,16,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1a, Figure 2a",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differences in bacterial taxa between patients with psoriatic arthritis  (PsA) compared to healthy controls (HLT),decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",2|74201|203494|48461|1647988|239934;2|1239|186801;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|46205;2|1239|186801|186802|216572|1263;2|74201;2|74201|203494;2|74201|203494|48461,Complete,Claregrieve1
bsdb:328/2/1,Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,healthy controls,skin psoriasis,patients fulfilling the skin psoriasis criteria of the Classification of Psoriatic arthritis (CASPAR),17,15,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1b, Figure 2b",10 January 2021,Rimsha Azhar,WikiWorks,Differences in bacterial taxa between patients with skin psoriasis (PS) compared to healthy controls (HLT),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota",2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|1239|186801;2|1239|526524|526525|128827;2|1239|526524;2|201174|1760;2|201174;2|1239|526524|526525|2810280|100883;2|1239|526524|526525;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|976,Complete,Claregrieve1
bsdb:328/3/1,Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,skin psoriasis,psoriatic arthiritis,patients fulfilling the psoriatic arthritis criteria of the Classification of Psoriatic arthritis (CASPAR),15,16,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1c, Figure 2c",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Difference in bacterial taxa between psoriatic arthiritis compared to psoriasis samples,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidota",2|1239|526524|526525|2810280|100883;2|976,Complete,Claregrieve1
bsdb:328/3/2,Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,skin psoriasis,psoriatic arthiritis,patients fulfilling the psoriatic arthritis criteria of the Classification of Psoriatic arthritis (CASPAR),15,16,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1c, Figure 2c",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Difference in bacterial taxa between psoriatic arthiritis compared to psoriasis samples,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|186801;2|1239|186801|186802;2|1239;2|74201;2|74201|203494|48461|203557,Complete,NA
bsdb:329/1/1,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,Postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota",2|1239|91061|186826|33958|1578;2|1239,Complete,Atrayees
bsdb:329/1/2,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,Postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Atrayees
bsdb:329/2/1,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP group (4-day old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Atrayees
bsdb:329/3/1,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP group (6-month old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota",2|1239|186801|186802|31979|1485;2|1239,Complete,Atrayees
bsdb:329/3/2,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP group (6-month old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3, Figure 5",6 July 2023,Atrayees,Atrayees,The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia,2|976|200643,Complete,Atrayees
bsdb:329/4/1,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:329/4/2,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549|815|816;2|976|200643,Complete,Atrayees
bsdb:329/5/1,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (4-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Atrayees
bsdb:329/6/1,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (6-month old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:329/6/2,Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (6-month old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3, Figure 5",6 July 2023,Atrayees,Atrayees,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia,2|976|200643,Complete,Atrayees
bsdb:330/1/1,Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 1,Finland,Homo sapiens,Placenta,UBERON:0001987,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ placenta sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 1 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in placenta samples negative and positive for HPV DNA,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|544448|2790996|2790998|2129;2|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
bsdb:330/2/1,Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 2,Finland,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ cervical sample determined by PCR and genotyped with Multimetrix,30,9,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in cervical samples negative and positive for HPV DNA,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|1239|91061|186826|33958|1578;2|544448|2790996|2790998|2129;2|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
bsdb:330/2/2,Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 2,Finland,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ cervical sample determined by PCR and genotyped with Multimetrix,30,9,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in cervical samples negative and positive for HPV DNA,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|186801|3082720|186804;2|1239|91061|186826|81852;2|1224|1236|135625|712|724;2|1239|186801|3082720|186804|1257,Complete,Fatima Zohra
bsdb:330/3/1,Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 3,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ oral sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 3 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in oral samples negative and positive for HPV DNA,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",2|201174|1760|85004|31953;2|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
bsdb:330/3/2,Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 3,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ oral sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 3 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in oral samples negative and positive for HPV DNA,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,Fatima Zohra
bsdb:331/1/1,Study 331,case-control,29320965,10.1089/thy.2017.0395,NA,"Zhao F, Feng J, Li J, Zhao L, Liu Y, Chen H, Jin Y, Zhu B , Wei Y",Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients,Thyroid : official journal of the American Thyroid Association,2018,"Hashimoto's thyroiditis, biomarker, clinical parameters, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"presence of euthyroidism, free thyroxine, and thyrotropin without hormonal therapy",27,50,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2a, 2b, table 3",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Comparisons of the relative abundance using LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730|42322;2|1239;2|1239|186801|3085636|186803|1407607;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803;2|1224|1236|135625|712;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263|438033;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:331/1/2,Study 331,case-control,29320965,10.1089/thy.2017.0395,NA,"Zhao F, Feng J, Li J, Zhao L, Liu Y, Chen H, Jin Y, Zhu B , Wei Y",Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients,Thyroid : official journal of the American Thyroid Association,2018,"Hashimoto's thyroiditis, biomarker, clinical parameters, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"presence of euthyroidism, free thyroxine, and thyrotropin without hormonal therapy",27,50,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 2a, 2b, table 3",10 January 2021,Rimsha Azhar,WikiWorks,Comparisons of the relative abundance using LEfSe analysis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Synergistota",2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838;2|976|200643|171549|171552|1283313;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|1506553;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|201174|1497346|1154584|1154585|1154586;2|976|200643|171549|815;2|976|200643|171549|171552;2|976|200643|171549|171551;2|1239|909932|1843488|909930;2|201174|1497346|1154584|1154585;2|976;2|508458,Complete,Atrayees
bsdb:332/1/1,Study 332,case-control,28903182,10.1016/j.biopha.2017.08.101,NA,"Ishaq HM, Mohammad IS, Guo H, Shahzad M, Hou YJ, Ma C, Naseem Z, Wu X, Shi P , Xu J",Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2017,"DGGE, Gut microbiota, Hashimoto’s thyroiditis, Hyporthyroidism, Pyrosequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"The Thyroid stimulating hormone(TSH) was higher than 5 μIU/ml, T4 was lower than 4.2 μg/dl, T3 was lower than 0.78 ng/ml, anti-thyroid peroxidase antibodies level was higher than 15 IU/ml, and anti-thyroglobulin antibodies was more than 30%",12,29,60 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Table 7,10 January 2021,Rimsha Azhar,WikiWorks,Hashimoto's thyroid gut microbial phylotypes from pyrosequencing,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,2|1239|186801|186802|216572|1263|1265,Complete,NA
bsdb:332/1/2,Study 332,case-control,28903182,10.1016/j.biopha.2017.08.101,NA,"Ishaq HM, Mohammad IS, Guo H, Shahzad M, Hou YJ, Ma C, Naseem Z, Wu X, Shi P , Xu J",Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2017,"DGGE, Gut microbiota, Hashimoto’s thyroiditis, Hyporthyroidism, Pyrosequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"The Thyroid stimulating hormone(TSH) was higher than 5 μIU/ml, T4 was lower than 4.2 μg/dl, T3 was lower than 0.78 ng/ml, anti-thyroid peroxidase antibodies level was higher than 15 IU/ml, and anti-thyroglobulin antibodies was more than 30%",12,29,60 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Table 7,10 January 2021,Rimsha Azhar,WikiWorks,Hashimoto's thyroid gut microbial phylotypes from pyrosequencing,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,2|1239|91061|186826|33958|1578|1596,Complete,NA
bsdb:333/1/1,Study 333,"cross-sectional observational, not case-control",30042470,https://doi.org/10.1038/s41372-018-0172-1,NA,"Imoto N, Morita H, Amanuma F, Maruyama H, Watanabe S , Hashiguchi N",Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study,Journal of perinatology : official journal of the California Perinatal Association,2018,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,without (non-Abx) use of maternal antimicrobial agents at delivery,infants with (Abx),Healthy infants,14,19,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Relative abundance of the six most common bacterial genera in all infants (n = 33) and in those with and without use of maternal antibiotics and with Cesarean or vaginal delivery,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
bsdb:333/2/1,Study 333,"cross-sectional observational, not case-control",30042470,https://doi.org/10.1038/s41372-018-0172-1,NA,"Imoto N, Morita H, Amanuma F, Maruyama H, Watanabe S , Hashiguchi N",Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study,Journal of perinatology : official journal of the California Perinatal Association,2018,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,NA,NA,Healthy infant not exposed to maternal antimicrobial,Healthy infant  exposed to maternal antimicrobial,"An infant or baby is the very young offspring of human beings. A newborn is, in colloquial use, an infant who is only hours, days, or up to one month old.",14,19,NA,16S,234,Illumina,"T-Test,ANOSIM,Spearman Correlation,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,NA,11 March 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,NA,NA,NA,NA,Complete,NA
bsdb:333/2/2,Study 333,"cross-sectional observational, not case-control",30042470,https://doi.org/10.1038/s41372-018-0172-1,NA,"Imoto N, Morita H, Amanuma F, Maruyama H, Watanabe S , Hashiguchi N",Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study,Journal of perinatology : official journal of the California Perinatal Association,2018,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,NA,NA,Healthy infant not exposed to maternal antimicrobial,Healthy infant  exposed to maternal antimicrobial,"An infant or baby is the very young offspring of human beings. A newborn is, in colloquial use, an infant who is only hours, days, or up to one month old.",14,19,NA,16S,234,Illumina,"T-Test,ANOSIM,Spearman Correlation,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,NA,11 March 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,NA,NA,NA,NA,Complete,NA
bsdb:334/1/1,Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,prenatal antibiotic free group (PAF group),infants(14-d old) exposed to prenatal antibiotic therapy (PAT group),Pre-term infants,12,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 1b, c; Figure 4a,b",10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe results on gut microbiomes of preterm infants,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Saccharicrinis,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales",2|976|200643|1970189|558415|1618113;2|29547;2|976|117743|200644,Complete,NA
bsdb:334/1/2,Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,prenatal antibiotic free group (PAF group),infants(14-d old) exposed to prenatal antibiotic therapy (PAT group),Pre-term infants,12,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 1b, c; Figure 4a,b",10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe results on gut microbiomes of preterm infants,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|186801|186802;2|1239|186801;2|201174|1760|85004|31953|1678,Complete,NA
bsdb:334/2/1,Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants exposed to antibiotic <=7day (L group),infants exposed to antibiotic >7day (H group),Pre-term infants,11,11,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 8,10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe analysis showed significant differences in microbial community structure between the H and L groups.,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,2|1224|28216,Complete,NA
bsdb:334/2/2,Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants exposed to antibiotic <=7day (L group),infants exposed to antibiotic >7day (H group),Pre-term infants,11,11,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 8,10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe analysis showed significant differences in microbial community structure between the H and L groups.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953,Complete,NA
bsdb:335/1/1,Study 335,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L, Hotte N, Kaplan GG, Vincent R, Tso R, Gänzle M, Rioux KP, Thiesen A, Barkema HW, Wine E , Madsen KL",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,NA,Experiment 1,Canada,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,healthy mice,Chronic treatment group,6-week old female wild-type 129/SvEv mice in chronic treatment group were fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,7,8,NA,16S,NA,Non-quantitative PCR,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Zyaijah Bailey,"WikiWorks,Claregrieve1",Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,increased,k__Bacteria|p__Verrucomicrobiota,2|74201,Complete,Claregrieve1
bsdb:335/2/1,Study 335,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L, Hotte N, Kaplan GG, Vincent R, Tso R, Gänzle M, Rioux KP, Thiesen A, Barkema HW, Wine E , Madsen KL",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,NA,Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,healthy mice,IL-10−/−  mice fed mouse chow with PM10,IL-10−/−  mice in chronic treatment group were  fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,9,7,NA,16S,NA,Non-quantitative PCR,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Zyaijah Bailey,"WikiWorks,Claregrieve1",Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),2|1239|91061|1385|186817|1386|1409,Complete,Claregrieve1
bsdb:335/2/2,Study 335,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L, Hotte N, Kaplan GG, Vincent R, Tso R, Gänzle M, Rioux KP, Thiesen A, Barkema HW, Wine E , Madsen KL",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,NA,Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,healthy mice,IL-10−/−  mice fed mouse chow with PM10,IL-10−/−  mice in chronic treatment group were  fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,9,7,NA,16S,NA,Non-quantitative PCR,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,10 January 2021,Zyaijah Bailey,"WikiWorks,Claregrieve1",Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Claregrieve1
bsdb:336/1/1,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"Chloe,WikiWorks",Composition Analysis of Microbiota,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinomycetota",2|976|200643|171549|815|816;2|976;2|1239|91061|186826|33958|1578;2|1224|28211|204457|41297|13687;2|201174,Complete,Chloe
bsdb:336/1/2,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,Composition Analysis of Microbiota,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Chloe
bsdb:336/2/1,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),piperacillin-tazobactam group (postnatal day 3),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"Chloe,WikiWorks",Composition Analysis of Microbiota,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota",2|201174;2|976,Complete,Chloe
bsdb:336/3/1,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),combination of penicillin and moxalactam group (postnatal day 7),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"Chloe,WikiWorks",Composition Analysis of Microbiota,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|976;2|1224|1236|91347|543|1940338,Complete,Chloe
bsdb:336/4/1,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),piperacillin-tazobactam group (postnatal day 7),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,Composition Analysis of Microbiota,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|976|200643|171549|815|816;2|1239|91061|186826|81852|1350,Complete,Chloe
bsdb:336/4/2,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),piperacillin-tazobactam group (postnatal day 7),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,Composition Analysis of Microbiota,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,2|1224|1236|91347|543|570,Complete,Chloe
bsdb:336/5/1,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,piperacillin-tazobactam group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Text,30 March 2022,Chloe,Chloe,NA,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Chloe
bsdb:336/6/1,Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,piperacillin-tazobactam group (postnatal day 7),combination of penicillin and moxalactam group (postnatal day 7),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Text,30 March 2022,Chloe,Chloe,NA,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Chloe
bsdb:337/1/1,Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,3-month old infants not exposed to antibiotics during the second trimester,3-month-old infants exposed to antibiotics in the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,56,12,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|186801|3085636|186803|1407607;2|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:337/1/2,Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,3-month old infants not exposed to antibiotics during the second trimester,3-month-old infants exposed to antibiotics in the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,56,12,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1, Table S2",15 July 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus antri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485|137838;2|1224|1236|91347|543;2|1239|91061|186826|33958|2742598|227943;2|1224|1236|135625|712;2|201174|1760|2037|2049|2529408|1660;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:337/3/1,Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,12-month-old infants not exposed to antibiotics during the second trimester,12-month-old infants exposed to antibiotics during the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,40,10,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:337/3/2,Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,12-month-old infants not exposed to antibiotics during the second trimester,12-month-old infants exposed to antibiotics during the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,40,10,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1, Table S2",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|1506553;2|1239|186801|3082720|186804;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:338/1/1,Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,4 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,"Figure 2, Text",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Relative abundance of microbial taxa in normal weight group vs obese group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1239|909932|909929|1843491|158846;2|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:338/1/2,Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,4 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,"Figure 2, Text",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Relative abundance of microbial taxa in normal weight group vs obese group,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:338/2/1,Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,"Lwaldron,Claregrieve1,WikiWorks",Relative abundance of microbial taxa in normal weight group vs obese group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum|s__Acetitomaculum ruminis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Pasteuriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",2|1239|186801|3085636|186803|31980|2382;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|28216|80840|506;2|1239|91061;2|1224|28216;2|1224|28216|80840;2|29547|3031852|213849|72294|194;2|1239|91061|186826|186828;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485|1502;2|1239|526524|526525|128827|2749846|31971;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|28050;2|1239|91061|186826;2|32066|203490|203491|1129771;2|1239|909932|909929|1843491|158846;2|201174|1760|85006|1268;2|1224|1236|135625;2|1239|91061|1385|538998;2|1239|186801|3082720|186804;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|387090;2|976|200643|171549|171552|2974251|165179;2|1224;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|3085636|186803|1506577|36835;2|1239|186801|3085636|186803|2316020|33038;2|1239|526524|526525|2810281,Complete,Claregrieve1
bsdb:338/2/2,Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Figure 5,10 January 2021,Mst Afroza Parvin,"Lwaldron,Claregrieve1,WikiWorks,Merit",Relative abundance of microbial taxa in normal weight group vs obese group,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella|s__Rickettsiella massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii",2|201174;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|626932;2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816|820;2|976|200643|171549|2005519;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1680;2|200940|3031449|213115|194924|35832;2|1239|186801|3082768|990719|990721;2|1239|186801|3082768|990719;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|186801|3085636|1185407|1185408;2|28221;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|186806|1730;2|1239|186801|186802|31979|1769729;2|1239|526524|526525|128827|61170;2|544448|31969;2|544448;2|1239|186801|186802|216572|119852;2|1224|28216|80840|75682|846;2|1224|28216|80840|75682|846|847;2|1224|28216|80840|75682;2|1224|28216|80840|2975441|93681|304;2|1239|186801|186802|186807;2|976|200643|171549|171552|838;2|1224|1236|118969|118968|59195|676517;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239|91061|186826|1300|1301|1302,Complete,Claregrieve1
bsdb:339/1/1,Study 339,laboratory experiment,28211537,10.1038/srep42906,NA,"Li R, Yang J, Saffari A, Jacobs J, Baek KI, Hough G, Larauche MH, Ma J, Jen N, Moussaoui N, Zhou B, Kang H, Reddy S, Henning SM, Campen MJ, Pisegna J, Li Z, Fogelman AM, Sioutas C, Navab M , Hsiai TK",Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites,Scientific reports,2017,NA,Experiment 1,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,vehicle control,mice exposed to UFP,C57BL/6 mice exposed to UFP (Ultrafine particles),11,12,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2 & Supplemental Figure S1& Text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",Differential microbial abundance between UFP-exposed mice and controls,increased,k__Bacteria|p__Verrucomicrobiota,2|74201,Complete,Claregrieve1
bsdb:339/1/2,Study 339,laboratory experiment,28211537,10.1038/srep42906,NA,"Li R, Yang J, Saffari A, Jacobs J, Baek KI, Hough G, Larauche MH, Ma J, Jen N, Moussaoui N, Zhou B, Kang H, Reddy S, Henning SM, Campen MJ, Pisegna J, Li Z, Fogelman AM, Sioutas C, Navab M , Hsiai TK",Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites,Scientific reports,2017,NA,Experiment 1,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,vehicle control,mice exposed to UFP,C57BL/6 mice exposed to UFP (Ultrafine particles),11,12,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2 & Supplemental Figure S1& Text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",Differential microbial abundance between UFP-exposed mice and controls,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota",2|201174;2|1117;2|1239,Complete,Claregrieve1
bsdb:340/1/1,Study 340,prospective cohort,33653942,https://doi.org/10.1128/mSystems.00984-20,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546988,NA,Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease,NA,NA,"pouchitis, UC, CD, mucin, butyrate, bile acids, oxidative stress, classifier, Crohn's disease, microbiome, ulcerative colitis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Normal pouch,Pouchitis,Patients with a pouch that developed inflammation,35,34,1 month (recent use) or 6 months off antibiotics,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 1,FIG 7,17 February 2024,Peace Sandy,Peace Sandy,Highest-scoring microbiome features identified by the classification models as the most informative for distinguishing between patients with a normal pouch and pouchitis and thus possibly predictive of pouchitis. The feature importance scores (averaged across 5-fold cross-validation) for (A) species.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|2887326|468|469;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|186803|572511|53443;2|1224|28216|80840|469610;2|1224|1236|1706369|1706371|10;2|1239|91061|186826|81852|1350|1352;2|1239|526524|526525|128827|658657;2|1239|526524|526525|128827|469614;2|1224|1236|91347|543|561|562;2|1239|186801|3085636|186803|658089;2|1239|186801|3085636|186803|2316020|33038;2|1239|909932|1843489|31977|906|187326;2|1224|28216|80840|995019|577310|487175;2|1239|91061|186826|1300|1301|1311;2|1239|909932|1843489|31977|29465|39778;2|1224|1236|91347|1903411|629;2|1239|526524|526525|128827|1522;2|1239|526524|526525|2810280|100883;2|1224|1236|91347|543|561;2|1224|1236|91347|1903414|586;2|201174|84998|1643822|1643826|84108;2|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:340/1/2,Study 340,prospective cohort,33653942,https://doi.org/10.1128/mSystems.00984-20,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546988,NA,Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease,NA,NA,"pouchitis, UC, CD, mucin, butyrate, bile acids, oxidative stress, classifier, Crohn's disease, microbiome, ulcerative colitis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Normal pouch,Pouchitis,Patients with a pouch that developed inflammation,35,34,1 month (recent use) or 6 months off antibiotics,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 2,FIG 7,17 February 2024,Peace Sandy,Peace Sandy,Highest-scoring microbiome features identified by the classification models as the most informative for distinguishing between patients with a normal pouch and pouchitis and thus possibly predictive of pouchitis. The feature importance scores (averaged across 5-fold cross-validation) for (A) species.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1239|526524|526525|128827|457422;2|1239|186801|186802|216572|216851|853;2|1224|1236|135625|712|724|249188;2|976|200643|171549|815|909656|204516;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|457412;2|1239|526524|526525|128827|123375|102148;2|1239|186801|3085636|186803|1213720|796942;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|197614;2|1239|91061|186826|1300|1301|1343;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|2316020|33039;2|1224|28211|356|772|773;2|1239|186801|3085636|186803|189330;2|1224|1236|135619|28256|2745;2|1239|91061|186826|33958|1253;2|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:341/1/1,Study 341,prospective cohort,30157953,10.1186/s40168-018-0531-3,NA,"Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M , Holtmann GJ",Influence of cigarette smoking on the human duodenal mucosa-associated microbiota,Microbiome,2018,"Cigarettes, Duodenum, Microbiome, Mucosa, Small intestine, Smoking",Experiment 1,Australia,Homo sapiens,Small intestine,UBERON:0002108,Smoking behavior,EFO:0004318,never smoked,"patients with FD, ID,or CD who currently smoked","patient with FD,ID or CD with who previously or currently smokes",41,61,2 months,16S,678,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3& Text,10 January 2021,Zyaijah Bailey,WikiWorks,Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:341/2/1,Study 341,prospective cohort,30157953,10.1186/s40168-018-0531-3,NA,"Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M , Holtmann GJ",Influence of cigarette smoking on the human duodenal mucosa-associated microbiota,Microbiome,2018,"Cigarettes, Duodenum, Microbiome, Mucosa, Small intestine, Smoking",Experiment 2,Australia,Homo sapiens,Small intestine,UBERON:0002108,Smoking behavior,EFO:0004318,never smoked,"patients with FD, ID,or CD who currently smokes","patient with FD,ID or CD with who previously or currently smokes",41,61,2 months,16S,678,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3 & Text,10 January 2021,Zyaijah Bailey,WikiWorks,Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:342/1/1,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,children who did not experience asthma exacerbation,Children who experienced exacerbation,"children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)",346,67,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between children with exacerbation and children without,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:342/2/1,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples with no rhinovirus infection,Samples with any rhinovirus infection,Samples with rhinovirus infection assessed by using quantitative PCR and partial sequencing to identify viral strain type,1883,1239,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus and samples without,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:342/2/2,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples with no rhinovirus infection,Samples with any rhinovirus infection,Samples with rhinovirus infection assessed by using quantitative PCR and partial sequencing to identify viral strain type,1883,1239,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus and samples without,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:342/3/1,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples that were RV-A negative-,Samples with rhinovirus-A (RV-A),Samples with rhinovirus-A,1883,386,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus-A and samples with no rhinovirus detected,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:342/3/2,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples that were RV-A negative-,Samples with rhinovirus-A (RV-A),Samples with rhinovirus-A,1883,386,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus-A and samples with no rhinovirus detected,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:342/5/1,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,children who did not experience exacerbation,Children who experienced exacerbation,"children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)",346,67,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between children with exacerbation and children without,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,2|1224|1236|2887326|468|475,Complete,Claregrieve1
bsdb:342/5/2,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,children who did not experience exacerbation,Children who experienced exacerbation,"children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)",346,67,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between children with exacerbation and children without,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|186826|186828|1651;2|201174|1760|85007|1653|1716;2|1224|1236|135625|712|724;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:342/7/1,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 7,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,samples with no rhinovirus infection,samples with any rhinovirus infection,samples with rhinovirus infection,1883,1239,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with any viral infection and samples without,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:342/7/2,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 7,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,samples with no rhinovirus infection,samples with any rhinovirus infection,samples with rhinovirus infection,1883,1239,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with any viral infection and samples without,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:342/8/1,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 8,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Rhinovirus-negative samples,Samples with rhinovirus A,Samples with rhinovirus A present,1883,386,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples infected with rhinovirus-A and samples with no rhinovirus detected,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:342/8/2,Study 342,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 8,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Rhinovirus-negative samples,Samples with rhinovirus A,Samples with rhinovirus A present,1883,386,None.,16S,4,Illumina,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples infected with rhinovirus-A and samples with no rhinovirus detected,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:343/1/1,Study 343,time series / longitudinal observational,31873965,10.1002/cncr.32641,NA,"Rashidi A, Kaiser T, Graiziger C, Holtan SG, Rehman TU, Weisdorf DJ, Dunny GM, Khoruts A , Staley C",Gut dysbiosis during antileukemia chemotherapy versus allogeneic hematopoietic cell transplantation,Cancer,2020,"dysbiosis, leukemia, microbiota, transplantation",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,Allogeneic Hematopoetic Stem Cell Transplant,Acute anti-leukemia treatment,Patients with leukemia who underwent intensive chemotherapy (any regimen involving 4 weeks or more of hospitalization) that did not have allo-HCT,20,20,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with acute leukemia treated with antileukemia regimens compared with allogeneic hematopoeitic stem cell transplant,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|815|816;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:343/1/2,Study 343,time series / longitudinal observational,31873965,10.1002/cncr.32641,NA,"Rashidi A, Kaiser T, Graiziger C, Holtan SG, Rehman TU, Weisdorf DJ, Dunny GM, Khoruts A , Staley C",Gut dysbiosis during antileukemia chemotherapy versus allogeneic hematopoietic cell transplantation,Cancer,2020,"dysbiosis, leukemia, microbiota, transplantation",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,Allogeneic Hematopoetic Stem Cell Transplant,Acute anti-leukemia treatment,Patients with leukemia who underwent intensive chemotherapy (any regimen involving 4 weeks or more of hospitalization) that did not have allo-HCT,20,20,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with acute leukemia treated with antileukemia regimens compared with allogeneic hematopoeitic stem cell transplant,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Claregrieve1
bsdb:344/1/1,Study 344,laboratory experiment,31935575,10.1016/j.chemosphere.2020.125879,NA,"Liu W, Zhou Y, Yong Li Y, Qin L, Yu R, Li Y, Chen Y , Xu",Effects of PM<sub>2.5</sub> exposure during gestation on maternal gut microbiota and pregnancy outcomes,Chemosphere,2020,"Gut microbiota, PM(2.5), Pregnancy outcomes, Short chain fatty acids",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed suspension from extracts of “blank” filter,mice exposed to Pm 2.5 suspension,exposed to PM2.5 suspension,12,12,NA,16S,34,Illumina,LEfSe,2,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,"Figure 4a, text",10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks,Merit","the most differentially abundant taxa between the two groups were identified through the LDA score which was generated from LEfSe analysis (phylum to genus: p, phylum; c, class; o, order; f, family; g, genus)",increased,"k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota,k__Archaea|p__candidate phylum NAG2,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.",2|28221;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|186801|186802|216572|946234;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|1239|186801|186802|216572|459786;2|1224;2157|1448937;2|1239|186801|186802|216572|459786|1945593;2|32066|203490|203491|203492|848|68766,Complete,Atrayees
bsdb:344/1/2,Study 344,laboratory experiment,31935575,10.1016/j.chemosphere.2020.125879,NA,"Liu W, Zhou Y, Yong Li Y, Qin L, Yu R, Li Y, Chen Y , Xu",Effects of PM<sub>2.5</sub> exposure during gestation on maternal gut microbiota and pregnancy outcomes,Chemosphere,2020,"Gut microbiota, PM(2.5), Pregnancy outcomes, Short chain fatty acids",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed suspension from extracts of “blank” filter,mice exposed to Pm 2.5 suspension,exposed to PM2.5 suspension,12,12,NA,16S,34,Illumina,LEfSe,2,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,"Figure 4a, text",10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees,Merit","the most differentially abundant taxa between the two groups were identified through the LDA score which was generated from LEfSe analysis (phylum to genus: p, phylum; c, class; o, order; f, family; g, genus)",decreased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Deferribacterota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Gemmatimonadota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",2|57723;2|1224|1236|72274|135621|351;2|1239|91061|1385;2|1239|91061;2|1239|91061|1385|186817|1386;2|200930|68337|191393|191394;2|200930|68337|191393;2|200930|68337;2|200930;2|1224|28216|80840|80864|80865;2|1224|1236;2|142182|219685|219686|219687;2|142182|219685|219686;2|142182|219685;2|142182;2|142182|219685|219686|219687|173479;2|201174|1760|85006|85023|55968;2|201174|1760|85006|85023;2|200930|68337|191393|2945020|248038;2|976|200643|171549|1853231|283168;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1239|909932|909929|1843491|970;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|976|200643|171549|1853231;2|1239|91061|186826|1300|1301|1306,Complete,Atrayees
bsdb:345/1/1,Study 345,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J, Lu W, Huang S, Le Maho Y, Habold C , Zhang Z","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 1,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Female hamsters Normal-protein diet (NPD) group,Female hamsters Low-protein diet (LPD) group,Female hamsters under low-protein diet LPD,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5 and Figure 5A,24 March 2024,Aleru Divine,Aleru Divine,Significant differential abundance in fecal microbiota of female hamster in Normal-protein diet (NPD) versus low-protein diet (LPD).,increased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Georgfuchsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|544448|31969|186332|186333|2086;2|976|200643|171549|815|816;2|976|200643|171549|2005520|156973;2|1224|28216|32003|2008793|690621;2|1239|91061|1385|186817;2|32066|203490|203491|203492;2|1224;2|1239|909932|1843489|31977,Complete,Peace Sandy
bsdb:345/1/2,Study 345,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J, Lu W, Huang S, Le Maho Y, Habold C , Zhang Z","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 1,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Female hamsters Normal-protein diet (NPD) group,Female hamsters Low-protein diet (LPD) group,Female hamsters under low-protein diet LPD,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5 and Figure 5A,24 March 2024,Aleru Divine,Aleru Divine,Significant differential abundance in fecal microbiota of female hamster in Normal-protein diet (NPD) versus low-protein diet (LPD).,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Millisia,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Oleomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",2|1224|1236|2887326|468|469;2|1239|526524|526525|128827|174708;2|201174|1760|85007|1653|1716|38286;2|976|117743|200644|2762318|308865;2|1239|186801|186802|204475;2|976|200643|171549|171551|1159323;2|201174|1760|85007|85026|264147;2|200930|68337|191393|2945020|248038;2|544448|31969|2085|2092|2093;2|1224|28211|204441|433|217063;2|1239|186801|186802|216572|119852;2|203691|203692|136|137|146;2|1239;2|976;2|1224|1236;2|976|200643|171549|171552|577309;2|1239|186801|3082720|186804;2|976|117743|200644|2762318,Complete,Peace Sandy
bsdb:345/3/1,Study 345,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J, Lu W, Huang S, Le Maho Y, Habold C , Zhang Z","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 3,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Offspring hamsters Normal-protein diet (NPD) group,Offspring hamsters Low-protein diet (LPD) group,Offspring hamsters under low-protein diet LPD,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table S6 and Figure 5C,24 March 2024,Aleru Divine,Aleru Divine,Significant differential abundance in fecal microbiota of offspring hamster in Normal-protein diet (NPD) versus low-protein diet (LPD).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Millisia,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Nitrobacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1224|1236|2887326|468|222991;2|544448|31969|186332|186333|2086;2|201174|1760|85006|1268|1663;2|201174|1760|85004|31953|1678;2|1224|28216|80840|506|517;2|1239|186801|3082768|990719|990721;2|1239|186801|186802|31979|1485;2|976|117743|200644|2762318|308865;2|1239|91061|186826|33958|1578;2|201174|1760|85007|85026|264147;2|200930|68337|191393|2945020|248038;2|1224|28211|204458|76892|267929;2|201174|84998|84999|1643824|133925;2|1224|1236|72274|135621|286;2|1224|1236|135614|32033|83618;2|201174|1760|2037;2|1224|28216|80840|80864;2|201174|84998|84999|84107;2|1239|91061|186826|33958;2|976|200643|171549|2005473;2|976|200643|171549|171552|577309;2|1239|186801|3082720|186804;2|976|200643|171549|171550,Complete,Svetlana up
bsdb:345/3/2,Study 345,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J, Lu W, Huang S, Le Maho Y, Habold C , Zhang Z","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 3,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Offspring hamsters Normal-protein diet (NPD) group,Offspring hamsters Low-protein diet (LPD) group,Offspring hamsters under low-protein diet LPD,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table S6 and Figure 5C,24 March 2024,Aleru Divine,Aleru Divine,Significant differential abundance in fecal microbiota of offspring hamster in Normal-protein diet (NPD) versus low-protein diet (LPD).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Proteiniborus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|415014;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239;2|1239|186801|3085636|186803;2|200940|3031449|213115|194924|872;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1224;2|203691|203692|1643686|143786|29521;2|203691|203692|136|137|146;2|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:345/4/1,Study 345,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J, Lu W, Huang S, Le Maho Y, Habold C , Zhang Z","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 4,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Offspring hamsters naicin+ group,Offspring hamsters niacin- group,Offspring hamsters under niacin-deficient (niacin-) diet.,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table S7 and Figure 5B,24 March 2024,Aleru Divine,Aleru Divine,Significant differential abundance in fecal microbiota of offspring hamster in niacin-supplemented diet (Niacin+) versus niacin-deficient diet (Niacin−).,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Proteiniborus",2|201174|1760|2037;2|203691|203692|136|137|146;2|1239|186801|186802|415014,Complete,Svetlana up
bsdb:345/4/2,Study 345,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J, Lu W, Huang S, Le Maho Y, Habold C , Zhang Z","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 4,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Offspring hamsters naicin+ group,Offspring hamsters niacin- group,Offspring hamsters under niacin-deficient (niacin-) diet.,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table S7 and Figure 5B,24 March 2024,Aleru Divine,Aleru Divine,Significant differential abundance in fecal microbiota of offspring hamster in niacin-supplemented diet (Niacin+) versus niacin-deficient diet (Niacin−).,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|1236|2887326|468|222991;2|201174|1760|85006|1268|1663;2|1239|186801|3085636|186803|241189;2|1239|91061|1385|90964|69965;2|200930|68337|191393|2945020|248038;2|1224|28216|80840|80864;2|976|200643|171549|171552|577309;2|976|200643|171549|171551;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:346/1/1,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,mild depression,severe depression,"Patients in this group were diagnosed with severe depression
(The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).",NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1A and 1B,10 January 2021,WikiWorks,"WikiWorks,Merit,ChiomaBlessing",Significant bacterial biomarkers among individuals with severe depression VS individuals with mild depression at admission,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA",2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|216572|1263|41978;2|1239|186801|3085636|186803|658655,Complete,ChiomaBlessing
bsdb:346/1/2,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,mild depression,severe depression,"Patients in this group were diagnosed with severe depression
(The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).",NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1A and 1B,10 January 2021,Fatima Zohra,"WikiWorks,Rukky,ChiomaBlessing,Joan Chuks",Significant bacterial biomarkers among individuals with severe depression VS individuals with mild depression at admission,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|201174;2|976|200643|171549|171550|239759|1288121;2|201174|1760|85004|31953|1678|1680;2|1224|28216|80840|75682|846|847;2|1239|186801|186802|216572|707003,Complete,Rukky
bsdb:346/2/1,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,mild depression,moderate depression,Patients in this group were diagnosed with moderate depression (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1A and 1B,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Significant bacterial biomarkers among individuals with moderate depression VS individuals with mild depression at admission,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|1239|186801|3085636|186803|33042|116085;2|1239|186801|186802|216572|946234;2|1239|91061|186826|1300|1301|1328;2|1239|186801|3085636|186803|1506553|1512,Complete,ChiomaBlessing
bsdb:346/3/1,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,mild anxiety,severe anxiety,Patients in this group were diagnosed with severe anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C and 1D,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,ChiomaBlessing",Significant bacterial biomarkers among individuals with severe anxiety VS individuals with mild anxiety at admission,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA",2|1239|91061|186826|1300|1301|1328;2|1239|186801|3085636|186803|658655,Complete,ChiomaBlessing
bsdb:346/3/2,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,mild anxiety,severe anxiety,Patients in this group were diagnosed with severe anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1C and 1D,10 January 2021,Fatima Zohra,"WikiWorks,Merit,ChiomaBlessing",Significant bacterial biomarkers among individuals with severe anxiety VS individuals with mild anxiety at admission,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|201174|1760;2|201174;2|1239|186801|3085636|186803|1766253|39491;2|976|200643|171549|171550|239759|28117;2|1239;2|201174|1760|85004|31953|1678|1680;2|1239|186801;2|1239|186801|3085636|186803|33042|116085;2|201174|1760|85007|1653;2|1239|186801|186802;2|1239|186801|186802|186806|1730|39496;2|201174|1760|85007|2805586|1847725;2|201174|1760|85007;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|41978,Complete,ChiomaBlessing
bsdb:346/4/1,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,mild anxiety,moderate anxiety,Patients in this group were diagnosed with moderate anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C and 1D,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,ChiomaBlessing",Significant bacterial biomarkers among individuals with moderate anxiety VS individuals with mild anxiety at admission,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|1239|91061|186826|1300|1357|1358;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|658081;2|1239|186801|186802|457421;2|201174|84998|1643822|1643826|84111,Complete,ChiomaBlessing
bsdb:346/5/1,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from depression at discharge,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A and 3B,20 February 2024,ChiomaBlessing,"ChiomaBlessing,Joan Chuks",Significant bacterial biomarkers among participants who achieved remission from depression (YES) VS participants who did not achieve remission from depression at discharge (NO),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|3085636|186803|1766253|39491;2|1224|28216|80840|506;2|1239;2|976|200643|171549|815|816|291645;2|1224|28216;2|1224|28216|80840;2|1239|186801;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|28050;2|1239|909932;2|1239|186801|186802|216572;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186807;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|3068309;2|1239|186801|186802|216572|1263|40519;2|1239|909932|909929;2|1239|186801|186802|216572|707003,Complete,ChiomaBlessing
bsdb:346/5/2,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from depression at discharge,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A and 3B,20 February 2024,ChiomaBlessing,ChiomaBlessing,Significant bacterial biomarkers among participants who achieved remission from depression (YES) VS participants who did not achieve remission from depression at discharge (NO),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1239|186801|186802|216572|1263|41978;2|1239|91061|1385;2|1239|91061|1385|186818;2|1239|91061|1385|186817|1433999;2|1224|1236|72274;2|1224|1236|72274|135621;2|1224|1236|72274|135621|286;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236;2|1239|186801|3085636|186803|572511|53443;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803|2316020|33038;2|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:346/6/1,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from anxiety at discharge,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C and 3D,20 February 2024,ChiomaBlessing,"ChiomaBlessing,Joan Chuks",Significant bacterial biomarkers among participants who achieved remission from anxiety (YES) VS participants who did not achieve remission from anxiety at discharge (NO),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|3085636|186803|1766253|39491;2|1224|28216|80840|506;2|1239;2|1224|28216;2|1224|28216|80840;2|1239|186801;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|1185407;2|1239|186801|186802;2|1239|186801|3085636|186803|665951;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40519;2|1239|186801|186802|216572|1263|41978;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|707003,Complete,ChiomaBlessing
bsdb:346/6/2,Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from anxiety at discharge,NA,NA,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C and 3D,20 February 2024,ChiomaBlessing,ChiomaBlessing,Significant bacterial biomarkers among participants who achieved remission from anxiety (YES) VS participants who did not achieve remission from anxiety at discharge (NO),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli",2|976|200643|171549|815|816|291645;2|1239|186801|3085636|186803|572511|53443;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|526524|526525|128827|658657;2|1224|1236|91347|543|1940338;2|1224|1236;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803|658081;2|1224;2|1239|91061|186826|1300|1301|1304;2|1224|1236|91347|543|561;2|1239|91061,Complete,ChiomaBlessing
bsdb:347/1/1,Study 347,case-control,30267022,10.1038/s41598-018-32730-6,NA,"Gao X, Jia R, Xie L, Kuang L, Feng L , Wan C",A study of the correlation between obesity and intestinal flora in school-age children,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese children,School children meeting WHO diagnostic criteria for obesity,38,39,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,"Table2, Table 3",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Comparisons of relative abundance of gut bacteria between the obesity and control groups at the level of Phylum & Species,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella|s__Allisonella histaminiformans,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|1239|909932|1843489|31977|209879|209880;2|976;2|200940|3031449|213115|194924|35832|35833;2|1239|909932|909929|1843491|158846|437897;2|1224|28216|80840|75682|846|847;2|976|200643|171549|2005525|375288|823;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|2974265|363265;2|1239|186801|3085636|186803|1506553|1512,Complete,Claregrieve1
bsdb:347/1/2,Study 347,case-control,30267022,10.1038/s41598-018-32730-6,NA,"Gao X, Jia R, Xie L, Kuang L, Feng L , Wan C",A study of the correlation between obesity and intestinal flora in school-age children,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese children,School children meeting WHO diagnostic criteria for obesity,38,39,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,"Table2, Table 3, text",10 January 2021,Mst Afroza Parvin,"Lwaldron,Claregrieve1,WikiWorks",Comparisons of relative abundance of gut bacteria between the obesity and control groups at the level of Phylum & Species,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes butyraticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor|s__Lactonifactor longoviformis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalispora|s__Faecalispora sporosphaeroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] sulci",2|201174;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171552|1283313|671218;2|1239|186801|3085636|186803|207244|645466;2|1239|186801|3085636|186803|207244|105841;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|818;2|1239|186801|3085636|186803|572511|89014;2|1239|186801|3085636|186803|572511|418240;2|95818;2|1239|91061|186826|81852|1350|44008;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|186802|216572|216851|853;2|1239;2|201174|84998|1643822|1643826|644652|471189;2|1239|186801|186802|31979|420345|341220;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|1300|1301|1304;2|74201;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|3115229|1549;2|1239|186801|186802|543314|143393,Complete,Claregrieve1
bsdb:348/1/1,Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Mst Afroza Parvin,WikiWorks,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",2|976|200643|171549|815|816|817;2|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:348/1/2,Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Mst Afroza Parvin,WikiWorks,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,Claregrieve1
bsdb:348/2/1,Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 2,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,overweight children,Healthy children who are considered overweight based on z-score of ≥ +1 and < +2,30,24,3 months,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Mst Afroza Parvin,WikiWorks,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",2|976|200643|171549|815|816|817;2|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:348/3/1,Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 3,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 6,10 January 2021,Mst Afroza Parvin,WikiWorks,Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,2|976|200643|171549|815|816|817,Complete,Claregrieve1
bsdb:348/3/2,Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 3,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table 6,10 January 2021,Mst Afroza Parvin,WikiWorks,Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,Claregrieve1
bsdb:348/4/1,Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 4,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,overweight children,Healthy children who are considered overweight based on z-score of ≥ +1 and < +2,30,24,3 months,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 6,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:349/1/1,Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 1,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure,women with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,100,89,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of cervical microbiota in the LEEP group and the Reference group,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2790998|2129|134821;2|544448|2790996|2895623|2895509|2098,Complete,Claregrieve1
bsdb:349/2/1,Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 2,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure,women with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,99,89,long-term antibiotic use,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,"age,contraception,marital status,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of cervical microbiota in the LEEP group and the Reference group,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:349/3/1,Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 3,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure (age <46),women <46 years old with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,48,75,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of the cervical microbiota in the LEEP group and the Reference group in women aged < 46 years,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2895623|2895509|2098;2|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:349/4/1,Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 4,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure,women <46 years old with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,48,75,long-term antibiotic use,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,"age,contraception,marital status,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of cervical microbiota in the LEEP group and the Reference group in women aged < 46 years,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:349/5/1,Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 5,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group 6 months post-procedure,women 6 months after Loop Electrosurgical Excision Procedure,100,77,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 2,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance between the cervical microbiota six months post treatment in the LEEP group and the cervical microbiota in the Reference group,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2895623|2895509|2098;2|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:349/6/1,Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 6,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group 12 months post-procedure,women 12 months after Loop Electrosurgical Excision Procedure,100,72,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 3,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance between cervical microbiota 12 months post treatment in the LEEP group and the cervical microbiota in the Reference group,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2895623|2895509|2098;2|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:350/1/1,Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obese children (O),Obesity was defined by body mass index (BMI) ≥ 95th percentile. Children in the O group were selected so that they did not have more than one trait matching the metabolic syndrome traits.,10,10,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in obese (O) children compared to normal weight (NW) children,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171551|836,Complete,ChiomaBlessing
bsdb:350/1/2,Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obese children (O),Obesity was defined by body mass index (BMI) ≥ 95th percentile. Children in the O group were selected so that they did not have more than one trait matching the metabolic syndrome traits.,10,10,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in obese (O) children compared to normal weight (NW) children,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,ChiomaBlessing
bsdb:350/2/1,Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obesity with metabolic syndrome (OMS),"OMS were defined by the presence of waist circumference > 75th by age and gender, and at least two of the following metabolic traits: (1) triglycerides > 1.1 mmol/L (100 mg/dL); (2) HDL cholesterol < 1.3 mmol/L (50 mg/dL), (3) glucose > 6.1 mmol/L (110 mg/dL) and (4) systolic blood pressure > 90th percentile for gender, age, and height.",10,7,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in Obesity with metabolic syndrome (OMS) children compared to normal weight (NW) children,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota",2|1239|91061;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|201174|84998;2|1239|526524|526525|128827;2|1224;2|1224|28216|80840|2975441|196013;2|1239|186801|3085636|186803;2|1239|186801|186802;2|1239,Complete,ChiomaBlessing
bsdb:350/2/2,Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obesity with metabolic syndrome (OMS),"OMS were defined by the presence of waist circumference > 75th by age and gender, and at least two of the following metabolic traits: (1) triglycerides > 1.1 mmol/L (100 mg/dL); (2) HDL cholesterol < 1.3 mmol/L (50 mg/dL), (3) glucose > 6.1 mmol/L (110 mg/dL) and (4) systolic blood pressure > 90th percentile for gender, age, and height.",10,7,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in Obesity with metabolic syndrome (OMS) children compared to normal weight (NW) children,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,2|976|200643|171549,Complete,ChiomaBlessing
bsdb:351/1/1,Study 351,"cross-sectional observational, not case-control",31934770,10.1089/chi.2019.0280,NA,"Da Silva CC, Monteil MA , Davis EM",Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota,Childhood obesity (Print),2020,"bifidobacterium, children, firmicutes, gut, microbiome, obesity",Experiment 1,Trinidad and Tobago,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal,overweight/obesity,school aged children (6-14 years),30,21,3 months,16S,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Table 2 & 3,10 January 2021,Mst Afroza Parvin,WikiWorks,The Relative Abundance (%) of the Most Dominant Bacterial Families & genus from Stool Samples at Varying Demographic and Anthropometric Measure,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
bsdb:351/1/2,Study 351,"cross-sectional observational, not case-control",31934770,10.1089/chi.2019.0280,NA,"Da Silva CC, Monteil MA , Davis EM",Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota,Childhood obesity (Print),2020,"bifidobacterium, children, firmicutes, gut, microbiome, obesity",Experiment 1,Trinidad and Tobago,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal,overweight/obesity,school aged children (6-14 years),30,21,3 months,16S,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Table 2 & 3,10 January 2021,Mst Afroza Parvin,WikiWorks,The Relative Abundance (%) of the Most Dominant Bacterial Families & genus from Stool Samples at Varying Demographic and Anthropometric Measure,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,NA
bsdb:352/1/1,Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Human papilloma virus infection,Cervical glandular intraepithelial neoplasia","EFO:1000165,EFO:0001668",Atypical Squamous Cells of Undetermined Significance,Low Grade Squamous Intraepithelial Lesion,low grade squamous intraepithelial lesion,6,18,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 58 introitus samples),decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae",2759|4751|4890|4891|4892|4893|4930;2759|4751|5204|162481|231213|1799696,Complete,Fatima Zohra
bsdb:352/2/1,Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Human papilloma virus infection,Cervical glandular intraepithelial neoplasia","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples),increased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,2759|4751|5204|1538075|162474|742845|55193,Complete,Fatima
bsdb:352/2/2,Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Human papilloma virus infection,Cervical glandular intraepithelial neoplasia","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples),decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,2759|4751|5204|162481|231213|1799696,Complete,Fatima
bsdb:352/3/1,Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Human papilloma virus infection","EFO:1000165,EFO:0001668",Atypical Squamous Cells of Undetermined Significance,Low Grade Squamous Intraepithelial Lesion,low grade squamus intraepithelial lesion,6,18,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"ChiomaBlessing,WikiWorks",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 55 cervical samples),decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,2759|4751|5204|162481|231213|1799696,Complete,Fatima Zohra
bsdb:352/4/1,Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 4,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,"Human papilloma virus infection,Cervical glandular intraepithelial neoplasia","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples),increased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,2759|4751|5204|1538075|162474|742845|55193,Complete,Fatima Zohra
bsdb:352/4/2,Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 4,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,"Human papilloma virus infection,Cervical glandular intraepithelial neoplasia","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples),decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,2759|4751|5204|162481|231213|1799696,Complete,Fatima Zohra
bsdb:353/1/1,Study 353,case-control,19849869,10.1017/S0007114509992182,NA,"Balamurugan R, George G, Kabeerdoss J, Hepsiba J, Chandragunasekaran AM , Ramakrishna BS",Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children,The British journal of nutrition,2010,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-obese,obese,(Private) School Children,13,15,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,class/grade level,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Mst Afroza Parvin,WikiWorks,Quantitative PCR of different bacterial groups from the faeces of obese (OB) and non-obese (NOB) participants,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:354/1/1,Study 354,case-control,22546742,10.1038/oby.2012.110,NA,"Karlsson CL, Onnerfält J, Xu J, Molin G, Ahrné S , Thorngren-Jerneck K",The microbiota of the gut in preschool children with normal and excessive body weight,"Obesity (Silver Spring, Md.)",2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (BMI at normal range),overweight/obese,Overweight/ obese children with BMI ranging 17.6-25.8 kg/m2,20,20,None,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Concentrations of specific bacterial groups in feces of overweight/ obese children compared to normal weight children,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:354/1/2,Study 354,case-control,22546742,10.1038/oby.2012.110,NA,"Karlsson CL, Onnerfält J, Xu J, Molin G, Ahrné S , Thorngren-Jerneck K",The microbiota of the gut in preschool children with normal and excessive body weight,"Obesity (Silver Spring, Md.)",2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (BMI at normal range),overweight/obese,Overweight/ obese children with BMI ranging 17.6-25.8 kg/m2,20,20,None,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 3,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Concentrations of specific bacterial groups in feces of overweight/ obese children compared to normal weight children,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|74201|203494|48461|1647988|239934|239935;2|200940|3031449|213115|194924|872,Complete,ChiomaBlessing
bsdb:355/1/1,Study 355,"cross-sectional observational, not case-control",23631345,10.1186/1757-4749-5-10,NA,"Bervoets L, Van Hoorenbeeck K, Kortleven I, Van Noten C, Hens N, Vael C, Goossens H, Desager KN , Vankerckhoven V",Differences in gut microbiota composition between obese and lean children: a cross-sectional study,Gut pathogens,2013,NA,Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (lean/normal weight),obese (obese/overweight/morbidly obese),Children who are obese by BMI (classified based on the international BMI cut-off values of the Extended International Obesity Task Force (IOTF) for children aged 2 to 18),27,26,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Mst Afroza Parvin,WikiWorks,Differences in bacterial genera between O/O and C group.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:355/1/2,Study 355,"cross-sectional observational, not case-control",23631345,10.1186/1757-4749-5-10,NA,"Bervoets L, Van Hoorenbeeck K, Kortleven I, Van Noten C, Hens N, Vael C, Goossens H, Desager KN , Vankerckhoven V",Differences in gut microbiota composition between obese and lean children: a cross-sectional study,Gut pathogens,2013,NA,Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (lean/normal weight),obese (obese/overweight/morbidly obese),Children who are obese by BMI (classified based on the international BMI cut-off values of the Extended International Obesity Task Force (IOTF) for children aged 2 to 18),27,26,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,10 January 2021,Mst Afroza Parvin,WikiWorks,Differences in bacterial genera between O/O and C group.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,2|976|200643|171549|815|909656|821,Complete,Claregrieve1
bsdb:356/1/1,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 3,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5 air,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,Figure 7a & text,10 January 2021,Zyaijah Bailey,WikiWorks,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|186801|3085636|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803;2|976|200643|171549|171550,Complete,Atrayees
bsdb:356/1/2,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 3,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5 air,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 2,Figure 7a & text,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|91061|186826|186827;2|1239|91061|186826|186827|66831;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1239|91061|1385|90964;2|1224|1236|91347|543|1940338,Complete,Atrayees
bsdb:356/2/1,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 2,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 10,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,Figure 7b & text,10 January 2021,Zyaijah Bailey,"Levitest,WikiWorks,Merit,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales",2|1239|186801|186802|31979;2|1224|1236|91347|1903414|583;2|201174|1760|85010,Complete,Atrayees
bsdb:356/3/1,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 3,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 7c & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Merit,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|91061|1385;2|1239|91061|1385|539738|1378;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|459786|1945593;2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:356/4/1,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 4,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,Figure 7d& text,10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300,Complete,Atrayees
bsdb:356/4/2,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 4,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 2,Figure 7d & text,8 August 2023,Atrayees,Atrayees,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|976|200643|171549|815|816;2|200940|3031449|213115|194924|872;2|976|200643|171549|815;2|1239|186801|186802|216572|244127,Complete,Atrayees
bsdb:356/5/2,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 5,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 10,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 7f & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees,Merit","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998|1643822|1643826|580024;2|976|200643|171549|171552;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:356/6/1,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 6,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7g & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Rukky","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp.",2|28221;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201;2|1239|186801|3085636|186803|207244|1872530,Complete,Atrayees
bsdb:356/6/2,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 6,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 7g & text,10 January 2021,Zyaijah Bailey,"Aiyshaaaa,WikiWorks,Merit,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Eukaryota|k__Viridiplantae|p__Streptophyta",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2759|33090|35493,Complete,Atrayees
bsdb:356/7/1,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 7,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 7h & text,10 January 2021,Zyaijah Bailey,WikiWorks,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,Atrayees
bsdb:356/7/2,Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 7,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 7h & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Merit,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3082720|186804;2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:357/1/1,Study 357,time series / longitudinal observational,30804895,10.3389/fmicb.2019.00054,NA,"Qin T, Zhang F, Zhou H, Ren H, Du Y, Liang S, Wang F, Cheng L, Xie X, Jin A, Wu Y, Zhao J , Xu J",High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition,Frontiers in microbiology,2019,"PM2.5/PM10, microbiome composition, pharynx, respiratory pathogen, smoking",Experiment 1,China,Homo sapiens,Cavity of pharynx,UBERON:0001731,Air pollution,ENVO:02500037,pre-smog swabs,post-smog swabs,Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours,83,83,NA,16S,34,Illumina,LEfSe,0.001,TRUE,4,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure S3,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe),increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1239|909932|1843489|31977;2|1239|91061;2|32066|203490|203491|1129771|32067,Complete,Claregrieve1
bsdb:357/1/2,Study 357,time series / longitudinal observational,30804895,10.3389/fmicb.2019.00054,NA,"Qin T, Zhang F, Zhou H, Ren H, Du Y, Liang S, Wang F, Cheng L, Xie X, Jin A, Wu Y, Zhao J , Xu J",High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition,Frontiers in microbiology,2019,"PM2.5/PM10, microbiome composition, pharynx, respiratory pathogen, smoking",Experiment 1,China,Homo sapiens,Cavity of pharynx,UBERON:0001731,Air pollution,ENVO:02500037,pre-smog swabs,post-smog swabs,Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours,83,83,NA,16S,34,Illumina,LEfSe,0.001,TRUE,4,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure S3,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe),decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:358/1/1,Study 358,"cross-sectional observational, not case-control",32546712,10.1038/s41598-020-66607-4,NA,"Tango CN, Seo SS, Kwon M, Lee DO, Chang HK , Kim MK",Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development,Scientific reports,2020,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Cervical cancer","EFO:1000165,MONDO:0002974",Healthy controls,CIN2/3-CC,patients diagnosed with CIN2/3 or cervical cancer during screening of the cervical tract,50,42,antibiotic therapy within 3 months,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,figure 2,10 January 2021,Cynthia Anderson,"WikiWorks,Peace Sandy",Diferences in relative abundances of microbial taxa (genus and species) between groups by LEfSe analysis,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus fornicalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia alkalitolerans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella koreensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|201174|1760|85007|1653|1716|43770;2|201174|1760|85009|31957|1912216;2|201174|1760|85009|31957|1912216|1747;2|1224|28211|356|212791;2|1224|28211|356|212791|225324;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|33958|1578|88164;2|1239|91061|186826|33958|2767885|1599;2|1224|28216|80840|75682|149698|286638;2|201174|1760|85006|1268|1269;2|201174|1760|85006|1268|1269|1270;2|976|200643|171549|171552|838|419005;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|33958|46255;2|1239|91061|186826|33958|46255|165096;2|1239|909932|1843489|31977|29465;2|1239|1737404|1737405|1570339;2|1224|1236|72274|135621|286;2|1224|1236|91347|543;2|201174|1760|85007|1653|1716;2|1224|28216|80840|75682|149698;2|544448|2790996|2790998|2129;2|1224|28211|204457|41297|13687;2|1239|186801|3085636|186803;2|201174|1760|85004|31953|2701,Complete,Peace Sandy
bsdb:358/1/2,Study 358,"cross-sectional observational, not case-control",32546712,10.1038/s41598-020-66607-4,NA,"Tango CN, Seo SS, Kwon M, Lee DO, Chang HK , Kim MK",Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development,Scientific reports,2020,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Cervical cancer","EFO:1000165,MONDO:0002974",Healthy controls,CIN2/3-CC,patients diagnosed with CIN2/3 or cervical cancer during screening of the cervical tract,50,42,antibiotic therapy within 3 months,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,figure 2,3 February 2024,Peace Sandy,Peace Sandy,Diferences in relative abundances of microbial taxa (genus and species) between groups by LEfSe analysis,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,2|201174|1760|85004|31953|2701,Complete,Peace Sandy
bsdb:359/1/1,Study 359,case-control,27015003,10.1038/ismej.2016.37,NA,"Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB , Ahn J",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between current and former smokers,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia",2|201174;2|201174|84998,Complete,Claregrieve1
bsdb:359/1/2,Study 359,case-control,27015003,10.1038/ismej.2016.37,NA,"Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB , Ahn J",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between current and former smokers,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota",2|1224|28216;2|976|117743;2|1224|1236;2|1224,Complete,Claregrieve1
bsdb:360/1/1,Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to MVE,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 10 & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota",2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979|1485;2|1239,Complete,Atrayees
bsdb:360/1/2,Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to MVE,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 10 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|119852;2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:360/2/1,Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 2,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to WS,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 10 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,2|976|200643|171549,Complete,Atrayees
bsdb:360/2/2,Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 2,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to WS,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 10 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|119852;2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:361/1/1,Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 1,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,all other mice,male mice exposed to cigarette smoke,male mice exposed to smoke,50,8,NA,16S,4,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 7,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks,Merit",Differentially abundant taxa in the smoke-exposed male mice versus all other mice,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Archaea|p__Candidatus Aenigmatarchaeota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2157|743724;2|1224|28211|204441;2|74201|203494;2|74201,Complete,Claregrieve1
bsdb:361/2/1,Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 2,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,all other mice,female mice exposed to cigarette smoke,female mice exposed to cigarette smoke,48,10,NA,16S,4,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,increased,NA,NA,NA,increased,Signature 1,Figure 7,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",Differentially abundant taxa in the smoke-exposed female mice versus all other mice,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|2005473,Complete,Claregrieve1
bsdb:361/3/1,Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 3,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,all other mice,ovariectomized female mice exposed to cigarette smoke,ovariectomized female mice exposed to smoke,48,10,NA,16S,4,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 7,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks,Merit",Differentially abundant taxa in the smoke-exposed ovariectomized female mice versus all other mice,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1239|186801|3085636|186803|830;2|976|200643|171549|171552;2|976|200643|171549|171550|28138;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:361/4/1,Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 4,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,control,mice exposed to smoke,"male, female or ovariectomized females mice exposed to smoke",30,28,NA,16S,4,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks,Merit",Differential microbial taxa between the control and smoke-exposed groups,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|1872421;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|186802|216572|459786;2|74201|203494;2|74201|203494|48461;2|74201,Complete,Claregrieve1
bsdb:361/4/2,Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 4,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,control,mice exposed to smoke,"male, female or ovariectomized females mice exposed to smoke",30,28,NA,16S,4,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Zyaijah Bailey,"Claregrieve1,Atrayees,WikiWorks,Merit",Differential microbial taxa between the control and smoke-exposed groups,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803;2|976|200643|171549|2005473;2|976|200643|171549|171550;2|976|200643|171549|194843;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|2049031,Complete,Claregrieve1
bsdb:362/1/1,Study 362,"cross-sectional observational, not case-control",32429742,10.1089/chi.2019.0312,NA,"Aguilar T, Nava GM, Olvera-Ramírez AM, Ronquillo D, Camacho M, Zavala GA, Caamaño MC, Acevedo-Whitehouse K, Rosado JL , García OP",Gut Bacterial Families Are Associated with Body Composition and Metabolic Risk Markers in School-Aged Children in Rural Mexico,Childhood obesity (Print),2020,"bacterial families, children, metabolic markers, microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese,School-aged children,56,16,4 months,16S,NA,RT-qPCR,ANOVA,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Figure A1,10 January 2021,Mst Afroza Parvin,WikiWorks,"Comparison of mean (ANOVA) between anthropometrical and biochemical variables and their association with the main bacterial families studied. (A) Comparison between normal weight, overweight, and obesity according to BMI for age.",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,Atrayees
bsdb:362/1/2,Study 362,"cross-sectional observational, not case-control",32429742,10.1089/chi.2019.0312,NA,"Aguilar T, Nava GM, Olvera-Ramírez AM, Ronquillo D, Camacho M, Zavala GA, Caamaño MC, Acevedo-Whitehouse K, Rosado JL , García OP",Gut Bacterial Families Are Associated with Body Composition and Metabolic Risk Markers in School-Aged Children in Rural Mexico,Childhood obesity (Print),2020,"bacterial families, children, metabolic markers, microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese,School-aged children,56,16,4 months,16S,NA,RT-qPCR,ANOVA,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Figure A1,10 January 2021,Mst Afroza Parvin,WikiWorks,"Comparison of mean (ANOVA) between anthropometrical and biochemical variables and their association with the main bacterial families studied. (A) Comparison between normal weight, overweight, and obesity according to BMI for age.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|815;2|976|200643|171549|171551;2|976|200643|171549|171552,Complete,Atrayees
bsdb:363/1/1,Study 363,"cross-sectional observational, not case-control",32341759,10.1080/20002297.2020.1742527,NA,"Sato N, Kakuta M, Uchino E, Hasegawa T, Kojima R, Kobayashi W, Sawada K, Tamura Y, Tokuda I, Imoto S, Nakaji S, Murashita K, Yanagita M , Okuno Y",The relationship between cigarette smoking and the tongue microbiome in an East Asian population,Journal of oral microbiology,2020,"East Asia, Oral cavity, cigarette smoking, microbiome, tongue",Experiment 1,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,never smokers,current smokers,participants who underwent tongue-coating analysis in 2016 and 2017,384,144,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,dental caries,number of teeth measurement,peridontal microbiome,sex",NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 3(a),10 January 2021,Victoria Goulbourne,"WikiWorks,Atrayees",The result of comparison of bacterial abundance at the genus level,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|201174|84998|84999|1643824|1380;2|1239|909932|1843489|31977|906;2|201174|1760|85007|1653|1716;2|976|200643|171549|2005523|346096;2|1239|186801|3082720|3030910|109326;2|976|200643|171549|2005525|195950;2|1239|186801|3082720|3118655|44259;2|544448|31969|2085|2092|2093,Complete,Atrayees
bsdb:363/1/2,Study 363,"cross-sectional observational, not case-control",32341759,10.1080/20002297.2020.1742527,NA,"Sato N, Kakuta M, Uchino E, Hasegawa T, Kojima R, Kobayashi W, Sawada K, Tamura Y, Tokuda I, Imoto S, Nakaji S, Murashita K, Yanagita M , Okuno Y",The relationship between cigarette smoking and the tongue microbiome in an East Asian population,Journal of oral microbiology,2020,"East Asia, Oral cavity, cigarette smoking, microbiome, tongue",Experiment 1,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,never smokers,current smokers,participants who underwent tongue-coating analysis in 2016 and 2017,384,144,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,dental caries,number of teeth measurement,peridontal microbiome,sex",NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 3(a),10 January 2021,Victoria Goulbourne,"WikiWorks,Atrayees",The result of comparison of bacterial abundance at the genus level,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1239|186801|186802|186807|2740;2|976|117743|200644|49546|1016;2|1224|28216|206351|481|482;2|1224|1236|135615|868|2717;2|1224|28216|80840|119060|47670;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|43996;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|1283313;2|976|200643|171549|171551|836;2|1239|186801|3085636|186803|1164882;2|32066|203490|203491|1129771|32067;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|186806|1730;2|29547|3031852|213849|72294|194;2|1239|526524|526525|128827|123375;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1213720;2|1239|91061|1385|539738|1378,Complete,Atrayees
bsdb:364/1/1,Study 364,case-control,31199220,10.1099/jmm.0.001003,NA,"Karabudak S, Ari O, Durmaz B, Dal T, Basyigit T, Kalcioglu MT , Durmaz R",Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology,Journal of medical microbiology,2019,"buccal microbiome, metagenomic analysis, next-generation sequencing, smoking",Experiment 1,Turkey,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behavior,EFO:0004318,non-smokers,smokers,"Participants who smoke cigarettes that fulfilled the inclusion criteria for good health: no use of antibiotics in the past 3 months, no respiratory infections, no oral aphthous lesions on buccal mucosa, and absence of dental problems",20,20,3 months,16S,23456789,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Victoria Goulbourne,WikiWorks,Comparison of statistically significant differences between smoker and non-smoker groups at genus and species levels,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",2|201174|1760|2037|2049|1654;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301|113107;2|976|200643|171549|171552|2974251|228604;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465|39777,Complete,Claregrieve1
bsdb:365/1/1,Study 365,laboratory experiment,30562947,10.3390/ijms19124079,NA,"Ishii C, Nakanishi Y, Murakami S, Nozu R, Ueno M, Hioki K, Aw W, Hirayama A, Soga T, Ito M, Tomita M , Fukuda S",A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet,International journal of molecular sciences,2018,"American diet, CE-TOFMS, intestinal microbiota, metabologenomics, metabolome, microbiome, multi-omics, next-generation sequencing",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Methionine measurement,EFO:0009771,mice fed control rodent diet.,mice fed American Diet,"C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber",6,5,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Tahiya Begum,"Claregrieve1,WikiWorks",Increased abundance of microbial taxa in AD mice compared with control mice,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263;2|976|200643|171549|171552;2|1239|186801|186802|539000;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|1239|91061|186826|1300|1357,Complete,Claregrieve1
bsdb:365/1/2,Study 365,laboratory experiment,30562947,10.3390/ijms19124079,NA,"Ishii C, Nakanishi Y, Murakami S, Nozu R, Ueno M, Hioki K, Aw W, Hirayama A, Soga T, Ito M, Tomita M , Fukuda S",A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet,International journal of molecular sciences,2018,"American diet, CE-TOFMS, intestinal microbiota, metabologenomics, metabolome, microbiome, multi-omics, next-generation sequencing",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Methionine measurement,EFO:0009771,mice fed control rodent diet.,mice fed American Diet,"C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber",6,5,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Tahiya Begum,"Claregrieve1,WikiWorks",Decreased abundance of microbial taxa in AD mice compared with control mice,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730|142586;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:366/1/1,Study 366,case-control,23454028,10.1016/j.cgh.2013.02.015,NA,"Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP , Rioux KP",Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease,Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association,2013,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,nonalcoholic fatty liver disease,Obese patients with a body mass index (BMI) greater than 30 kg/m2 and clinically suspected non-alcoholic fatty liver disease,30,30,3 months,16S,NA,Roche454,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Rimsha Azhar,WikiWorks,Significant taxa distinguishing in control and NAFLD,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1224|28211|204441|597359;2|1224|1236|135625|712;2|1239|91061|186826|33958;2|1239|909932|1843489|31977;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|588605;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|189330,Complete,Claregrieve1
bsdb:366/1/2,Study 366,case-control,23454028,10.1016/j.cgh.2013.02.015,NA,"Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP , Rioux KP",Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease,Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association,2013,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,nonalcoholic fatty liver disease,Obese patients with a body mass index (BMI) greater than 30 kg/m2 and clinically suspected non-alcoholic fatty liver disease,30,30,3 months,16S,NA,Roche454,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Rimsha Azhar,WikiWorks,Significant taxa distinguishing in control and NAFLD,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|1239|186801|186802|541000;2|976|200643|171549|171551;2|1239|186801|186802|216572|459786,Complete,Claregrieve1
bsdb:367/1/1,Study 367,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S, Ulloa-Martínez M, Martínez-Rojano H, Galván-Rodríguez FM, Miranda-Brito C, Romano MC, Piña-Escobedo A, Pizano-Zárate ML, Hoyo-Vadillo C , García-Mena J",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Unrelated children, 9–11 years old",81,80,3 months,16S,3,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Mst Afroza Parvin,WikiWorks,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.",2|1239|186801|186802|216572|216851|1971605;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|33042|2049024;2|1224|1236|91347|543;2|1239|186801|3085636|186803|841|2049040,Complete,NA
bsdb:367/1/2,Study 367,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S, Ulloa-Martínez M, Martínez-Rojano H, Galván-Rodríguez FM, Miranda-Brito C, Romano MC, Piña-Escobedo A, Pizano-Zárate ML, Hoyo-Vadillo C , García-Mena J",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Unrelated children, 9–11 years old",81,80,3 months,16S,3,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Mst Afroza Parvin,WikiWorks,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1224|1236|135624|83763|83770|2053619;2|1224|1236|91347|1903409|551|558;2|1239|186801|186802|216572|119852,Complete,NA
bsdb:368/1/1,Study 368,"cross-sectional observational, not case-control",32640977,10.1186/s12866-020-01883-8,NA,"Halboub E, Al-Ak'hali MS, Alamir AH, Homeida HE, Baraniya D, Chen T , Al-Hebshi NN",Tongue microbiome of smokeless tobacco users,BMC microbiology,2020,"Microbiota, Mouth neoplasms, Rothia mucilaginosa, high-throughput nucleotide sequencing, Tobacco, Tongue",Experiment 1,Saudi Arabia,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,non-shammah users,shammah users,participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use,23,29,3 months,16S,123,Illumina,LEfSe,0.015,TRUE,NA,sex,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3 a & b,10 January 2021,Victoria Goulbourne,WikiWorks,Differentially abundant taxa,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus gastricus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|419014;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1306;2|201174|1760|2037|2049|2529408|52773;2|201174|1760|85004|31953|419014|419015;2|1239|91061|186826|33958|2742598|227942;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1343;2|1224|1236|135625|712|724|249188;2|1224|28216|206351|481|482|484;2|1239|909932|1843489|31977|29465|29466;2|1224|28216|206351|481|482|34026;2|32066|203490|203491|1129771|32067|554406;2|201174|1760|2037|2049|1654|29317;2|1239|91061|186826|1300|1301|1305;2|1224|28216|206351|481|482|495,Complete,Atrayees
bsdb:368/1/2,Study 368,"cross-sectional observational, not case-control",32640977,10.1186/s12866-020-01883-8,NA,"Halboub E, Al-Ak'hali MS, Alamir AH, Homeida HE, Baraniya D, Chen T , Al-Hebshi NN",Tongue microbiome of smokeless tobacco users,BMC microbiology,2020,"Microbiota, Mouth neoplasms, Rothia mucilaginosa, high-throughput nucleotide sequencing, Tobacco, Tongue",Experiment 1,Saudi Arabia,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,non-shammah users,shammah users,participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use,23,29,3 months,16S,123,Illumina,LEfSe,0.015,TRUE,NA,sex,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3 a & b,10 January 2021,Victoria Goulbourne,WikiWorks,Differentially abundant taxa,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Archangiaceae|g__Archangium",2|1224|28216|206351|481|538;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|265975;2|1224|28216|206351|481|538|539;2|1239|91061|186826|1300|1301|1306;2|1239|186801|3085636|186803|265975|1501332;2|1239|186801|3085636|186803|265975|237576;2|32066|203490|203491|1129771|32067|104608;2|2818505|32015|29|39|47,Complete,Atrayees
bsdb:369/1/1,Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 1,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,children aged 2-9 years,34,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:369/1/2,Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 1,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,children aged 2-9 years,34,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|976|200643|171549|171552;2|1239|186801|3082768|990719;2|1239|1737404|1737405|1737406;2|201174|84998|1643822|1643826|84108;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|119852,Complete,NA
bsdb:369/2/1,Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 2,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,before onset of obesity,after onset of obesity,children aged 2-9 years,36,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224;2|1239|526524|526525|2810280|135858;2|1224|28216|80840|506;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:369/2/2,Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 2,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,before onset of obesity,after onset of obesity,children aged 2-9 years,36,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|91061|186826|33958;2|1239|186801|186802|31979;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1263,Complete,NA
bsdb:370/1/1,Study 370,time series / longitudinal observational,27836847,10.1128/AEM.02149-16,NA,"Stanaway IB, Wallace JC, Shojaie A, Griffith WC, Hong S, Wilder CS, Green FH, Tsai J, Knight M, Workman T, Vigoren EM, McLean JS, Thompson B , Faustman EM",Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure,Applied and environmental microbiology,2017,"16S rRNA, azinphos-methyl, bacteria, buccal mucosa, farmworkers, microbiome, oral, sequencing",Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Air pollution,ENVO:02500037,Winter individuals,Spring/Summer individuals,Individuals for whom sequencing was performed had previous spring/summer blood azinphos-methyl detection by mass spectrometry as evidence of pesticide exposure.,82,101,NA,16S,56,Ion Torrent,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Table 1,10 January 2021,Victoria Goulbourne,"Lwaldron,Atrayees,WikiWorks,Aiyshaaaa",Wilcoxon's rank sum test of azinphos-methyl blood detection groups for compositional pertubation,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|1236|135619|28256|2745;2|201174|1760|85006;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:371/1/1,Study 371,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,"anorexic, lean, and overweight subjects",obese subjects,patients who were obese by BMI (BMI>30 kg m−2),128,134,6 months,WMS,NA,RT-qPCR,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks,Folakunmi",Differential microbial abundance between the obese group and all the other groups,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Claregrieve1
bsdb:371/2/1,Study 371,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean and anorexic subjects,obese and overweight subjects,patients who were overweight or obese by BMI,91,171,6 months,WMS,NA,RT-qPCR,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks,Folakunmi",Differential microbial abundance between the obese and overweight group and the lean and anorexic group,decreased,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,2157|28890|183925|2158|2159|2172|2173,Complete,Claregrieve1
bsdb:371/3/1,Study 371,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean subjects,obese subjects,obese patients defined by BMI  (BMI>30 kg m−2),64,108,6 months,WMS,NA,RT-qPCR,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks,Folakunmi",Differential microbial abundance between obese and lean subjects (species level),decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,2|201174|1760|85004|31953|1678|28025,Complete,Claregrieve1
bsdb:371/3/2,Study 371,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean subjects,obese subjects,obese patients defined by BMI  (BMI>30 kg m−2),64,108,6 months,WMS,NA,RT-qPCR,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 1,9 August 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between obese and lean subjects,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,2|1239|91061|186826|33958|2742598|1598,Complete,Folakunmi
bsdb:371/4/1,Study 371,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean subjects,overweight subjects,patients who were overweight by BMI  (BMI>25 and <30 kg m−2),64,32,6 months,WMS,NA,RT-qPCR,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between overweight and lean subjects,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,2|1239|91061|186826|33958|2742598|1598,Complete,Folakunmi
bsdb:371/5/1,Study 371,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,"anorexic, lean, and overweight subjects (species level)",obese subjects (species level),patients who were obese by BMI (BMI>30 kg m−2),111,108,6 months,WMS,NA,RT-qPCR,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,9 August 2022,Claregrieve1,"Claregrieve1,Folakunmi",Differential microbial abundance between the obese group and all the other groups at the species level,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,2|201174|1760|85004|31953|1678|28025,Complete,Folakunmi
bsdb:371/6/1,Study 371,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 6,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean and anorexic subjects,obese and overweight subjects,patients who were overweight or obese by BMI,79,140,6 months,WMS,NA,RT-qPCR,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,29 January 2024,Folakunmi,Folakunmi,Differential microbial abundance between the obese and overweight group and the lean and anorexic group at species level,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,2|1239|91061|186826|33958|2742598|1598,Complete,Folakunmi
bsdb:372/1/1,Study 372,laboratory experiment,31559135,10.1002/advs.201900972,NA,"Li X, Sun H, Li B, Zhang X, Cui J, Yun J, Yang Y, Zhang L, Meng Q, Wu S, Duan J, Yang H, Wu J, Sun Z, Zou Y , Chen R",Probiotics Ameliorate Colon Epithelial Injury Induced by Ambient Ultrafine Particles Exposure,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2019,"Lactobacillus, air pollution, colonic epithelium, gut microbiota, ultrafine particles",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed to FRA,Diesel exhaust particle (DEP) exposed mice,mice exposed to Diesel exhaust particles (DEP),30,37,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C & text,10 January 2021,Zyaijah Bailey,WikiWorks,LEfSe histogram of fecal microbiota profiling from DEPs group (fecal samples from male n = 20 and female n = 17) and FRA group (fecal samples from male n = 15 and female n = 15) following 7‐day exposure.,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958|1578,Complete,NA
bsdb:372/1/2,Study 372,laboratory experiment,31559135,10.1002/advs.201900972,NA,"Li X, Sun H, Li B, Zhang X, Cui J, Yun J, Yang Y, Zhang L, Meng Q, Wu S, Duan J, Yang H, Wu J, Sun Z, Zou Y , Chen R",Probiotics Ameliorate Colon Epithelial Injury Induced by Ambient Ultrafine Particles Exposure,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2019,"Lactobacillus, air pollution, colonic epithelium, gut microbiota, ultrafine particles",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed to FRA,Diesel exhaust particle (DEP) exposed mice,mice exposed to Diesel exhaust particles (DEP),30,37,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C & text,10 January 2021,Zyaijah Bailey,"Aiyshaaaa,WikiWorks,Merit",LEfSe histogram of fecal microbiota profiling from DEPs group (fecal samples from male n = 20 and female n = 17) and FRA group (fecal samples from male n = 15 and female n = 15) following 7‐day exposure.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|1239;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|31979;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1506;2|976|200643|171549,Complete,NA
bsdb:373/1/1,Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,overweight children,"overweight, but otherwise healthy children (7-12 years)",9,9,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2, text",10 January 2021,Mst Afroza Parvin,"WikiWorks,Merit,Atrayees,Folakunmi",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus timonensis",2|1239|186801|3085636|186803|1766253|39491;2|201174|1760|85004|31953|1678|1681;2|1239|186801|3085636|186803|33042;2|1239|91061|186826|1300|1301|1335;2|1239|186801|3085636|186803|3342669|45851;2|1239|1737404|1737405|1570339|162289|1268254,Complete,Folakunmi
bsdb:373/1/2,Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,overweight children,"overweight, but otherwise healthy children (7-12 years)",9,9,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi,Scholastica,Welile",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera stadtmanae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__uncultured Lachnoclostridium sp.",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|1288121;2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|976|200643|171549|2005519|397864|487174;2|201174|1760|85004|31953|1678|28025;2|200940|3031449|213115|194924|35832|35833;2157|28890|183925|2158|2159|2316|2317;2|976|200643|171549|171552|577309|454154;2|976|200643|171549|815|909656|821;2|201174|84998|84999|84107|1473205|1473216;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|1506553|1586779,Complete,Folakunmi
bsdb:373/2/1,Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 2,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,Overweight children,"overweight, but otherwise healthy children (7-12 years)",9,7,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2",10 January 2021,Mst Afroza Parvin,"WikiWorks,Merit,Folakunmi",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus timonensis",2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|418240;2|1239|526524|526525|2810280|135858|100886;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485|1506;2|1239|186801|3085636|186803|1506553;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|186802|543314|2137877;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|216572|1263|1160721;2|201174|84998|1643822|1643826|84111|84112;2|1239|91061|186826|1300|1301|1335;2|1239|1737404|1737405|1570339|162289|1268254,Complete,Folakunmi
bsdb:373/2/2,Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 2,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,Overweight children,"overweight, but otherwise healthy children (7-12 years)",9,7,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",2|201174|84998|84999|84107|1473205|1473216;2|1239|186801|3085636|186803|33042|33043;2|976|200643|171549|171552|2974251|165179;2|1239|186801|186802|216572|1263|40519;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|28050;2|1239|186801|3082768|990719,Complete,Folakunmi
bsdb:373/3/1,Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 3,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,normal weight children,healthy children with normal weight (7-12 years),7,9,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2",30 January 2024,Folakunmi,"Folakunmi,Joan Chuks",Composition of fecal pools used as inocula according to dominant taxa classified at the species level.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera stadtmanae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.",2|201174|84998|1643822|1643826|447020|446660;2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|818;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|28025;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|418240;2|1239|526524|526525|2810280|135858|100886;2|1239|186801|3085636|186803|189330|88431;2|1239|1737404|1737405|1570339|150022|1260;2|1239|186801|3082720|186804|1505657|261299;2157|28890|183925|2158|2159|2316|2317;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|204516;2|1239|186801|186802|216572|1263|1160721;2|1239|909932|1843488|909930|40840;2|877428;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|1506553|2028282,Complete,Folakunmi
bsdb:373/3/2,Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 3,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,normal weight children,healthy children with normal weight (7-12 years),7,9,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",30 January 2024,Folakunmi,"Folakunmi,Joan Chuks",Composition of fecal pools used as inocula according to dominant taxa classified at the species level.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|1263|40519;2|976|200643|171549|171552|1283313;2|1239|526524|526525|128827|331630,Complete,Folakunmi
bsdb:374/1/1,Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal controls,cervical intraepithelial neoplasia cases,women with histology proven CIN2/3,18,17,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,10 January 2021,Cynthia Anderson,"Cynthia Anderson,LGeistlinger,WikiWorks","Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Thermotogota|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia",2|1239|186801|3082720|3118656|114627;2|200918|188708|2419|188709|1643951;2|1224|28211|766|942|953,Complete,Claregrieve1
bsdb:374/1/2,Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal controls,cervical intraepithelial neoplasia cases,women with histology proven CIN2/3,18,17,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,10 January 2021,Cynthia Anderson,WikiWorks,"Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter",2|1224|1236|135622|267888|53246;2|1224|1236|2887326|468|497,Complete,Claregrieve1
bsdb:374/2/1,Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 2,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,normal control,cervical cancer,histology proven cervical cancer,18,12,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,10 January 2021,Cynthia Anderson,WikiWorks,"Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Thermotogota|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia",2|1239|186801|3082720|3118656|114627;2|200918|188708|2419|188709|1643951;2|1224|28211|766|942|953,Complete,Claregrieve1
bsdb:374/2/2,Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 2,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,normal control,cervical cancer,histology proven cervical cancer,18,12,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,10 January 2021,Cynthia Anderson,"Cynthia Anderson,LGeistlinger,WikiWorks","Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Endolissoclinum",2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1224|28211|204441|41295|1263978,Complete,Claregrieve1
bsdb:375/1/1,Study 375,"cross-sectional observational, not case-control",26745497,10.1159/000442479,NA,"Radilla-Vázquez RB, Parra-Rojas I, Martínez-Hernández NE, Márquez-Sandoval YF, Illades-Aguiar B , Castro-Alarcón N",Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects,Obesity facts,2016,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,obese individuals (BMI >=30) both sexes aged between 18 to 25 years,32,32,4 weeks,WMS,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance in obese and normal-weight young subjects,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|186801|186802|216572|1535;2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:375/1/2,Study 375,"cross-sectional observational, not case-control",26745497,10.1159/000442479,NA,"Radilla-Vázquez RB, Parra-Rojas I, Martínez-Hernández NE, Márquez-Sandoval YF, Illades-Aguiar B , Castro-Alarcón N",Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects,Obesity facts,2016,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,obese individuals (BMI >=30) both sexes aged between 18 to 25 years,32,32,4 weeks,WMS,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance in obese and normal-weight young subjects,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|91347|543|561|562;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:376/1/1,Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took amoxiclav,took amoxiclav for 7 days,7,7,2 months,16S,4,"RT-qPCR,Roche454",ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Results within text- Page 3, 2nd paragraph under sub-heading ""Effect of B-lactams""",10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by amoxiclav, before and after exposure",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota",2|976|200643|171549;2|976|200643|171549|815|816;2|976,Complete,ChiomaBlessing
bsdb:376/1/2,Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took amoxiclav,took amoxiclav for 7 days,7,7,2 months,16S,4,"RT-qPCR,Roche454",ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Results within text- Page 3, 2nd paragraph under sub-heading ""Effect of B-lactams""",10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by amoxiclav, before and after exposure",decreased,k__Bacteria|p__Bacillota,2|1239,Complete,ChiomaBlessing
bsdb:376/2/1,Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took levofloxacin,took levofloxacin for 7 days,8,8,2 months,16S,4,"RT-qPCR,Roche454",ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Supporting Info file: Table S2,10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by levofloxacin, before and after exposure",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:376/2/2,Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took levofloxacin,took levofloxacin for 7 days,8,8,2 months,16S,4,"RT-qPCR,Roche454",ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Supporting Info file: Table S2,10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by levofloxacin, before and after exposure",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,2|1239|186801|3085636|186803|572511,Complete,ChiomaBlessing
bsdb:377/1/1,Study 377,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,e-cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette smokers",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between e-cig smokers and never smokers,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri",2|32066|203490|203491|203492|848|860;2|32066|203490|203491|203492|848|68766;2|1239|186801|3085636|186803|1164882|979627;2|1224|28216|80840|119060|47670|47671;2|1239|186801|3085636|186803|265975|1501329;2|1239|186801|186802|186807|2740|2049038;2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301|1303;2|976|200643|171549|171551|836|1583331,Complete,Claregrieve1
bsdb:377/1/2,Study 377,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,e-cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette smokers",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between e-cig smokers and never smokers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|s__uncultured Bacteroidetes bacterium",2|201174|1760|85004|31953|419014|419015;2|1239|186801|186802;2|1239|186801|3082720|3118655|44259|143361;2|508458|649775|649776|3029087|1434006|651822;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|1300|1357|1358;2|1239|909932|909929|1843491|52225|2049034;2|1224|28216|206351|481|482|267212;2|1239|186801|3085636|186803|265975|1969407;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|52228|310514;2|976|200643|171549|171552|2974251|28135;2|976|200643|171549|171552|838|59823;2|1239|909932|909929|1843491|970|671224;2|1239|909932|909929|1843491|970|135079;2|201174|84998|1643822|1643826|84108|84109;2|1239|91061|1385|90964|1279|29388;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977;2|976|152509,Complete,Claregrieve1
bsdb:377/2/1,Study 377,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,never smokers,cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and never smokers,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",2|1239|91061|186826|186827|46123|46125;2|201174|1760|2037|2049|1654|52769;2|976|117743|200644|49546|1016|1017;2|976|117743|200644|49546|1016|45243;2|976|117743|200644|49546|1016|327575;2|976|117743|200644|49546|1016|1019;2|1224|1236|135615|868|2717|2718;2|1239|186801|3085636|186803|43996|43997;2|201174|1760|85007|1653|1716|61592;2|1224|28216|206351|481|538|539;2|32066|203490|203491|203492|848|860;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|724|726;2|1224|1236|135625|712|724|735;2|1224|1236|135625|712|724|740;2|1239|186801|3085636|186803|1164882|979627;2|1224|28216|80840|119060|47670|47671;2|1224|28216|206351|481|482|1107316;2|1224|28216|206351|481|482|192066;2|1239|186801|3085636|186803|265975|1501329;2|1239|186801|186802|541000;2|1224|28216|80840|80864|219181|1898956;2|1239|186801|186802|186807|2740|2049038;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|59823;2|201174|1760|85006|1268|32207|43675;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|1303;2|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:377/2/2,Study 377,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,never smokers,cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S2,10 January 2021,Victoria Goulbourne,"Lwaldron,Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and never smokers,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174|1760|2037|2049|1654|114702;2|201174|1760|85004|31953|419014|419015;2|200940|3031451|3024411|213121|893|895;2|1239|186801|186802;2|1239|186801|3082720|3118655|44259|143361;2|508458|649775|649776|3029087|1434006|651822;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|1300|1357|1358;2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|906|2023260;2|1239|909932|909929|1843491|52225|2049034;2|544448|31969;2|1239|186801|3085636|186803|265975|1969407;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|2974251|439703;2|976|200643|171549|171552|52228|310514;2|976|200643|171549|171552|2974257|28134;2|976|200643|171549|171552|2974251|28135;2|976|200643|171549|171552|2974251|28136;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552|838|28137;2|508458|649775|649776|3029088|638847|638849;2|201174|1760|85004|31953|196081|230143;2|1239|909932|909929|1843491|970|671224;2|1239|909932|909929|1843491|970|135079;2|201174|84998|1643822|1643826|84108|84109;2|1239|91061|186826|1300|1301|1318;2|203691|203692|136|2845253|157|158;2|203691|203692|136|2845253|157|51160;2|203691|203692|136|2845253|157|166;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|1926307;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:377/3/1,Study 377,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,cigarette smoker,E-cigarette smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette users",40,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and e-cigarette smokers,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",2|976|117743|200644|49546|1016|1017;2|976|117743|200644|49546|1016|45243;2|976|117743|200644|49546|1016|1019;2|1224|1236|135615|868|2717|2718;2|1239|186801|3085636|186803|43996|43997;2|201174|1760|85007|1653|1716|61592;2|1224|28216|206351|481|538|539;2|32066|203490|203491|203492|848|860;2|1224|1236|135625|712|724|726;2|1224|1236|135625|712|724|740;2|1224|28216|80840|119060|47670|47671;2|1224|28216|206351|481|482|1107316;2|1224|28216|206351|481|482|192066;2|1239|186801|186802|541000;2|1239|186801|186802|186807|2740|2049038;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|59823;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:377/3/2,Study 377,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,cigarette smoker,E-cigarette smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette users",40,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and e-cigarette smokers,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobotulus|s__Desulfobotulus sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|201174|1760|2037|2049|1654|114702;2|201174|1760|85004|31953|419014|419015;2|200940|3024418|213118|213119|48001|1940337;2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301|1318,Complete,Claregrieve1
bsdb:378/1/1,Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 4),35,35,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Figure 2B,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus- host disease patients.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1239|91061|186826|1300|1357;2|1224|28216|80840|119060|47670;2|1224|1236|135614|32033|40323;2|1224|1236|135614|32033;2|1224|1236|135614;2|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:378/1/2,Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 4),35,35,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Figure 2B,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus- host disease patients.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",2|1224|28211;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1239|186801;2|1239|526524|526525|2810280|1505663;2|1239|186801|186802;2|1239|186801|186802|216572|946234;2|1239|91061|1385|539738|1378;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|459786;2|1239|186801|186802|541000;2|1224|28211|204441;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|1769710,Complete,Claregrieve1
bsdb:378/2/1,Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3),35,35,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Figure 2C,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus-host disease patients.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|135614|32033|40323;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:378/2/2,Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3),35,35,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Figure 2C,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus- host disease patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|572511;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|186802|216572|216851|1946507;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1769710;2|1239|186801|186802|541000,Complete,Claregrieve1
bsdb:379/1/1,Study 379,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y, Cai Q, Zheng W, Steinwandel M, Blot WJ, Shu XO , Long J",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,"16S rRNA gene sequencing; Southern Community Cohort Study; Probiotic taxa, Oral microbiome, obesity",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Obesity,EFO:0001073,obese,non-obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",647,969,1 year,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking status","age,alcohol drinking,number of teeth measurement,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,10 January 2021,Victoria Goulbourne,WikiWorks,Probiotic bacterial taxa showing a significantly higher prevelance in non-obese than obese individuals,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium subtile,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus ultunensis",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|158787;2|201174|1760|85004|31953|1678|77635;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|47493;2|1239|91061|186826|33958|1578|227945,Complete,NA
bsdb:379/2/1,Study 379,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y, Cai Q, Zheng W, Steinwandel M, Blot WJ, Shu XO , Long J",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,"16S rRNA gene sequencing; Southern Community Cohort Study; Probiotic taxa, Oral microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Obesity,EFO:0001073,non-obese,obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",969,647,1 year,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking behavior","age,alcohol drinking,number of teeth measurement,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 3,10 January 2021,Victoria Goulbourne,"Atrayees,WikiWorks",Common bacterial taxa showing a significantly higher prevelance in obese than in non-obese individuals,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",2|201174|1760|2037|2049|1654|29317;2|1239|91061|186826|186828;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186828|117563|46124;2|1239|91061|186826|1300|1301|45634,Complete,NA
bsdb:379/2/2,Study 379,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y, Cai Q, Zheng W, Steinwandel M, Blot WJ, Shu XO , Long J",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,"16S rRNA gene sequencing; Southern Community Cohort Study; Probiotic taxa, Oral microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Obesity,EFO:0001073,non-obese,obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",969,647,1 year,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking behavior","age,alcohol drinking,number of teeth measurement,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 4,10 January 2021,Victoria Goulbourne,"Atrayees,WikiWorks",Rare taxa showing a significantly higher prevelance in obese or non-obese individuals,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 512",2|201174|1760|85004|31953|419014;2|1239|909932|1843489|31977|156454;2|1224|1236|135625|712|416916|712149,Complete,NA
bsdb:380/1/1,Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,patients post allogenic hematopoietic cell transplant/pre Fecal Microbiota Transplant,patients preallogenic hematopoietic cell transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,increased,NA,Signature 1,Figure 4B,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
bsdb:380/2/1,Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 180,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 4B,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
bsdb:380/3/1,Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 7,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,decreased,NA,Signature 1,Figure 5,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
bsdb:380/4/1,Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 30,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,decreased,NA,Signature 1,Figure 5,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
bsdb:381/1/1,Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,healthy volunteers,hematopoietic stem cell transplant recipients,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,18,50,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Text, Figure 1",10 January 2021,Nadine Ulysse,WikiWorks,Clinical and Microbime Predictors of Acute GastroIntestinal Graft-vs- Host Disease,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Fatima Zohra
bsdb:381/1/2,Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,healthy volunteers,hematopoietic stem cell transplant recipients,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,18,50,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Text, Figure 1",10 January 2021,Nadine Ulysse,WikiWorks,Clinical and Microbime Predictors of Acute GastroIntestinal Graft-vs- Host Disease,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|3085636|186803|46205;2|1239|186801|186802|216572|292632,Complete,Fatima Zohra
bsdb:381/2/1,Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,low fecal butyrate levels,high fecal butyrate levels,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,50,50,NA,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 3, Supplemental figure 2",10 January 2021,Nadine Ulysse,WikiWorks,Differences in fecal metabolites among hemapoietic stem cell transplant (HSCT) recipients at baseline,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|1239|186801;2|1239|186801|186802;2|1239|186801|3085636|186803;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|572511;2|1239|526524;2|1239|526524|526525;2|1239|526524|526525|128827;2|1239|186801|3085636|186803|46205;2|1239|526524|526525|2810280|1505663,Complete,Fatima Zohra
bsdb:381/2/2,Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,low fecal butyrate levels,high fecal butyrate levels,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,50,50,NA,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 3, Supplemental figure 2",10 January 2021,Nadine Ulysse,WikiWorks,Differences in fecal metabolites among hemapoietic stem cell transplant (HSCT) recipients at baseline,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|91061|186826;2|1239|91061,Complete,Fatima Zohra
bsdb:382/1/1,Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 1,Italy,Homo sapiens,Endocervix,UBERON:0000458,Chlamydia trachomatis infectious disease,EFO:0007205,healthy control,patient with chlamydia infection,patient with Chlamydia infection,7,7,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii",2|1239|91061|186826|186827|1375;2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375|87541,Complete,Fatima Zohra
bsdb:382/1/2,Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 1,Italy,Homo sapiens,Endocervix,UBERON:0000458,Chlamydia trachomatis infectious disease,EFO:0007205,healthy control,patient with chlamydia infection,patient with Chlamydia infection,7,7,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239;2|1239|91061,Complete,Fatima Zohra
bsdb:382/2/1,Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 2,Italy,Homo sapiens,Endocervix,UBERON:0000458,"Chlamydophila infectious disease,Human papilloma virus infection","EFO:0001668,EFO:1000863",HPV positive women,patient with chlamydia infection,patient with Chlamydia infection,7,8,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,increased,"k__Bacteria|p__Chlamydiota,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae,k__Bacteria|p__Chlamydiota|c__Chlamydiia,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis",2|204428;2|204428|204429|51291|809;2|204428|204429;2|204428|204429|51291;2|204428|204429|51291|809|810;2|204428|204429|51291|809|810|813,Complete,Fatima Zohra
bsdb:382/2/2,Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 2,Italy,Homo sapiens,Endocervix,UBERON:0000458,"Chlamydophila infectious disease,Human papilloma virus infection","EFO:0001668,EFO:1000863",HPV positive women,patient with chlamydia infection,patient with Chlamydia infection,7,8,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826;2|1239,Complete,Fatima Zohra
bsdb:383/1/1,Study 383,prospective cohort,28632934,10.1111/all.13232,NA,"Savage JH, Lee-Sarwar KA, Sordillo J, Bunyavanich S, Zhou Y, O'Connor G, Sandel M, Bacharier LB, Zeiger R, Sodergren E, Weinstock GM, Gold DR, Weiss ST , Litonjua AA",A prospective microbiome-wide association study of food sensitization and food allergy in early childhood,Allergy,2018,"Dorea, food allergy, food sensitization, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,no food sensitization,child with food sensitization,"child with serum-specific IgE to milk, egg, peanut, soy, wheat, and walnut greater than 0.35 kU/L at age 3",131,85,1 week,16S,345,Roche454,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2a,10 January 2021,Lucy Mellor,WikiWorks,Significant associations between food sensitization and bacterial genera. The log2 fold change is plotted for each bacterial genus significantly associated with food sensitization,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:383/2/1,Study 383,prospective cohort,28632934,10.1111/all.13232,NA,"Savage JH, Lee-Sarwar KA, Sordillo J, Bunyavanich S, Zhou Y, O'Connor G, Sandel M, Bacharier LB, Zeiger R, Sodergren E, Weinstock GM, Gold DR, Weiss ST , Litonjua AA",A prospective microbiome-wide association study of food sensitization and food allergy in early childhood,Allergy,2018,"Dorea, food allergy, food sensitization, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,no food allergy,child with food allergy,"child with healthcare provider-diagnosed allergy to milk, egg, peanut, wheat, soy, or other nut allergy prior to age 3 years with evidence of IgE sensitization to that food (>0.1 kU/L) at age 3 years",202,14,1 week,16S,345,Roche454,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2b,10 January 2021,Lucy Mellor,WikiWorks,Significant associations between food allergy and bacterial genera. The log2 fold change is plotted for each bacterial genus significantly associated with food allergy,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1224|1236|91347|543|544;2|1239|186801|186802|216572|119852;2|1239|91061|186826|1300|1357;2|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:384/1/1,Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,FSCZ,first-episode drug naive schizophrenia (FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsychotic medications before,69,40,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees","Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|186801|3082768|990719;2|1224|1236|91347|543;2|256845|1313211|278082|255528;2|1239|91061|186826|81852;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|81852|1350,Complete,Atrayees
bsdb:384/1/2,Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,FSCZ,first-episode drug naive schizophrenia (FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsychotic medications before,69,40,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Atrayees,WikiWorks","Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|1236|135625|712;2|1224|1236|135624|83763;2|1239|526524|526525|2810281;2|1239|186801|3082720|186804;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|906;2|1224|1236|135625|712|713;2|1239|909932|1843489|31977,Complete,Atrayees
bsdb:384/2/1,Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|186801|3082768|990719;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1224|1236|91347|543|561;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:384/2/2,Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Aiyshaaaa,WikiWorks,Atrayees","Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|1224|1236|135625|712;2|1239|526524|526525|2810281;2|1224|1236|135625|712|713;2|1239|909932|1843489|31977|906,Complete,Atrayees
bsdb:384/3/1,Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,FSCZ,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",40,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3082720|186804;2|1239|909932|1843489|31977;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1224|1236|91347|543|561;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|906;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:384/3/2,Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,FSCZ,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",40,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:385/1/1,Study 385,case-control,30619779,10.3389/fcimb.2018.00433,NA,"Hu YL, Pang W, Huang Y, Zhang Y , Zhang CJ",The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics,Frontiers in cellular and infection microbiology,2018,"gastric adenocarcinoma, human, inflammation, microbiome, shotgun metagenomics",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric adenocarcinoma,EFO:0000503,Superficial gastritis (SG),Gastric adenocarcinoma (GC),SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies,5,6,Use of antibiotics within 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 2A and Figure 2B,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy",Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313;2|1224|1236;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|490;2|1224|1236|135625|712;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1313;2|976|200643|171549|171551|836;2|976|200643|171549|171551;2|976|200643|171549|171551|836|28124;2|1224|1236|135625|712|416916|739;2|1224|28216|206351|481,Complete,Peace Sandy
bsdb:385/1/2,Study 385,case-control,30619779,10.3389/fcimb.2018.00433,NA,"Hu YL, Pang W, Huang Y, Zhang Y , Zhang CJ",The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics,Frontiers in cellular and infection microbiology,2018,"gastric adenocarcinoma, human, inflammation, microbiome, shotgun metagenomics",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric adenocarcinoma,EFO:0000503,Superficial gastritis (SG),Gastric adenocarcinoma (GC),SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies,5,6,Use of antibiotics within 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 2A and Figure 2B,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy,MyleeeA",Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Blastomonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium xenophagum",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|55565;2|1224|28211;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953;2|1224|28211|204457|41297|150203;2|201174|84998|84999|84107;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|1884818;2|1239|186801|186802;2|1239|186801|3085636|186803;2|201174|84998|84999|1643824|2767353|1382;2|1239|186801|3085636|186803|265975|237576;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28129;2|201174|1760|85006|1268|32207|43675;2|1224|28211|204457|41297|165695;2|1224|28211|204457|41297|165695|13690;2|1224|28211|204457|41297;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|45634;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1305;2|1239|186801|186802|543314|56774;2|1224|28211|204457|41297|165695|121428,Complete,Peace Sandy
bsdb:386/1/1,Study 386,case-control,31001490,10.3389/fcimb.2019.00090,NA,"Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B , Sun Z",The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients,Frontiers in cellular and infection microbiology,2019,"human gut microbiota, metabolic potential, metagenomic sequencing, microbial diversity, tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,healthy controls,Tuberculosis (TB) patients,"patients diagnosed with TB by assessing symptoms, including the results of acid-fast bacilli (AFB) smear microscopy, culture, the T-SPOT.TB test and a chest radiograph.",31,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 2A, Text (results)",10 January 2021,Yu Wang,"WikiWorks,Peace Sandy","(A) Differentially abundant species between the C and P groups. P-values for all differentially abundant species between groups are plotted above (Wilcoxon rank-sum test, FDR < 0.1, respectively). Species (present in at least 10% samples) with mean relative abundances of more than 0.001 were considered.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|33042,Complete,Peace Sandy
bsdb:386/1/2,Study 386,case-control,31001490,10.3389/fcimb.2019.00090,NA,"Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B , Sun Z",The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients,Frontiers in cellular and infection microbiology,2019,"human gut microbiota, metabolic potential, metagenomic sequencing, microbial diversity, tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,healthy controls,Tuberculosis (TB) patients,"patients diagnosed with TB by assessing symptoms, including the results of acid-fast bacilli (AFB) smear microscopy, culture, the T-SPOT.TB test and a chest radiograph.",31,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 2A, Text (results)",10 January 2021,Yu Wang,"Lwaldron,WikiWorks,Peace Sandy","(A) Differentially abundant species between the C and P groups. P-values for all differentially abundant species between groups are plotted above (Wilcoxon rank-sum test, FDR < 0.1, respectively). Species (present in at least 10% samples) with mean relative abundances of more than 0.001 were considered.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|1239|186801|3085636|186803|1766253|39491;2|74201|203494|48461|1647988|239934|239935;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|40520;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|33042|2049024;2|1239|186801|3085636|186803|33042|751585;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|28050|39485;2|1239|909932|909929|1843491|158846|437897;2|1239|909932|909929|1843491|158846|158847;2|1239|909932|909929|1843491|158846|491921;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1224|28216|80840|995019|40544|40545;2|1239|186801|3085636|186803|2316020|46228,Complete,Peace Sandy
bsdb:387/1/1,Study 387,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE , Weintraub A",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,"antibiotics, culture, intestinal microbiota, pyrosequencing",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before ciprofloxacin exposure,after ciprofloxacin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were given ciprofloxacin",9,9,3 months,16S,567,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Text (results),10 January 2021,Gina Celentano,"Claregrieve1,WikiWorks",Human normal intestinal microbiota before versus after antibiotic administration,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:387/1/2,Study 387,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE , Weintraub A",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,"antibiotics, culture, intestinal microbiota, pyrosequencing",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before ciprofloxacin exposure,after ciprofloxacin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were given ciprofloxacin",9,9,3 months,16S,567,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Text (results),10 January 2021,Gina Celentano,"Claregrieve1,WikiWorks",Human normal intestinal microbiota before versus after antibiotic administration,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:387/2/1,Study 387,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE , Weintraub A",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,"antibiotics, culture, intestinal microbiota, pyrosequencing",Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Before clindamycin exposure,after clindamycin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were exporsed to clindamycin",9,9,3 months,16S,567,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Text (results),10 January 2021,Gina Celentano,"Claregrieve1,WikiWorks",Human normal intestinal microbiota before versus after antibiotic administration,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|186802;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:388/1/1,Study 388,"cross-sectional observational, not case-control",32753953,10.2147/CMAR.S251021,NA,"Zhou J, Wang L, Yuan R, Yu X, Chen Z, Yang F, Sun G , Dong Q",Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model,Cancer management and research,2020,"microbiome, oral squamous cell carcinoma, predicted functions, random forest machine learning",Experiment 1,China,Homo sapiens,Mucosa of oral region,UBERON:0003343,Oral squamous cell carcinoma,EFO:0000199,paracancerous tissues,cancerous  lesions,patients at different stages of OSCC were enrolled in the study,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2A,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Relative abundance of genera enriched in cancerous tissues VS paracancerous tissues,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|91061|186826|186828|2747;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,ChiomaBlessing
bsdb:388/1/2,Study 388,"cross-sectional observational, not case-control",32753953,10.2147/CMAR.S251021,NA,"Zhou J, Wang L, Yuan R, Yu X, Chen Z, Yang F, Sun G , Dong Q",Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model,Cancer management and research,2020,"microbiome, oral squamous cell carcinoma, predicted functions, random forest machine learning",Experiment 1,China,Homo sapiens,Mucosa of oral region,UBERON:0003343,Oral squamous cell carcinoma,EFO:0000199,paracancerous tissues,cancerous  lesions,patients at different stages of OSCC were enrolled in the study,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2A,10 January 2021,Rimsha Azhar,"Atrayees,WikiWorks,ChiomaBlessing",Relative abundance of genera enriched in cancerous tissues VS paracancerous tissues,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Eukaryota|k__Viridiplantae|p__Streptophyta",2|201174|1760|85006|1268|1663;2|1224|28211|204458|76892|41275;2|200940|3031449|213115|194924|872;2|201174|1760|85006|85023|33882;2|200930|68337|191393|2945020|248038;2|1239|91061|1385|186822|44249;2759|33090|35493,Complete,ChiomaBlessing
bsdb:389/1/1,Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,121,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,WikiWorks,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:389/1/2,Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,121,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,"WikiWorks,Atrayees","Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",2|1224|28216|206351|481|482|28449;2|976|200643|171549|171552|838;2|976|117743|200644|2762318,Complete,Atrayees
bsdb:389/2/1,Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,mania,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,62,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,WikiWorks,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas",2|1239|91061|186826|1300|1301;2|1224|28216|80840|2975441|215579,Complete,Atrayees
bsdb:389/2/2,Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,mania,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,62,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,"WikiWorks,Atrayees","Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",2|1224|28216|206351|481|482|28449;2|976|200643|171549|171552|838;2|976|117743|200644|2762318,Complete,Atrayees
bsdb:390/1/1,Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2A,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,Folakunmi",Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|186802|216572|258514;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|1239|186801|186802|216572|244127;2|200940|3031449|213115|194924|35832;2|28221;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|186801|186802|216572|946234;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|216572|1508657;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:390/1/2,Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2A,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|526524|526525|128827|1774107;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802|1392389;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:390/2/1,Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,scizophrenia during remission,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2B,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi,Welile",Characterization of fecal microbiota to distinguish toxigenic types by linear discriminant analysis method,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|201174|1760|2037|2049|1654;2|1239|186801|186802|186806|264995;2|1239|186801|186802|216572|244127;2|201174|84998|84999|1643824|1380;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|2383;2|1239|186801|3082768|990719;2|1239|186801|186802|31979|1485;2|1224|28216|80840|80864|283;2|1239|186801|186802|216572|946234;2|1239|526524|526525|128827|61170;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|31979|420345;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|526524|526525|128827|123375;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:390/2/2,Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,scizophrenia during remission,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2B,10 January 2021,WikiWorks,"WikiWorks,Folakunmi",Characterization of fecal microbiota to distinguish toxigenic types by lineear discriminant analysis method,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|1239|186801|186802|3085642|580596;2|1239|526524|526525|128827|1774107;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802|1392389;2|976|200643|171549|171552|577309;2|1239|526524|526525|2810280|3025755,Complete,Folakunmi
bsdb:390/3/1,Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,symptomatic remission,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi,MyleeeA",Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|186802|31979;2|1239|186801|3082720|186804;2|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:391/1/1,Study 391,"cross-sectional observational, not case-control",31841737,10.1016/j.jneuroim.2019.577126,NA,"Shi Z, Qiu Y, Wang J, Fang Y, Zhang Y, Chen H, Du Q, Zhao Z, Yan C, Yang M , Zhou H",Dysbiosis of gut microbiota in patients with neuromyelitis optica spectrum disorders: A cross sectional study,Journal of neuroimmunology,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Neuromyelitis optica,EFO:0004256,healthy controls,neuromyelitis optica spectrum disorder,Each patient met the 2015 international diagnostic criteria for NMOSD and tested positive for serum AQP4-IgG using cell-based assays,20,20,currently taking antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Abundance of gut microbiota between the NMOSD and HS groups,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1224|1236|91347;2|1224|1236|91347|543;2|1224;2|1224|1236;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061;2|1239|91061|1385;2|1239|91061|186826;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572|1486725;2|1239|909932|1843489|31977|156454;2|1239|186801|186802|216572|946234;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300,Complete,Atrayees
bsdb:391/1/2,Study 391,"cross-sectional observational, not case-control",31841737,10.1016/j.jneuroim.2019.577126,NA,"Shi Z, Qiu Y, Wang J, Fang Y, Zhang Y, Chen H, Du Q, Zhao Z, Yan C, Yang M , Zhou H",Dysbiosis of gut microbiota in patients with neuromyelitis optica spectrum disorders: A cross sectional study,Journal of neuroimmunology,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Neuromyelitis optica,EFO:0004256,healthy controls,neuromyelitis optica spectrum disorder,Each patient met the 2015 international diagnostic criteria for NMOSD and tested positive for serum AQP4-IgG using cell-based assays,20,20,currently taking antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3, text",10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",Abundance of gut microbiota between the NMOSD and HS groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|33042;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552;2|1239|186801|186802;2|1239|186801;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:392/1/1,Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy controls,non-IgE mediated cow's milk allergy,"children aged 1-26 months with a diagnosis of non-IgE mediated cow's milk allergy based on clinical history, negative result of skin prick test, and/or negative level of IgE serum-specific anti-cow's milk proteins",23,23,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between cow's milk allergy non IgE patients at diagnosis and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1239|186801|186802|31979|1266,Complete,Claregrieve1
bsdb:392/2/1,Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE mediated cow's milk allergy treated with EHCF,23,9,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF and non-IgE mediated cow's milk allergy patients at diagnosis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:392/3/1,Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,23,14,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients at diagnosis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:392/3/2,Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,23,14,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table S1,31 December 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients at diagnosis,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,2|201174|1760|85011|2062|1883,Complete,Claregrieve1
bsdb:392/4/1,Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,9,14,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients treated with EHCF,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|28050;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:392/4/2,Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,9,14,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy treated with EHCF + LGG and non-IgE mediated cow's milk allergy treated with EHCF,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|39948,Complete,Claregrieve1
bsdb:393/1/1,Study 393,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M, Guadamuro L, Espinosa-Martos I, Mancabelli L, Jiménez S, Molinos-Norniella C, Pérez-Solis D, Milani C, Rodríguez JM, Ventura M, Bousoño C, Gueimonde M, Margolles A, Díaz JJ , Delgado S",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,"cow’s milk protein, fecal microbiota, non-IgE mediated allergy, protein hydrolyzed formulas, tolerance acquisition",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy non-tolerant to cow's milk protein,infant with non-IgE-mediated cow's milk allergy tolerant to cow's milk protein,infant with non-IgE mediated cow's milk allergy tolerant to cow's milk after a period of six months dairy-free diet,3,14,4 weeks,16S,34,Illumina,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Lucy Mellor,WikiWorks,"Significant differences in fecal microbial abundances (%) between tolerant and non-tolerant infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) after
a period with a diet free of cow’s milk protein (CMP)",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004|31953;2|201174|84998|84999|84107;2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:393/2/1,Study 393,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M, Guadamuro L, Espinosa-Martos I, Mancabelli L, Jiménez S, Molinos-Norniella C, Pérez-Solis D, Milani C, Rodríguez JM, Ventura M, Bousoño C, Gueimonde M, Margolles A, Díaz JJ , Delgado S",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,"cow’s milk protein, fecal microbiota, non-IgE mediated allergy, protein hydrolyzed formulas, tolerance acquisition",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy control,infant with non-IgE-mediated cow's milk allergy,"infant with cow's milk protein allergy confirmed by a negative skin prick test, values lower than 0.35 kU/L cow’s milk-specific IgE determined in their blood, and a clear positive standardized oral challenge (SOC), performed under medical supervision",10,17,4 weeks,16S,34,Illumina,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differences in relative abundances (%) of sequences in fecal samples of infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) and non-allergic control infants,increased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,2|201174|84998|84999|84107,Complete,Atrayees
bsdb:393/2/2,Study 393,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M, Guadamuro L, Espinosa-Martos I, Mancabelli L, Jiménez S, Molinos-Norniella C, Pérez-Solis D, Milani C, Rodríguez JM, Ventura M, Bousoño C, Gueimonde M, Margolles A, Díaz JJ , Delgado S",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,"cow’s milk protein, fecal microbiota, non-IgE mediated allergy, protein hydrolyzed formulas, tolerance acquisition",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy control,infant with non-IgE-mediated cow's milk allergy,"infant with cow's milk protein allergy confirmed by a negative skin prick test, values lower than 0.35 kU/L cow’s milk-specific IgE determined in their blood, and a clear positive standardized oral challenge (SOC), performed under medical supervision",10,17,4 weeks,16S,34,Illumina,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Differences in relative abundances (%) of sequences in fecal samples of infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) and non-allergic control infants,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Atrayees
bsdb:394/1/1,Study 394,prospective cohort,31676759,10.1038/s41467-019-12989-7,NA,"Thorsen J, Rasmussen MA, Waage J, Mortensen M, Brejnrod A, Bønnelykke K, Chawes BL, Brix S, Sørensen SJ, Stokholm J , Bisgaard H",Infant airway microbiota and topical immune perturbations in the origins of childhood asthma,Nature communications,2019,NA,Experiment 1,Denmark,Homo sapiens,Hypopharynx,UBERON:0001051,Asthma,MONDO:0004979,healthy control,child with asthma at age 6,"asthma at age 6 years diagnosed using a pre-defined validated quantitative symptom algorithm based on parental registration of troublesome lung symptoms on structured daily diary cards from birth, verified by study pediatricians at each clinic visit",438,135,NA,16S,4,Illumina,Cox Proportional-Hazards Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplemental Table 1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks","Associations between log-relative abundances at one month and asthma development by age six years, assessed with Cox proportional hazards regression",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:395/1/1,Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"Chronic kidney disease,Stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",healthy controls,peritoneal dialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in peritoneal dialysis group VS healthy control group,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota",2|201174;2|1239,Complete,Atrayees
bsdb:395/1/2,Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"Chronic kidney disease,Stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",healthy controls,peritoneal dialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Figure 2,14 July 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in peritoneal dialysis group VS healthy control group,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Atrayees
bsdb:395/2/1,Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,"Chronic kidney disease,Stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",healthy controls,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in hemodialysis  group VS healthy control group,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Atrayees
bsdb:395/3/1,Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,"Chronic kidney disease,Stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",peritoneal dialysis,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",8,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in the hemodialysis group VS peritoneal dialysis group,decreased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Atrayees
bsdb:395/3/2,Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,"Chronic kidney disease,Stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",peritoneal dialysis,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",8,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,increased,NA,NA,increased,Signature 2,Figure 2,14 July 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in the hemodialysis group VS peritoneal dialysis group,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|201174;2|976|200643,Complete,Atrayees
bsdb:396/1/1,Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 7a, 7b",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline atopic dermatitis lesional sites versus control skin,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061;2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:396/1/2,Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 7a, 7b",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline atopic dermatitis lesional sites versus control skin,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus",2|201174|1760;2|1224|28211;2|976|200643;2|1224|28216;2|1239|186801;2|201174|84998;2|1239|526524;2|201174|84995;2|74201|203494;2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060|106589,Complete,Claregrieve1
bsdb:396/2/1,Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS + Bleach,child with moderate to severe atopic dermatitis after treatment with TCS + bleach,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7c,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS + bleach treatment group at baseline and after treatment,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|2887326|468|469;2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:396/2/2,Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS + Bleach,child with moderate to severe atopic dermatitis after treatment with TCS + bleach,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7c,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS + bleach treatment group at baseline and after treatment,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:396/3/1,Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS only,child with moderate to severe atopic dermatitis after treatment with TCS only,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7d,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS only treatment group at baseline and after treatment,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|2887326|468|469;2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:396/3/2,Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS only,child with moderate to severe atopic dermatitis after treatment with TCS only,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7d,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS only treatment group at baseline and after treatment,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:397/1/1,Study 397,case-control,31152265,10.1007/s10096-019-03598-9,NA,"Zheng Y, Wang Q, Ma L, Chen Y, Gao Y, Zhang G, Cui S, Liang H, He C , Song L",Alterations in the skin microbiome are associated with disease severity and treatment in the perioral zone of the skin of infants with atopic dermatitis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2019,"Atopic dermatitis, Bacterial diversity, Perioral skin, Prevotella melaninogenica",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,severe atopic dermatitis,child with severe atopic dermatitis based on eczema area and severity index (EASI) local rating method,20,20,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,increased,NA,decreased,Signature 1,"Table 2, Table 3",10 January 2021,Lucy Mellor,WikiWorks,Different genera of average relative abundance >=0.1% in healthy and severe atopic dermatitis groups,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae",2|1239|91061|1385|90964|1279;2|201174|1760|85007|85025|1827;2|1239|91061|186826|186828|1651;2|1224|28216|80840|114248;2|1239|91061|1385|90964|1279|1280;2|201174|1760|85007|1653|1716|146827;2|1224|28211|204457|41297|13687|172044,Complete,Folakunmi
bsdb:397/1/2,Study 397,case-control,31152265,10.1007/s10096-019-03598-9,NA,"Zheng Y, Wang Q, Ma L, Chen Y, Gao Y, Zhang G, Cui S, Liang H, He C , Song L",Alterations in the skin microbiome are associated with disease severity and treatment in the perioral zone of the skin of infants with atopic dermatitis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2019,"Atopic dermatitis, Bacterial diversity, Perioral skin, Prevotella melaninogenica",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,severe atopic dermatitis,child with severe atopic dermatitis based on eczema area and severity index (EASI) local rating method,20,20,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,increased,NA,decreased,Signature 2,"Table 2, Table 3",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Different genera of average relative abundance >=0.1% in healthy and severe atopic dermatitis groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|1224|28211|356|82115|357;2|201174|84998|84999|1643824|1380;2|976|200643|171549|171552|2974257|425941;2|32066|203490|203491|1129771|32067;2|1224|28216|80840|119060|131079;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|186828|117563,Complete,Folakunmi
bsdb:398/1/1,Study 398,prospective cohort,27609659,10.1016/j.jaci.2016.07.029,NA,"Kennedy EA, Connolly J, Hourihane JO, Fallon PG, McLean WHI, Murray D, Jo JH, Segre JA, Kong HH , Irvine AD",Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year,The Journal of allergy and clinical immunology,2017,"16S sequencing, Staphylococcus aureus, atopic dermatitis, longitudinal birth cohort, microbiome, skin",Experiment 1,Ireland,Homo sapiens,Skin of forearm,UBERON:0003403,Atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child with atopic dermatis at month 12 diagnosed by experienced health care personnel using the UK Working Party Diagnostic Criteria,10,10,NA,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of major taxa in antecubital fossa at month 2 between subjects that went on to be affected with atopic dermatits at month 12 and those who went on to be unaffected,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
bsdb:399/1/1,Study 399,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:399/1/2,Study 399,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 2, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Candidatus Absconditabacteria|s__candidate division SR1 bacterium",2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157;2|1224|28216|206351|481|538;2|1224|28216|80840|119060|47670;2|1239|186801|3085636|186803|43994;2|1224|1236|135615|868|2717;2|1224|28216|80840|80864|283;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848|68766;2|201174|1760|85009|31957|1743;2|1224|1236|135625|712|724|740;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836;2|1239|186801|3082720|3120161|1481960;2|221235|2044938,Complete,Claregrieve1
bsdb:399/2/1,Study 399,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4a, Figure 5, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|1224|1236|91347|543|561;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301;2|544448|31969;2|1239|186801|186802|1898207;2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|46205;2|1239|186801|186802|216572|1508657,Complete,Claregrieve1
bsdb:399/2/2,Study 399,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4a, Figure 5, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium",2|74201|203494|48461|1647988|239934;2|976|200643|171549|815|816;2|1239|526524|526525|128827;2|1239|186801|3085636|186803;2|201174|84998|1643822|1643826|84108;2|1239|186801|186802|543314|2137877,Complete,Claregrieve1
bsdb:400/1/1,Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy control,asthma,child age 4-7 years with physician diagnosed asthma,24,34,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text (Association between gut metabolites and microbiota for rhinitis and asthma)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differential expression of genera of bacteria between children with asthma and health controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:400/1/2,Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy control,asthma,child age 4-7 years with physician diagnosed asthma,24,34,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text (Association between gut metabolites and microbiota for rhinitis and asthma)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differential expression of genera of bacteria between children with asthma and health controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:400/2/1,Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,child age 4-7 years with physician diagnosed allergic rhinitis,24,27,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text",10 January 2021,Lucy Mellor,WikiWorks,Differential expression of genera of bacteria between children with allergic rhinitis and health controls,increased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,2|201174|84998|1643822|1643826|447020,Complete,Folakunmi
bsdb:400/2/2,Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,child age 4-7 years with physician diagnosed allergic rhinitis,24,27,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differential expression of genera of bacteria between children with allergic rhinitis and health controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330,Complete,Folakunmi
bsdb:401/1/1,Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Asthma,MONDO:0004979,healthy control,asthma,"child age 3-5 diagnosed as ever having asthma with the occurrence of recurrent wheeze in the last 12 months, or current use of asthma medication",32,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differences and comparisons of bacteria in phyla and genera among children with asthma and health controls,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,2|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:401/1/2,Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Asthma,MONDO:0004979,healthy control,asthma,"child age 3-5 diagnosed as ever having asthma with the occurrence of recurrent wheeze in the last 12 months, or current use of asthma medication",32,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differences and comparisons of bacteria in phyla and genera among children with asthma and health controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|1239|186801|3085636|186803|830;2|1239|1737404|1737405|1570339|543311,Complete,Claregrieve1
bsdb:401/2/1,Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,"child age 3-5 diagnosed as having symptoms such as sneezing, nasal congestion, itching, and rhinorrhea in the last 12 months",32,23,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 2, Text",10 January 2021,Lucy Mellor,WikiWorks,Differences and comparisons of bacteria in phlya and genera among children with allergic rhinitis and health controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota",2|1224|1236|2887326|468|475;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836;2|1224,Complete,Claregrieve1
bsdb:401/2/2,Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,"child age 3-5 diagnosed as having symptoms such as sneezing, nasal congestion, itching, and rhinorrhea in the last 12 months",32,23,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Table 2, Text",10 January 2021,Lucy Mellor,WikiWorks,Differences and comparisons of bacteria in phlya and genera among children with allergic rhinitis and health controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",2|1239|186801|3085636|186803|830;2|1224|1236|135625|712|416916;2|1239|186801|3085636|186803|437755,Complete,Claregrieve1
bsdb:402/1/1,Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,IgE associated eczema,1 week old Infants with typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index,8,6,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"delivery procedure,medical procedure",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,WikiWorks,"Relative abundance >1% of dominant phyla, classes, families and genera in stool samples at 1 week of age infants that remained non-allergic (controls) and in infants developing IgE-associated eczema",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,Folakunmi
bsdb:402/2/1,Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,mothers whose infants remained non-allergic,Mothers whose infants developed IgE associated eczema,Mothers whose infants developed typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index,10,9,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"delivery procedure,medical procedure",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,WikiWorks,"Relative abundance >1% of dominant phyla, classes, families and genera in stool samples of mothers who's infants that remained non-allergic (controls) or infants developed IgE-associated eczema",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:402/3/1,Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,vaginally delivered infant,caesarean delivered infant,infant born by caesarean section,7,7,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1a, Text (Effects of delivery mode on gut microbiome establishment )",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Folakunmi
bsdb:402/3/2,Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,vaginally delivered infant,caesarean delivered infant,infant born by caesarean section,7,7,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1a, Text (Effects of delivery mode on gut microbiome establishment )",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week,decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Folakunmi
bsdb:403/1/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia",2|1239|186801|3085636|186803|841;2|1224|1236|91347|1903409|551,Complete,Lwaldron
bsdb:403/1/2,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|547,Complete,Lwaldron
bsdb:403/2/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3b,10 January 2021,Lucy Mellor,"Lwaldron,WikiWorks",Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale",2|1239|186801;2|1239|186801|186802;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|31979|1485|137838,Complete,Lwaldron
bsdb:403/2/2,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Pseudomonadota",2|201174;2|201174|1760;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|216816|1679;2|1224,Complete,Lwaldron
bsdb:403/3/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3c,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,2|1224|1236|91347|1903409|551,Complete,Lwaldron
bsdb:403/3/2,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3c,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050,Complete,Lwaldron
bsdb:403/4/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3d,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",2|1239|909932|1843489|31977|29465|29466;2|976|200643|171549|815|816|817,Complete,Lwaldron
bsdb:403/4/2,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3d,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,2|201174|1760|85004|31953|1678|1681,Complete,Lwaldron
bsdb:403/5/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3e,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,2|1224|1236|91347|1903409|551,Complete,Lwaldron
bsdb:403/5/2,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3e,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",2|201174|1760|85004|31953|1678;2|1239|91061|186826|1300|1301;2|29547|3031852|213849|72294|194,Complete,Lwaldron
bsdb:403/6/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3f,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|201174;2|201174|1760;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|216816|1679;2|1224|1236|91347|543|547,Complete,Lwaldron
bsdb:403/7/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 1-2 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,10 January 2021,Lucy Mellor,"WikiWorks,Merit",Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|547;2|1224|1236|91347|543|570;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Lwaldron
bsdb:403/8/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 1-2 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3h,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years,decreased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Lwaldron
bsdb:403/9/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 2-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3i,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|201174|1760|85004|31953|1678;2|1224|28216|80840|995019|40544;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|200940|3031449|213115|194924|35832,Complete,Lwaldron
bsdb:403/10/1,Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 2-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3j,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota",2|1239|186801|3085636|186803;2|201174;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1224,Complete,Lwaldron
bsdb:404/1/1,Study 404,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,infants (<1 year old) diagnosed with atopic dermatitis based on the SCORAD scoring system,5,15,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|186802|216572|1263;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|140625;2|1239|909932|909929|1843491|158846;2|1239|186801|3085636|186803|207244;2|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:404/1/2,Study 404,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,infants (<1 year old) diagnosed with atopic dermatitis based on the SCORAD scoring system,5,15,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1224|1236|91347|543,Complete,Claregrieve1
bsdb:404/2/1,Study 404,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age 1-6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,15,58,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:404/2/2,Study 404,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age 1-6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,15,58,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810280|100883,Complete,Claregrieve1
bsdb:404/3/1,Study 404,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age >6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,22,17,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Bacterial genera that are distinctive between the AD and the non-AD patients age >6 years old,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella",2|1239|186801|3082720|186804;2|1239|186801|3085636|186803|588605,Complete,Claregrieve1
bsdb:404/3/2,Study 404,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age >6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,22,17,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Bacterial genera that are distinctive between the AD and the non-AD patients age >6 years old,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1239|186801|186802|216572|244127;2|976|200643|171549|1853231|574697;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|1239|186801|186802;2|1239|526524|526525|128827|61170;2|1239|186801|186802|541000;2|976|200643|171549|171552|577309;2|976|200643|171549|171551,Complete,Claregrieve1
bsdb:405/1/1,Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment",531,58,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:405/1/2,Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment",531,58,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:405/2/1,Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers with asthma,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment and mother with asthma",122,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Lucy Mellor,WikiWorks,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:405/2/2,Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers with asthma,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment and mother with asthma",122,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"WikiWorks,Suwaiba,Atrayees",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|976|200643|171549|171550|239759;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511;2|976|200643|171549|2005525|375288;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|946234;2|74201|203494|48461|1647988|239934,Complete,Atrayees
bsdb:405/3/1,Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers without asthma,child with asthma at 5 years old among mothers without asthma,409,33,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,20 July 2023,Atrayees,Atrayees,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to non-asthmatic mothers,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|1263;2|74201|203494|48461|1647988|239934,Complete,Atrayees
bsdb:405/3/2,Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers without asthma,child with asthma at 5 years old among mothers without asthma,409,33,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,20 July 2023,Atrayees,Atrayees,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to non-asthmatic mothers,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|207244;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|946234,Complete,Atrayees
bsdb:406/1/1,Study 406,case-control,30524957,10.3389/fonc.2018.00520,NA,"Yang J, Mu X, Wang Y, Zhu D, Zhang J, Liang C, Chen B, Wang J, Zhao C, Zuo Z, Heng X, Zhang C , Zhang L",Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers,Frontiers in oncology,2018,"biomarker, dysbiosis, lung cancer, non-smoking female patient, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,healthy controls,non-smoking female lung cancer patients,female and have confirmed diagnosis of non-small-cell lung cancer,172,75,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,"age,sex,smoking status",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"WikiWorks,Claregrieve1",Differentially abundant taxa between lung cancer and control groups,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Blastomonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales",2|1224|28211|204457|41297|150203;2|976|117743|200644;2|976|117743;2|1224|28216|80840|75682|963;2|1224|28216|80840|75682;2|1224;2|1224|28216|206389|75787;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|976|117743|200644|2762318;2|1224|28216|206389,Complete,Claregrieve1
bsdb:406/1/2,Study 406,case-control,30524957,10.3389/fonc.2018.00520,NA,"Yang J, Mu X, Wang Y, Zhu D, Zhang J, Liang C, Chen B, Wang J, Zhao C, Zuo Z, Heng X, Zhang C , Zhang L",Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers,Frontiers in oncology,2018,"biomarker, dysbiosis, lung cancer, non-smoking female patient, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,healthy controls,non-smoking female lung cancer patients,female and have confirmed diagnosis of non-small-cell lung cancer,172,75,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,"age,sex,smoking status",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between lung cancer and control groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacteroidota",2|1224|1236|2887326|468|469;2|1239|91061;2|976;2|1224|28216;2|1224|28216|80840;2|976|117743|200644|2762318|59732;2|1224|28216|80840|80864;2|1224|28216|80840|80864|283;2|1224|1236|91347;2|1224|1236|91347|543;2|1239;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|135614|32033;2|1224|1236|135614;2|1224|1236|72274|135621;2|976,Complete,Claregrieve1
bsdb:407/1/1,Study 407,prospective cohort,32733243,10.3389/fphar.2020.01000,NA,"Wang B, Zhang Y, Zhao Q, Yan Y, Yang T, Xia Y , Chen H",Patients With Reflux Esophagitis Possess a Possible Different Oral Microbiota Compared With Healthy Controls,Frontiers in pharmacology,2020,"biomarker, dysbiosis, high-throughput sequencing, oral microbiota, reflux esophagitis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Peptic esophagitis,EFO:1001095,healthy controls,reflux esophagus patients,symptoms such as heartburn and regurgitation were in accordance with the endoscopic criteria of Los Angeles Grade and taken no drugs as treatment,51,55,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,"Atrayees,WikiWorks",Bacterial taxa diversities between Reflux Esophigitis (RE) and healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Neomegalonemataceae|g__Neomegalonema",2|201174|84998|84999|1643824|1380;2|976|200643|171549;2|976|200643;2|976;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1224|28211|356|119045;2|1239|909932;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|909929;2|1239|526524|526525|128827|123375;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1224|28211|204455|2814874|356797,Complete,Atrayees
bsdb:407/1/2,Study 407,prospective cohort,32733243,10.3389/fphar.2020.01000,NA,"Wang B, Zhang Y, Zhao Q, Yan Y, Yang T, Xia Y , Chen H",Patients With Reflux Esophagitis Possess a Possible Different Oral Microbiota Compared With Healthy Controls,Frontiers in pharmacology,2020,"biomarker, dysbiosis, high-throughput sequencing, oral microbiota, reflux esophagitis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Peptic esophagitis,EFO:1001095,healthy controls,reflux esophagus patients,symptoms such as heartburn and regurgitation were in accordance with the endoscopic criteria of Los Angeles Grade and taken no drugs as treatment,51,55,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks,Merit",Bacterial taxa diversities between Reflux Esophigitis (RE) and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae|g__Granulicella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Lactivibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Wolinella,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Cyanobacteriota",2|201174|1760|2037;2|1224|1236|135625|712|416916;2|1239|91061|1385;2|1239|91061|1385|539003;2|1239|91061;2|1224|28216;2|1224|28216|80840;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|29547;2|1239|91061|186826|186828;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|538;2|1239|186801|3082720|3118655|44259;2|201174|1760|85004|31953|2701;2|1239|91061|1385|539738|1378;2|57723|204432|204433|204434|940557;2|976|200643|171549|171552|52228;2|1239|186801|3085636|186803|43994;2|508458|649775|649776|3029087|1508421;2|1239|91061|186826;2|201174|1760|85006|1268;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1224;2|1239|186801|186802|186806|113286;2|201174|1760|85006|1268|32207;2|203691|203692|136|137;2|203691|203692|136;2|203691|203692;2|203691;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775;2|508458;2|1239|186801|186802|68298;2|203691|203692|136|2845253|157;2|29547|3031852|213849|72293|843;2759|33090|35493;2|1117,Complete,Atrayees
bsdb:408/1/1,Study 408,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, Azad MB, Subbarao P, Mandhane P, Becker A, Sears MR, Kollmann TR, Mohn WW, Finlay BB , Turvey SE",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 3 months,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,DESeq2,0.05,TRUE,NA,"antibiotic exposure,cesarean section,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1a,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant OTUs Identified by Deseq2 analysis at 3 months,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239;2|1239|186801|186802|31979,Complete,Folakunmi
bsdb:408/1/2,Study 408,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, Azad MB, Subbarao P, Mandhane P, Becker A, Sears MR, Kollmann TR, Mohn WW, Finlay BB , Turvey SE",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 3 months,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,DESeq2,0.05,TRUE,NA,"antibiotic exposure,cesarean section,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1a,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant OTUs Identified by Deseq2 analysis at 3 months,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Folakunmi
bsdb:408/2/1,Study 408,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, Azad MB, Subbarao P, Mandhane P, Becker A, Sears MR, Kollmann TR, Mohn WW, Finlay BB , Turvey SE",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 1 year,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,DESeq2,0.05,TRUE,NA,"antibiotic exposure,delivery procedure,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1b,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant OTUs Identified by Deseq2 analysis at 1 year,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|186801|3085636|186803;2|201174|1760|85006|1268|32207,Complete,Folakunmi
bsdb:408/2/2,Study 408,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, Azad MB, Subbarao P, Mandhane P, Becker A, Sears MR, Kollmann TR, Mohn WW, Finlay BB , Turvey SE",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 1 year,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,DESeq2,0.05,TRUE,NA,"antibiotic exposure,delivery procedure,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1b,23 January 2024,Folakunmi,Folakunmi,Differentially abundant OTUs Identified by Deseq2 analysis at 1 year,decreased,NA,NA,Complete,Folakunmi
bsdb:409/1/1,Study 409,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA , Nagler CR",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy controls,IgE mediated cow's milk allergy,diagnosis of IgE mediated cow's milk allergy based on clinical history and level of IgE serum-specific anti-cow's milk proteins,20,19,4 weeks,16S,4,Illumina,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,"Figure 1d, Text (""The gut microbiota of cow's milk allergic infants exhibits significantly increased diversity and altered composition""), Supplemental Table 2",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:409/1/2,Study 409,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA , Nagler CR",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy controls,IgE mediated cow's milk allergy,diagnosis of IgE mediated cow's milk allergy based on clinical history and level of IgE serum-specific anti-cow's milk proteins,20,19,4 weeks,16S,4,Illumina,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 2,"Figure 1d, Text(""The gut microbiota of cow's milk allergic infants exhibits significantly increased diversity and altered composition""), Supplemental Table 2",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1224|1236|91347|543|561;2|1239|91061|186826|1300,Complete,Folakunmi
bsdb:409/2/1,Study 409,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA , Nagler CR",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,pre EHCF with LGG,post EHCF with LGG,cow milk allergic infants post treatment with EHCF with LGG,12,12,4 weeks,16S,4,Illumina,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,"text (""Treatment with LGG-supplemented EHCF increases the relative abundance of butyrate-producing bacteria and fecal butyrate levels""), Supplemental Table 2",24 January 2024,Folakunmi,Folakunmi,Differentially abundant taxa between pre EHCF with LGG and post EHCF with LGG groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|33042,Complete,Folakunmi
bsdb:409/3/1,Study 409,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA , Nagler CR",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Lactobacillus rhamnosus GG,NCBITAXON:568703,Post EHCF treatment,Post EHCF with LGG,cow milk allergic infants post treatment with EHCF with LGG,7,12,4 weeks,16S,4,Illumina,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,"Within text result (""Treatment with LGG-supplemented EHCF increases the relative abundance of butyrate-producing bacteria and fecal butyrate levels"", lines 10-12), supplemental table 2",24 January 2024,Folakunmi,Folakunmi,Differentially abundant taxa between Post EHCF and Post EHCF with LGG groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis",2|1239|186801|3085636|186803|841;2|1239|186801|186802|186806|264995,Complete,Folakunmi
bsdb:410/1/1,Study 410,"cross-sectional observational, not case-control",28118207,10.1097/QAD.0000000000001409,NA,"Nowak RG, Bentzen SM, Ravel J, Crowell TA, Dauda W, Ma B, Liu H, Blattner WA, Baral SD , Charurat ME","Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria","AIDS (London, England)",2017,NA,Experiment 1,Nigeria,Homo sapiens,Rectum,UBERON:0001052,HIV infection,EFO:0000764,HIV-uninfected MSM,ART-treated HIV infected MSM,Men who have sex with men (MSM) with HIV that has been treated with antiretroviral therapy (ART),55,34,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Michael Lutete,"WikiWorks,Folakunmi","Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1239|1737404|1737405|1570339|165779;2|29547|3031852|213849|72294|194;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289,Complete,Folakunmi
bsdb:410/1/2,Study 410,"cross-sectional observational, not case-control",28118207,10.1097/QAD.0000000000001409,NA,"Nowak RG, Bentzen SM, Ravel J, Crowell TA, Dauda W, Ma B, Liu H, Blattner WA, Baral SD , Charurat ME","Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria","AIDS (London, England)",2017,NA,Experiment 1,Nigeria,Homo sapiens,Rectum,UBERON:0001052,HIV infection,EFO:0000764,HIV-uninfected MSM,ART-treated HIV infected MSM,Men who have sex with men (MSM) with HIV that has been treated with antiretroviral therapy (ART),55,34,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Michael Lutete,"WikiWorks,Folakunmi","Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:411/1/1,Study 411,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM , Aldrovandi GM",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,"men who have sex with men (MSM), pre-exposure prophylaxis (PrEP), rectal microbiome",Experiment 1,United States of America,Homo sapiens,Rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,Linear Regression,0.1,TRUE,NA,"age,alcohol drinking,anal intercourse,drug dependence,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1, Figure 2, Text",10 January 2021,Michael Lutete,WikiWorks,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",2|1239|91061|186826|1300|1301;2|32066|203490|203491|203492|848;2|1239|909932|909929|1843491|52225,Complete,NA
bsdb:411/1/2,Study 411,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM , Aldrovandi GM",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,"men who have sex with men (MSM), pre-exposure prophylaxis (PrEP), rectal microbiome",Experiment 1,United States of America,Homo sapiens,Rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,Linear Regression,0.1,TRUE,NA,"age,alcohol drinking,anal intercourse,drug dependence,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1, Figure 2, Text",10 January 2021,Michael Lutete,WikiWorks,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,NA
bsdb:411/2/1,Study 411,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM , Aldrovandi GM",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,"men who have sex with men (MSM), pre-exposure prophylaxis (PrEP), rectal microbiome",Experiment 2,United States of America,Homo sapiens,Rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,NA,0.05,TRUE,NA,"age,alcohol drinking,anal intercourse,drug dependence,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2, Text",10 January 2021,Michael Lutete,WikiWorks,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
bsdb:412/1/1,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Rectum,UBERON:0001052,"HIV infection,Methamphetamine dependence","EFO:0000764,EFO:0004701",HIV-positive non-MA users,HIV-positive MA users,HIV-positive Men who have sex with men (MSM) who self-reported methamphetamine (MA) use in the past six months,81,101,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Table S2, Figure 3",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differential abundance of bacterial genera between HIV+ methamphetamine users and non-users,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|75984;2|1239|909932|1843489|31977|909928;2|32066|203490|203491|1129771|34104,Complete,Claregrieve1
bsdb:412/2/1,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,non-users,Methamphetamine users,MSM who self-reported methamphetamine (MA) use in the past six months,225,156,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Table S2",10 January 2021,Michael Lutete,WikiWorks,Differential abundance of bacterial genera between MA users and non-users,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|1239|1737404|1737405|1570339|1161127;2|1224|1236|135625|712|724;2|1239|186801|186802|186806|1730;2|1239|909932|1843489|31977|29465;2|201174|1760|85007|85029|37914;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|150022;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|1239|186801|3082720|186804|1257;2|1239|1737404|1737405|1570339|165779;2|1239|186801|3082720|3030910|86331,Complete,Claregrieve1
bsdb:412/2/2,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,non-users,Methamphetamine users,MSM who self-reported methamphetamine (MA) use in the past six months,225,156,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Table S2",10 January 2021,Michael Lutete,WikiWorks,Differential abundance of bacterial genera between MA users and non-users,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|1239|186801|186802|3085642|580596;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|1283313,Complete,Claregrieve1
bsdb:412/3/1,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,MSM who did not test positive on MA urine drug screening,MSM who tested positive on MA urine drug screening,MSM who tested positive for methamphetamine (MA) use in a urine drug screening,329,52,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Supplementary Figure S6, Results within text (Page 5, under subheading ""Dose-response analysis of bacterial counts on increasing frequency of MA use""",10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Sensitivity analysis using urine toxicology screening to define MA use,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|1239|1737404|1737405|1570339|165779;2|201174|1760|85007|1653|1716;2|201174|1760|85007|85029|37914;2|1239|186801|186802|186806|1730;2|1239|1737404|1737405|1570339|150022;2|32066|203490|203491|203492|848;2|1239|186801|3082720|3030910|86331;2|1239|1737404|1737405|1570339|1161127;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:412/3/2,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,MSM who did not test positive on MA urine drug screening,MSM who tested positive on MA urine drug screening,MSM who tested positive for methamphetamine (MA) use in a urine drug screening,329,52,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Figure 4-6",10 January 2021,Michael Lutete,WikiWorks,Sensitivity analysis using urine toxicology screening to define MA use,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Lentisphaerota|c__Oligosphaeria|o__Oligosphaerales|f__Oligosphaeraceae|g__Oligosphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|1239|186801|186802|216572|216851;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578;2|256845|1313207|1313208|1313209|1313210;2|1224|1236|135624|83763|83770,Complete,Claregrieve1
bsdb:412/4/1,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-positive men who have sex with men who did not test positive in a methamphetamine drug screening,HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening,HIV-positive Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,81,21,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Figure 4-6",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differential microbial abundance between MA+ and MA- stratified by HIV (Using urine toxicology screening to define MA use in HIV-positive MSM),increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,2|32066|203490|203491|1129771|34104,Complete,Claregrieve1
bsdb:412/4/2,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-positive men who have sex with men who did not test positive in a methamphetamine drug screening,HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening,HIV-positive Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,81,21,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Figure 4-6",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differential microbial abundance between MA+ and MA- in HIv+ patients (Using urine toxicology screening to define MA use in HIV-positive MSM),decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,2|1224|28216|80840|75682|846,Complete,Claregrieve1
bsdb:412/5/1,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 5,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-negative MSM who did not test positive in a MA drug screening,HIV-negative MSM who tested positive in a MA drug screening,HIV-negative Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,248,31,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Figure S6,10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks,ChiomaBlessing",Differential microbial abundance between MA+ and MA- in HIV- men,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Claregrieve1
bsdb:412/5/2,Study 412,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 5,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-negative MSM who did not test positive in a MA drug screening,HIV-negative MSM who tested positive in a MA drug screening,HIV-negative Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,248,31,NA,16S,4,Illumina,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Figure S6,10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks,ChiomaBlessing",Differential microbial abundance between MA+ and MA- in HIV- men,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|976|200643|171549|2005519|397864;2|1239|91061|186826|186828|117563;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|34104;2|1239|186801|186802|216572|292632,Complete,Claregrieve1
bsdb:413/1/1,Study 413,"cross-sectional observational, not case-control",32307692,10.1111/acps.13175,NA,"Turna J, Grosman Kaplan K, Anglin R, Patterson B, Soreni N, Bercik P, Surette MG , Van Ameringen M",The gut microbiome and inflammation in obsessive-compulsive disorder patients compared to age- and sex-matched controls: a pilot study,Acta psychiatrica Scandinavica,2020,"OCD, anxiety, cytokine, gut microbiota, gut-brain axis, inflammation",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,healthy controls,OCD,non-depressed medication free individuals or individuals with mild depressive symptoms (MADRS score<16) with a primary DSM-5 diagnosis of OCD as per the MINI or at least moderate OCD (Y-BOCS score >= 20),22,21,8 weeks,16S,3,Illumina,ANCOM,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,decreased,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Relative abundance of gut microbiome in OCD patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|1239|186801|186802|216572|119852;2|976|200643|171549|1853231|283168;2|1239|186801|3085636|186803|207244,Complete,Fatima
bsdb:414/1/1,Study 414,time series / longitudinal observational,30701077,10.1038/s41522-018-0073-2,NA,"Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterström CK, Allander T, Andersson B, Borenstein E, Dahlin M , Prast-Nielsen S",The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy,NPJ biofilms and microbiomes,2019,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,after keto diet,before keto diet,children with therapy resistent inoperabe epilepsy or a diagnosis of a neorometablic disorder in which KD is recommended,12,12,3 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",Statistical changes at all taxonomic levels during dietary interventaion (keto diet) using LEFse method,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",2|1239|186801|3085636|186803|1766253|39491;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|39948;2|201174;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|1680,Complete,Folakunmi
bsdb:414/1/2,Study 414,time series / longitudinal observational,30701077,10.1038/s41522-018-0073-2,NA,"Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterström CK, Allander T, Andersson B, Borenstein E, Dahlin M , Prast-Nielsen S",The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy,NPJ biofilms and microbiomes,2019,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,after keto diet,before keto diet,children with therapy resistent inoperabe epilepsy or a diagnosis of a neorometablic disorder in which KD is recommended,12,12,3 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Statistical changes at all taxonomic levels during dietary interventaion (keto diet) using LEFse method,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|561;2|1224|1236;2|1224|1236|91347|543;2|1224|1236|91347;2|1224,Complete,Folakunmi
bsdb:415/1/1,Study 415,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,Age-matched HIV-uninfected women,HIV-positive women who have been taking ART for more than 1 year,HIV-positive women who have been taking antiretroviral therapy (ART) for more than 1 year,3,3,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Differences in abundance of salivary bacteria between HIV uninfected women and HIV-positive women on ART,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|437755,Complete,Folakunmi
bsdb:415/2/1,Study 415,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,"HIV infection,Oral candidiasis","EFO:0000764,EFO:0007406",Age-matched HIV-uninfected womenn,HIV-positive women with oral candidiasis,HIV-positive women with oral candidiasis,3,3,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Differences in abundance of salivary bacteria between HIV uninfected women and HIV-positive women coinfected with oral candidiasis,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:415/3/1,Study 415,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Age,EFO:0000246,HIV uninfected women who are less than 35 years of age,HIV uninfected women who are 50 years of age or older,HIV-negative women who are 50 years of age or older,4,4,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Differences in abundance of salivary bacteria between young HIV uninfected women and old HIV uninfected women,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|437755,Complete,Folakunmi
bsdb:415/4/1,Study 415,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Coinfection,Age","EFO:0010716,EFO:0000246",young HIV-infected group without coinfection,aging HIV-infected women with coinfections,"aging HIV-infected women with coinfections; Hairy leukoplakia, oral candida, kaposi's sarcoma, HPV",4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5,24 August 2023,Atrayees,"Atrayees,Folakunmi",LEfSe was performed to identify statistically different bacterial taxa in their relative abundance between young adult HIV-infected women versus aging HIV-infected women with coinfection.,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria",2|200940|3031449|213115|194924|872|885;2|1239|91061|186826|33958|1578|1591;2|1239|91061|186826|33958|2742598|1598;2|200930|68337|191393|2945020|248038|248039;2|976|200643|171549|1853231|283168|1965233;2|1239|91061|186826|186827;2|1239|186801|186802|31979;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1357|44273;2|1239|186801|186802|216572|119852;2,Complete,Folakunmi
bsdb:415/4/2,Study 415,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Coinfection,Age","EFO:0010716,EFO:0000246",young HIV-infected group without coinfection,aging HIV-infected women with coinfections,"aging HIV-infected women with coinfections; Hairy leukoplakia, oral candida, kaposi's sarcoma, HPV",4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5,24 August 2023,Atrayees,Atrayees,LEfSe was performed to identify statistically different bacterial taxa in their relative abundance between young adult HIV-infected women versus aging HIV-infected women with coinfection.,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Mycoplasmatota",2|1239|526524|526525|128827|123375|102148;2|1239|526524|526525|128827|118747|2704657;2|1239|909932|1843489|31977|29465|29466;2|544448,Complete,Folakunmi
bsdb:416/1/1,Study 416,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR , Prendergast AJ",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,NA,Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,"HIV infection,Antimicrobial agent","EFO:0000764,CHEBI:33281",stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,"Text, Figure S3, Figure S2",10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis",2|976|200643|171549|815|816|371601;2|1224|1236|91347|543|561|562;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|328812;2|976|200643|171549|2005525|375288|387661;2|1239|186801|3085636|186803|841|166486;2|976|200643|171549|171550|239759|2585118,Complete,Atrayees
bsdb:416/1/2,Study 416,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR , Prendergast AJ",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,NA,Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,"HIV infection,Antimicrobial agent","EFO:0000764,CHEBI:33281",stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Text, Figure S3",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks,Atrayees",Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",2|1224|1236|135625|712|724|729;2|1239|526524|526525|128827|1573535|1735;2|1239|91061|186826|1300|1301|1318;2|1239|186801|186802|216572|216851|853;2|1239|91061|186826|1300|1301|1304;2|976|200643|171549|171550|239759|328813;2|1239|186801|3082720|186804|1505657|261299;2|201174|84998|1643822|1643826|84111|84112;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|1300|1301|1343,Complete,Atrayees
bsdb:417/1/1,Study 417,"cross-sectional observational, not case-control",30366816,10.1016/j.ebiom.2018.10.037,NA,"Moon JY, Zolnik CP, Wang Z, Qiu Y, Usyk M, Wang T, Kizer JR, Landay AL, Kurland IJ, Anastos K, Kaplan RC, Burk RD , Qi Q","Gut microbiota and plasma metabolites associated with diabetes in women with, or at high risk for, HIV infection",EBioMedicine,2018,"Diabetes, Gut microbiota, HIV, Metabolite",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"HIV infection,Diabetes mellitus","EFO:0000764,EFO:0000400",Women without diabetes,Women with diabetes,Women with or at high risk for HIV infection who have diabetes,26,22,NA,16S,4,Illumina,Linear Regression,0.1,TRUE,NA,NA,"HIV infection,age",NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Text, Figure 2, Table 2",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differentially abundant genera by diabetes status in women with HIV or at high risk for HIV,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|150022;2|32066|203490|203491|1129771|168808;2|201174|84998|1643822|1643826|447020,Complete,Claregrieve1
bsdb:418/1/1,Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological non-responders assigned to treatment for 12 weeks,HIV-infected immunological non-responders (INR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|200940|3031449|213115|194924|872;2|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:418/1/2,Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological non-responders assigned to treatment for 12 weeks,HIV-infected immunological non-responders (INR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979,Complete,Folakunmi
bsdb:418/2/1,Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological responders assigned to treatment for 12 weeks,HIV-infected immunological responders (IR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|200940|3031449|213115|194924|872;2|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:418/2/2,Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological responders assigned to treatment for 12 weeks,HIV-infected immunological responders (IR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979,Complete,Folakunmi
bsdb:419/1/1,Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks,Persons with HIV,27,27,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Text, Supplementary Figure 3",10 January 2021,Michael Lutete,WikiWorks,Effect of Probiotic LGG on Gut Microbiota Composition,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:419/1/2,Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks,Persons with HIV,27,27,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Text, Supplementary Figure 3",10 January 2021,Michael Lutete,WikiWorks,Effect of Probiotic LGG on Gut Microbiota Composition,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1224|1236|91347|543;2|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:419/3/1,Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,NA,Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,individuals with no change in uptake,individuals with decreased F-2-fluoro-2-deoxy-D-glucose (F-FDG) uptake on positron emission tomography (PET)/magnetic resonance imaging (MRI),Persons with HIV,7,5,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Text, Figure 2",10 January 2021,Michael Lutete,WikiWorks,Changes in relative abundance of Enterobacteriaceae after LGG supplementation in responders and nonresponders,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Claregrieve1
bsdb:420/1/1,Study 420,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B, Nowak P, Nwosu FC, Kvale D, Thalme A, Sonnerborg A, Ueland PM, Holm K, Birkeland SE, Dahm AE, Sandset PM, Rudi K, Hov JR, Dyrhol-Riise AM , Trøseid M",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,NA,Experiment 1,"Norway,Sweden",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline probiotic group,Probiotic group after 8 weeks of intervention,HIV-infected on antiretroviral therapy allocated to probiotic group after 8 weeks of intervention,11,11,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3 & Supplementary figure S4A,10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Gut microbiota composition after probiotic intervention at 8 weeks compared to baseline group (in HIV-infected individuals on stable antiretroviral therapy (ART)),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174|1760;2|1239;2|201174|1760|85004|31953|1678;2|1239|186801|186802|541000,Complete,ChiomaBlessing
bsdb:420/1/2,Study 420,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B, Nowak P, Nwosu FC, Kvale D, Thalme A, Sonnerborg A, Ueland PM, Holm K, Birkeland SE, Dahm AE, Sandset PM, Rudi K, Hov JR, Dyrhol-Riise AM , Trøseid M",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,NA,Experiment 1,"Norway,Sweden",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline probiotic group,Probiotic group after 8 weeks of intervention,HIV-infected on antiretroviral therapy allocated to probiotic group after 8 weeks of intervention,11,11,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3 & Supplementary figure S4A,10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Gut microbiota composition after probiotic intervention at 8 weeks compared to baseline group (in HIV-infected individuals on stable antiretroviral therapy (ART)),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota",2|976|200643|171549|815|816;2|976,Complete,ChiomaBlessing
bsdb:420/2/1,Study 420,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B, Nowak P, Nwosu FC, Kvale D, Thalme A, Sonnerborg A, Ueland PM, Holm K, Birkeland SE, Dahm AE, Sandset PM, Rudi K, Hov JR, Dyrhol-Riise AM , Trøseid M",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,NA,Experiment 2,"Norway,Sweden",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-probiotic intervention group (after 8 weeks),Probiotic intervention group (after 8 weeks),Probiotic intervention group (after 8 weeks),13,11,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Gut microbiota composition after probiotic intervention at 8 weeks compared to non-probiotic group (in HIV-infected individuals on stable antiretroviral therapy (ART)),increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:421/1/1,Study 421,randomized controlled trial,32708743,10.3390/nu12072112,NA,"Sainz T, Gosalbes MJ, Talavera-Rodríguez A, Jimenez-Hernandez N, Prieto L, Escosa L, Guillén S, Ramos JT, Muñoz-Fernández MÁ, Moya A, Navarro ML, Mellado MJ , Serrano-Villar S",Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study,Nutrients,2020,"HIV, children and adolescents, microbiota, vertical transmission",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-uninfected siblings or children born to HIV-infected mothers,Vertically HIV-infected children,Vertically HIV-infected children,10,23,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Text (results), Figure 4",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Comparison of basal samples from vertically HIV-infected children vs. healthy controls,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|74201|203494|48461|1647988|239934;2|1239|526524|526525|2810280|100883;2|1224|1236|91347|543|561;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:421/1/2,Study 421,randomized controlled trial,32708743,10.3390/nu12072112,NA,"Sainz T, Gosalbes MJ, Talavera-Rodríguez A, Jimenez-Hernandez N, Prieto L, Escosa L, Guillén S, Ramos JT, Muñoz-Fernández MÁ, Moya A, Navarro ML, Mellado MJ , Serrano-Villar S",Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study,Nutrients,2020,"HIV, children and adolescents, microbiota, vertical transmission",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-uninfected siblings or children born to HIV-infected mothers,Vertically HIV-infected children,Vertically HIV-infected children,10,23,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Text (results), Figure 4",28 December 2022,Claregrieve1,Claregrieve1,Comparison of basal samples from vertically HIV-infected children vs. healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|186807|51514;2|1239|91061|186826|1300|1357;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:422/1/1,Study 422,case-control,30518941,10.1038/s41598-018-35877-4,NA,"Kaur US, Shet A, Rajnala N, Gopalan BP, Moar P, D H, Singh BP, Chaturvedi R , Tandon R",High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy,Scientific reports,2018,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected age-matched controls,Perinatally HIV-infected children,Perinatally HIV-infected children,14,29,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,age,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Text, Figure 1, Figure 3, Table S1",10 January 2021,Michael Lutete,WikiWorks,Perinatally HIV-infected children show a distinct pattern of gut microbiota compared to uninfected controls,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",2|976;2|203691;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|906;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|909932|909929|1843491|970;2|1239|186801|186802|31979|1485;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067;2|1224|1236|91347|1903409|53335;2|1224|1236|135624|84642;2|32066;2|32066|203490;2|32066|203490|203491,Complete,Atrayees
bsdb:422/1/2,Study 422,case-control,30518941,10.1038/s41598-018-35877-4,NA,"Kaur US, Shet A, Rajnala N, Gopalan BP, Moar P, D H, Singh BP, Chaturvedi R , Tandon R",High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy,Scientific reports,2018,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected age-matched controls,Perinatally HIV-infected children,Perinatally HIV-infected children,14,29,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,age,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Text, Figure 1, Figure 3, Table S1",10 January 2021,Michael Lutete,"Aiyshaaaa,WikiWorks,Merit",Perinatally HIV-infected children show a distinct pattern of gut microbiota compared to uninfected controls,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Chloroflexota|c__Anaerolineae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales",2|201174;2|200795|292625;2|1239;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|186802|31979;2|1117;2|1239|186801|186802|186807|51514;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803;2|256845|1313211;2|256845;2|200795|292625|292629|292628|475961;2|1239|186801|186802|541000;2|74201|203494|48461|203557|48463;2|1224|28211|766;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|256845|1313211|278082|255528;2|256845|1313211|278082,Complete,Atrayees
bsdb:423/1/1,Study 423,case-control,32747678,10.1038/s41598-020-69845-8,https://pubmed.ncbi.nlm.nih.gov/32747678/,"Zeng Q, Shen J, Chen K, Zhou J, Liao Q, Lu K, Yuan J , Bi F",The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Amyotrophic lateral sclerosis,MONDO:0004976,Healthy controls,Amyotrophic lateral sclerosis - ALS patients,Patients clinically diagnosed with probably or definite ALS according to the revised El Escorial criteria in the neurology department.,20,20,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,age,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2F,14 January 2021,Fatima,"Fatima,Peace Sandy","The bar chart shows the biomarkers with diferential abundance between the groups and larger than the preset value (LDA score >4, p<0.05). The LDA score indicates the extent to which the corresponding group is affected by the diferential microbes.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549;2|976|200643;2|976;2|976|200643|171549|171551,Complete,Peace Sandy
bsdb:423/1/2,Study 423,case-control,32747678,10.1038/s41598-020-69845-8,https://pubmed.ncbi.nlm.nih.gov/32747678/,"Zeng Q, Shen J, Chen K, Zhou J, Liao Q, Lu K, Yuan J , Bi F",The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Amyotrophic lateral sclerosis,MONDO:0004976,Healthy controls,Amyotrophic lateral sclerosis - ALS patients,Patients clinically diagnosed with probably or definite ALS according to the revised El Escorial criteria in the neurology department.,20,20,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,age,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2F,14 January 2021,Fatima,"Fatima,Peace Sandy","The bar chart shows the biomarkers with diferential abundance between the groups and larger than the preset value (LDA score >4, p<0.05). The LDA score indicates the extent to which the corresponding group is affected by the diferential microbes.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1239|909932|909929|1843491|158846;2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489|31977;2|1239|909932|909929|1843491|158846,Complete,Peace Sandy
bsdb:424/1/1,Study 424,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,Pancreatic cancer patients,Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.,13,30,8 weeks,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2a,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1",Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",2|74201|203494|48461|1647988|239934;2|976|200643|171549;2|1239|909932|1843489|31977|906;2|976|200643|171549|1853231|283168;2|1239|909932|1843489|31977;2|1239|186801|3085636|186803|1898203,Complete,Claregrieve1
bsdb:424/1/2,Study 424,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,Pancreatic cancer patients,Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.,13,30,8 weeks,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2a,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1",Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|s__uncultured bacterium",2|1239|186801|3085636|186803|207244;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|186802|541000;2|1239|186801|186802|216572|292632;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|216572|2485925;2|77133,Complete,Claregrieve1
bsdb:424/3/1,Study 424,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 3,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,NBO PC,BO PC,Bile duct-obstructed pancreatic cancer patients.,16,11,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3b,4 February 2021,Yu Wang,"Yu Wang,Fatima",Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,2|1239|186801|3085636|186803|572511,Complete,Claregrieve1
bsdb:424/3/2,Study 424,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 3,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,NBO PC,BO PC,Bile duct-obstructed pancreatic cancer patients.,16,11,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3b,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1",Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|909929;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:424/4/1,Study 424,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 4,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,NBO PC,Non-Bile duct-obstructed pancreatic cancer patients.,13,16,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3c,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1",Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 001,k__Bacteria|p__Mycoplasmatota|c__Mollicutes",2|1239|186801|186802|216572|216851;2|1239|186801|186802|541000;2|1239|186801|186802|31979|1485|1970093;2|544448|31969,Complete,Claregrieve1
bsdb:424/4/2,Study 424,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 4,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,NBO PC,Non-Bile duct-obstructed pancreatic cancer patients.,13,16,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3c,4 February 2021,Yu Wang,"Claregrieve1,Fatima,Yu Wang",Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|74201|203494|48461|1647988|239934;2|976|200643|171549,Complete,Claregrieve1
bsdb:425/1/1,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,34,38,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2c,17 February 2021,Manuela,Manuela,NA,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Lwaldron
bsdb:425/1/2,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,34,38,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2c,17 February 2021,Manuela,Manuela,NA,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Verrucomicrobiota",2|976;2|74201,Complete,Lwaldron
bsdb:425/2/1,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Middle Altitude (MHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,49,38,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2g,17 February 2021,Manuela,Manuela,NA,decreased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Pseudomonadota",2|95818;2|1224,Complete,Lwaldron
bsdb:425/2/2,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Middle Altitude (MHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,49,38,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2g,17 February 2021,Manuela,Manuela,NA,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Lwaldron
bsdb:425/3/1,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2d,17 February 2021,Manuela,Manuela,NA,decreased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota",2|95818;2|32066;2|1224,Complete,Lwaldron
bsdb:425/3/2,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2d,17 February 2021,Manuela,Manuela,NA,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Lwaldron
bsdb:425/4/1,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Middle Altitude (MHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2h,17 February 2021,Manuela,Manuela,NA,decreased,k__Bacteria|p__Candidatus Saccharibacteria,2|95818,Complete,Lwaldron
bsdb:425/5/1,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Han Hypertensive at Middle Altitude (MHH),Han hypertensive participants living at middle altitude.,34,49,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2e,17 February 2021,Manuela,Manuela,NA,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Lwaldron
bsdb:425/5/2,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Han Hypertensive at Middle Altitude (MHH),Han hypertensive participants living at middle altitude.,34,49,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2e,17 February 2021,Manuela,Manuela,NA,increased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Verrucomicrobiota",2|57723;2|976;2|95818;2|544448;2|74201,Complete,Lwaldron
bsdb:425/6/1,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Han Healthy at Middle Altitude (MHN),Han healthy participants living at middle altitude.,35,35,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2f,17 February 2021,Manuela,Manuela,NA,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Lwaldron
bsdb:425/6/2,Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Han Healthy at Middle Altitude (MHN),Han healthy participants living at middle altitude.,35,35,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2f,17 February 2021,Manuela,Manuela,NA,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota",2|1239;2|32066,Complete,Lwaldron
bsdb:426/1/1,Study 426,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y, Li Y, Yan L, Sun C, Miao Q, Wang Q, Xiao X, Lian M, Li B, Chen Y, Zhang J, Li Y, Huang B, Li Y, Cao Q, Fan Z, Chen X, Fang JY, Gershwin ME, Tang R , Ma X",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,"autoimmune hepatitis, intestinal microbiology",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex","age,antibiotic exposure,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,25 February 2021,Valentina,Valentina,LDA effect size analysis of 11 genera was significantly different between AIH and the control group.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:426/1/2,Study 426,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y, Li Y, Yan L, Sun C, Miao Q, Wang Q, Xiao X, Lian M, Li B, Chen Y, Zhang J, Li Y, Huang B, Li Y, Cao Q, Fan Z, Chen X, Fang JY, Gershwin ME, Tang R , Ma X",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,"autoimmune hepatitis, intestinal microbiology",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex","age,antibiotic exposure,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,3 March 2021,Valentina,"Valentina,Atrayees",LDA effect size analysis of taxa that was significantly different between AIH and the control group.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:426/2/NA,Study 426,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y, Li Y, Yan L, Sun C, Miao Q, Wang Q, Xiao X, Lian M, Li B, Chen Y, Zhang J, Li Y, Huang B, Li Y, Cao Q, Fan Z, Chen X, Fang JY, Gershwin ME, Tang R , Ma X",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,"autoimmune hepatitis, intestinal microbiology",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,NA,16S,34,Illumina,Logistic Regression,0.05,FALSE,NA,"age,body mass index,sex","age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:427/1/1,Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegetarians,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table S2,11 February 2021,Lorakasselman,"Lorakasselman,Claregrieve1",Differential microbial abundance between omnivores and vegetarians,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,2|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:427/1/2,Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegetarians,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Table S2,1 January 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between omnivores and vegetarians,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977,Complete,NA
bsdb:427/2/1,Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegans,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S2,11 February 2021,Lorakasselman,"Lorakasselman,Claregrieve1",Differential microbial abundance between omnivores and vegans,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|28050;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:427/2/2,Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegans,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S2,1 January 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between omnivores and vegans,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:427/3/1,Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegans,vegetarians,individuals who do not eat meat but do eat other animal products,51,51,3 months,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S2,1 January 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between vegetarians and vegans,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,2|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:428/1/1,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs,78,87,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,28 May 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|33039;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|47678;2|74201|203494|48461|1647988|239934|239935,Complete,Fatima
bsdb:428/1/2,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs,78,87,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,28 May 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans",2|201174|1760|85004|31953|1678|1680;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|292632;2|201174|1760|85004|31953|1678|28026;2|1239|186801|186802|216572|216851|853;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330|39486,Complete,Fatima
bsdb:428/2/1,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs,78,13,Patients whose COVID-19 treatment included antibiotics were excluded,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|201174|1760|85004|31953|1678|1689;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|2719313|208479;2|1239|91061|186826|33958|2767887|1623;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|375288|1869337;2|976|200643|171549|171552|2974251|165179;2|1239|186801|186802|216572|1263|457412;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|3085636|186803|1506553|1512,Complete,Fatima
bsdb:428/2/2,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs,78,13,Patients whose COVID-19 treatment included antibiotics were excluded,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|976|200643|171549|171550|239759|28117;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|28026;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|216572|292632,Complete,Fatima
bsdb:428/3/1,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,"Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs, treated with antibiotics during course of COVID-19",78,14,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",2|201174|1760|85004|31953|1678|1689;2|1239|91061|186826|33958|2767887|1623;2|976|200643|171549|2005525|375288|823;2|1239|91061|186826|81852|1350|1351;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|1506553|1512;2|1239|909932|1843489|31977|29465|29466,Complete,Fatima
bsdb:428/3/2,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,"Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs, treated with antibiotics during course of COVID-19",78,14,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|216851|853;2|201174|1760|85004|31953|1678|28026;2|1239|186801|186802|216572|292632;2|201174|84998|84999|84107|102106|74426;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|186802|216572|1263|457412;2|1239|186801|3085636|186803|572511|40520;2|976|200643|171549|171552|2974251|165179;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|976|200643|171549|171550|239759|28117;2|1239|91061|186826|1300|1301|1304;2|1239|186801|3085636|186803|2569097|39488,Complete,Fatima
bsdb:428/4/1,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients treated with antibiotics,"Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs, treated with antibiotics",78,34,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S3,11 June 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples from patients were treated with antibiotics and non-COVID-19 samples,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.",2|201174|1760|85004|31953|1678|1680;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|216572|292632|2053618;2|1224|1236|91347|543|570|573;2|201174|84998|1643822|1643826|447020|446660;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|216572|1535;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|186802|216572|292632|665956;2|1239|91061|186826|81852|1350|33945;2|1239|186801|186802|186806|1730|39496;2|1224|1236|91347|543|544|1896336,Complete,Fatima
bsdb:428/4/2,Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients treated with antibiotics,"Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs, treated with antibiotics",78,34,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S3,11 June 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples from patients were treated with antibiotics and non-COVID-19 samples,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium|s__Cryptobacterium curtum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella|s__Shuttleworthella satelles,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia|s__Parascardovia denticolens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. ICM7,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.",2|1239|186801|3085636|186803|2569097|39488;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|28116;2|1239|186801|186802|216572|1263|457412;2|201174|1760|85004|31953|196081|78259;2|201174|1760|85009|31957|1912216|1747;2|201174|84998|1643822|1643826|84162|84163;2|1239|186801|3085636|186803|177971|177972;2|201174|1760|85004|31953|196082|78258;2|1239|91061|186826|81852|1350|1353;2|1239|186801|3085636|186803|1164882|936594;2|1239|186801|3085636|186803|265975|652706;2|1239|186801|3085636|186803|658089;2|201174|84998|1643822|1643826|84108|2049041;2|201174|84998|84999|1643824|133925|138595;2|1239|186801|3085636|186803|33042|116085;2|201174|84998|84999|1643824|2767353|1383;2|1239|91061|1385|90964|1279|1280;2|201174|1760|85006|1268|32207|172042;2|1239|91061|186826|186827|46123|46125;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|1213720|796942;2|1239|91061|1385|90964|1279|1282;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|186802|186806|1730|39490;2|201174|1760|85004|31953|196081|230143;2|1224|28216|80840|995019|40544|40545;2|976|200643|171549|171550|239759|328813;2|1239|526524|526525|2810280|100883;2|201174|84998|84999|1643824|133925|133926;2|976|200643|171549|2005525|375288|1869337,Complete,Fatima
bsdb:429/1/1,Study 429,case-control,32937864,https://doi.org/10.3390/cancers12092619,NA,"Gunathilake M, Lee J, Choi IJ, Kim YI, Yoon J, Sul WJ, Kim JF , Kim J",Alterations in Gastric Microbial Communities Are Associated with Risk of Gastric Cancer in a Korean Population: A Case-Control Study,Cancers,2020,"case-control, gastric cancer, gastric microbiome, microbial dysbiosis index, pathways",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy controls,gastric cancer patients,"patients with histologically confirmed early gastric cancer (invasive carcinoma confined to the mucosa, regardless of lymph node metastasis status) within the preceding 3 months",288,268,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,increased,Signature 1,Figure 2,29 June 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between gastric cancer patients and healthy controls,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|29547|3031852|213849|72294|194|197;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:429/1/2,Study 429,case-control,32937864,https://doi.org/10.3390/cancers12092619,NA,"Gunathilake M, Lee J, Choi IJ, Kim YI, Yoon J, Sul WJ, Kim JF , Kim J",Alterations in Gastric Microbial Communities Are Associated with Risk of Gastric Cancer in a Korean Population: A Case-Control Study,Cancers,2020,"case-control, gastric cancer, gastric microbiome, microbial dysbiosis index, pathways",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy controls,gastric cancer patients,"patients with histologically confirmed early gastric cancer (invasive carcinoma confined to the mucosa, regardless of lymph node metastasis status) within the preceding 3 months",288,268,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,increased,Signature 2,Figure 2,29 June 2022,Claregrieve1,"Claregrieve1,Merit",Differential microbial abundance between gastric cancer patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella taiwanensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",2|1239|91061|1385|539738|1378|1179787;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|28133;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1306,Complete,Claregrieve1
bsdb:430/1/1,Study 430,prospective cohort,32690600,10.1136/gutjnl-2020-322294,NA,"Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK , Ng SC",Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19,Gut,2021,"diagnostic virology, gut inflammation, infectious disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Patients with low-to-none SARS CoV-2 infectivity,Patients with high SARS CoV-2 infectivity,"SARS CoV-2 infection confirmed by two consecutive RT-OCR tests. High SARS-CoV2 infectivity defined as higher 3' vs 5', end coverage of SARS CoV-2 genome in fecal viral RNA metagenome.",15,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 March 2021,Fatima,"Fatima,Claregrieve1",Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii",2|976|200643|171549|815|816|46506;2|1239|186801|3085636|186803|1898203;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171550|239759|328813,Complete,Fatima
bsdb:430/1/2,Study 430,prospective cohort,32690600,10.1136/gutjnl-2020-322294,NA,"Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK , Ng SC",Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19,Gut,2021,"diagnostic virology, gut inflammation, infectious disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Patients with low-to-none SARS CoV-2 infectivity,Patients with high SARS CoV-2 infectivity,"SARS CoV-2 infection confirmed by two consecutive RT-OCR tests. High SARS-CoV2 infectivity defined as higher 3' vs 5', end coverage of SARS CoV-2 genome in fecal viral RNA metagenome.",15,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,4 March 2021,Fatima,"Fatima,Claregrieve1",Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis",2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107|102106|626935;2|1224|1236|91347|1903414|581|582;2|1239|91061|186826|1300|1301|68892,Complete,Fatima
bsdb:431/1/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,18 March 2021,Cynthia Anderson,"Cynthia Anderson,Fatima",Differential florae types in the comparison of the microbiota between high-risk human papillomavirus (HPV) persistent infection higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Commensalibacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Stappia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",2|1224|28216|80840|506|222;2|1224|28216|80840|80864|283;2|1224|28211|204441|433|1079922;2|1239|1737404|1737405|1570339|162290;2|1224|1236|135619|28256|2745;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|1224|1236|135614|32033|68;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045|407;2|201174|1760|85009|85015|1839;2|1224|28211|204455|31989|265;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|75682|1522432;2|1224|1236|72274|135621|286;2|201174|1497346|588673|320599|207599;2|1224|28211|356|2821832|152161;2|1239|186801|3085636|186803|84036;2|1297|188787|68933|188786|270,Complete,Fatima
bsdb:431/2/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 2,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with LSIL,transient HPV+ with HSIL,high-risk HPV transient infection (HPV has regressed within 1 year) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,19 March 2021,Cynthia Anderson,Cynthia Anderson,comparison of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum",2|1224|1236|135614|32033;2|1239|526524|526525|128827|1522,Complete,Fatima
bsdb:431/3/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 3,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,transient HPV+ with LSIL,high-risk HPV transient infection (HPV has regressed within 1 year) with low grade squamus intraepithelial lesion,31,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,19 March 2021,Cynthia Anderson,Cynthia Anderson,Comparison of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|32066|203490|203491|1129771|168808;2|1239|186801|3085636|186803|177971;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827|1522;2|1239|909932|1843489|31977|906;2|1224|28211|356|2831106|46913;2|1224|1236|135614|32033;2|201174|1760|85004|31953|2701,Complete,Fatima
bsdb:431/4/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 4,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with high grade squamus intraepithelial lesion,31,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,19 March 2021,Cynthia Anderson,"Cynthia Anderson,Fatima",Comparison of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|1239|909932|1843489|31977|906;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|177971;2|32066|203490|203491|1129771|168808,Complete,Fatima
bsdb:431/5/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 5,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,2|1239|91061|186826|1300|1301|1311,Complete,Fatima
bsdb:431/5/2,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 5,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter|s__Pseudarthrobacter oxydans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Deinococcota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Deinococcota|c__Deinococci,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|186801|186802|216572|216851;2|1239|91061|1385|186818;2|201174|1760|85007|1653|1716|38304;2|201174|1760|85007|2805586|1847725;2|1239|526524|526525;2|201174|1760|85006|1268;2|201174|1760|85006|1268|1742993|1671;2|201174|1760|85007|1653|1716|169292;2|1239|1737404|1737405|1570339|162289;2|201174|1760|2037|2049;2|1239|1737404|1737405|1570339|165779;2|1239|186801|3085636|186803|2316020|33039;2|976|200643|171549|171552|838|28130;2|201174|1760|85007|85025;2|1239|909932|1843489|31977|39948;2|1297;2|201174|1760|2037;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|2701;2|1297|188787;2|1239|91061|186826|33958|1243;2|1224|28216|32003|206379;2|1224|1236|135614;2|1239|186801|186802|404402;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|2981628|755172;2|201174|1760|85004|31953|1678|1689;2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964;2|1239|91061|1385;2|1239|91061|186826|81852|1350|53345;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|91061|186826|33958|2767887|1624;2|1239|909932|1843489|31977|39948|309120;2|1239|909932|909929;2|1239|909932;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|91061|186826|1300,Complete,Fatima
bsdb:431/6/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 6,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with HSIL,persistent HPV+ with LSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,2|1239|186801|3085636|186803|2316020|33039,Complete,Fatima
bsdb:431/6/2,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 6,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with HSIL,persistent HPV+ with LSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Eukaryota|k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichinellidae|g__Trichinella|s__Trichinella pseudospiralis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gelidilacus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides faecis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas",2|976|200643|171549|171551|836;2759|33208|6231|119088|6329|6332|6333|6337;2|1239|909932|1843489|31977|1567;2|1239|186801|3085636|186803|1506577;2|976|117743|200644|49546|237|206041;2|976|200643|171549|2005525|375288|1217282;2|1224|28216|206389|2008795|73029,Complete,Fatima
bsdb:431/7/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 7,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with LSIL,transient HPV+ with HSIL,high-risk HPV transient infection with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV transient infection with HSIL group and high-risk HPV transient infection with LSIL group,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella|s__Dyella koreensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gelidilacus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides faecis",2|976|117743;2|976|117743|200644;2|976|117743|200644|2762318|501783;2|1239|91061|186826|33958|1578;2|1224|1236|135614|1775411|231454|311235;2|976|117743|200644|49546|237|206041;2|1224|1236|135614|1775411|231454;2|976|200643|171549|2005525|375288|1217282,Complete,Fatima
bsdb:431/8/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 8,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,transient HPV+ with LSIL,high-risk HPV transient infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4D,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia|s__Devosia riboflavina,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1224|28211|356|2831106|46913|46914;2|95818;2|32066|203490|203491|1129771|168808;2|1239|91061|186826|33958|1578;2|1224|1236|72274|135621|286;2|1239|186801|3085636|186803|177971;2|32066|203490|203491|1129771;2|1239|186801|186802|541000;2|1224|1236|72274|135621,Complete,Fatima
bsdb:431/9/1,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 9,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,increased,"k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella",2|201174|1497346|588673;2|1224|1236|91347|1903414|581,Complete,Fatima
bsdb:431/9/2,Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 9,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus equicursoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|39948;2|1239|91061|186826|33958|1578|420645;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544;2|1239|186801|3082720|186804|1257;2|1224|1236|72274|135621|286;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171552|838|28130;2|1239|186801|186802|541000,Complete,Fatima
bsdb:432/1/1,Study 432,"cross-sectional observational, not case-control",33490017,10.3389/fpubh.2020.587298,NA,"Wei ZT, Chen HL, Wang CF, Yang GL, Han SM , Zhang SL",Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection,Frontiers in public health,2020,"16s rRNA, bacterial vaginosis, human papillomavirus, persistent infection, vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by Hybrid Capture II assay,30,30,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2E,19 March 2021,Cynthia Anderson,Cynthia Anderson,Bacterial taxa analysis of the HPV-positive and HPV-negative groups.,increased,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,2|544448|31969|2085|2092|2093,Complete,Claregrieve1
bsdb:432/1/2,Study 432,"cross-sectional observational, not case-control",33490017,10.3389/fpubh.2020.587298,NA,"Wei ZT, Chen HL, Wang CF, Yang GL, Han SM , Zhang SL",Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection,Frontiers in public health,2020,"16s rRNA, bacterial vaginosis, human papillomavirus, persistent infection, vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by Hybrid Capture II assay,30,30,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2E,19 March 2021,Cynthia Anderson,"Cynthia Anderson,Claregrieve1",Bacterial taxa analysis of the HPV-positive and HPV-negative groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae|g__Sporolactobacillus",2|1239|91061;2|1239|91061|186826;2|1239|91061|1385|186821;2|1239|91061|1385|186821|2077,Complete,Claregrieve1
bsdb:433/1/1,Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 1,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN 2+,Patients with cervical intraepithelial neoplasia 2 or higher,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 2A, 2B, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees",Comparative analysis of vaginal microbiota profiles,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota",2|201174|1760|85004|31953|2701;2|201174;2|976,Complete,Atrayees
bsdb:433/1/2,Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 1,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN 2+,Patients with cervical intraepithelial neoplasia 2 or higher,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 2A, 2B, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees",Comparative analysis of vaginal microbiota profiles,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826,Complete,Atrayees
bsdb:433/2/1,Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 2,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,Patients with cervical cancer,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,"Figure 2C, 2D, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees",Comparative analysis of vaginal microbiota profiles,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|165779;2|1239|186801;2|1239|1737404|1737405;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|200643|171549;2|976|200643;2|1239;2|1224,Complete,Atrayees
bsdb:433/2/2,Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 2,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,Patients with cervical cancer,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,"Figure 2C, 2D, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees",Comparative analysis of vaginal microbiota profiles,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Actinomycetota",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826;2|201174,Complete,Atrayees
bsdb:434/1/1,Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,healthy control,HPV +,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,2|1239|909932|1843489|31977|906,Complete,Atrayees
bsdb:434/2/1,Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,LSIL,women with low-grade squamous intraepithelial lesions confirmed by biopsy,78,51,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,2|976|200643|171549|171552|838|419005,Complete,Atrayees
bsdb:434/3/1,Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 3,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,HSIL,women with high-grade squamous intraepithelial lesions confirmed by biopsy,68,23,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis",2|976|200643|171549|171552|838;2|1239|186801;2|1239|186801|186802;2|976|200643|171549|171552;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|177971;2|1239|91061|186826|1300;2|976|200643|171549|171552|2974257|386414,Complete,Atrayees
bsdb:434/4/1,Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 4,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical cancer,MONDO:0002974,healthy control,cervical cancer,women with cervical cancer confirmed by biopsy,68,9,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus|s__Oceanobacillus profundus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis",2|1239|91061|1385;2|32066|203490|203491;2|32066|203490;2|32066;2|1239|91061|1385|186817;2|1224;2|1239|91061|1385|186817|1386;2|976|200643;2|976|200643|171549;2|976;2|1224|28216;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771;2|1224|28216|80840|80864;2|1224|28216|80840;2|1224|28216|80840|80864|12916;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|1239|91061|1385|186817|182709;2|1239|91061|1385|186817|182709|372463;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977;2|1239|909932;2|1239|909932|909929;2|1239|186801|186802;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|171551|836|281920,Complete,Atrayees
bsdb:434/5/1,Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 5,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,Healthy control,HPV+,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Fig 3, 4",28 June 2023,Atrayees,Atrayees,Relative abundance of taxa across the samples,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",2|976;2|32066|203490;2|1224;2|976|200643|171549|171552|838;2|1239|91061|1385|186817|1386;2|32066|203490|203491|1129771|168808;2|1239|909932|1843489|31977|906;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|165779,Complete,Atrayees
bsdb:434/5/2,Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 5,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,Healthy control,HPV+,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,"Figure 3, 4",28 June 2023,Atrayees,Atrayees,Relative abundance of taxa across the samples,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",2|1239;2|201174|84998|84999|1643824|1380,Complete,Atrayees
bsdb:435/1/1,Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls and HPV+ transient patients,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,9,6,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,LEfSe Analysis. A: LDA value distribution histogram,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium papyrosolvens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1224;2|1224|28211;2|201174;2|1239|186801;2|1239|186801|186802;2|1224|28211|356;2|976;2|976|200643;2|1224|1236;2|1224|28211|356|82115;2|1224|28211|356|69277|28100;2|1239|909932|1843489|31977;2|976|200643|171549;2|976|200643|171549|171552;2|1224|28211|204457;2|1224|28211|204457|41297;2|1224|28211|204457|41297|13687;2|1239|1737404|1737405|1570339|165779;2|1224|28211|204457|41297|13687|68569;2|976|200643|171549|171552|838;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|815|909656|310298;2|1224|28216|80840|119060;2|1239|186801|186802|216572|1508657|29362;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|162289,Complete,Folakunmi
bsdb:435/1/2,Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls and HPV+ transient patients,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,9,6,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,Folakunmi",LEfSe Analysis. A: LDA value distribution histogram,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|1239|91061;2|1239;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:435/2/1,Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 2,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls and HPV+ persistent patients,HPV+ transient,HPV infection cleared within 12 months,11,4,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,LEfSe Analysis. A: LDA value distribution histogram,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,2|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:435/3/1,Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 3,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV+ transient,HPV+ persistent,patients whose HPV infection persisted for 12 months,6,4,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,supplementary figure s1,6 February 2024,Folakunmi,Folakunmi,Lefse analysis between  persistent HPV infection group and transient HPV infection group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota",2|976|200643|171549|171552;2|1224|28216|80840|119060;2|1224|1236;2|1224|28211|204457|41297|13687|68569;2|1224|28211|204457|41297|13687;2|976|200643|171549|171552;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|356|69277|28100;2|976|200643|171549;2|1224|28211|356|82115;2|1239|186801;2|1239|186801|186802;2|976|200643;2|201174;2|1224|1236;2|1224|28211;2|1224,Complete,Folakunmi
bsdb:435/3/2,Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 3,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV+ transient,HPV+ persistent,patients whose HPV infection persisted for 12 months,6,4,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,supplementary figure s1,6 February 2024,Folakunmi,Folakunmi,Lefse analysis between persistent HPV infection group and transient HPV infection group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria",2|1239|91061;2|1239;2|1239|91061|186826|81850;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|147802;2,Complete,Folakunmi
bsdb:435/4/1,Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,5,6,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,supplementary figure s1,9 February 2024,Folakunmi,Folakunmi,Lefse analysis between persistent HPV infection group and transient HPV infection group,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota",2|32066|203490|203491|1129771|168808|40543;2|1224|1236|135622|267889|28228;2|1224|1236|135622|267889;2|976|117743|200644|246874;2|976|200643|171549|1853231|283168;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552;2|1224|28216|80840|119060;2|1224|1236;2|976|200643|171549|171552|838;2|32066|203490|203491;2|32066|203490;2|1224|1236|91347|543;2|1224|1236|91347;2|1239|1737404|1737405|1570339|165779;2|1117;2|1224|28211|204457|41297|13687|68569;2|1224|28211|204457|41297;2|976|117747|200666;2|1224|28211|204457|41297|13687;2|1239|186801|186802;2|976|200643|171549|171552;2|1224|28211|356|69277|28100;2|1224|28211|356|82115;2|1224|28211|356;2|976|200643|171549;2|1224|1236;2|976|200643;2|1239|909932|1843489|31977;2|1239|909932|909929;2|1239|909932;2|201174;2|201174;2|1224|28211;2|1224,Complete,Folakunmi
bsdb:435/4/2,Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,5,6,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,supplementary figure s1,9 February 2024,Folakunmi,Folakunmi,Lefse analysis between persistent HPV infection group and transient HPV infection group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|1385|186817|1386;2|1239;2|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:436/1/1,Study 436,"cross-sectional observational, not case-control",32941440,10.1371/journal.pone.0238705,NA,"So KA, Yang EJ, Kim NR, Hong SR, Lee JH, Hwang CS, Shim SH, Lee SJ , Kim TJ",Changes of vaginal microbiota during cervical carcinogenesis in women with human papillomavirus infection,PloS one,2020,NA,Experiment 1,South Korea,Homo sapiens,Vaginal fluid,UBERON:0036243,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN2+/cervical cancer,patients with cervical intraepithelial neoplasia 2+ or cervical cancer confirmed by biopsy,10,20,NA,16S,34,Illumina,Chi-Square,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,21 March 2021,Cynthia Anderson,"Cynthia Anderson,Claregrieve1",Differential microbial abundance between healthy controls and patients with cervical disease with CIN 2 or 3 and cervical cancer,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis",2|1239|909932|1843489|31977|39948|218538;2|201174|84998|84999|1643824|2767327|82135;2|1239|1737404|1737405|1570339|150022|1260;2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171552|2974257|28127;2|976|200643|171549|171552|2974257|386414,Complete,Claregrieve1
bsdb:437/1/1,Study 437,"cross-sectional observational, not case-control",32656096,10.3389/fcimb.2020.00286,NA,"Yang Q, Wang Y, Wei X, Zhu J, Wang X, Xie X , Lu W",The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing,Frontiers in cellular and infection microbiology,2020,"HPV infection, cervical cancer, metabolism, shotgun metagenomic sequencing, vaginal microbiome",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,Healthy control,HPV-16+,Patients with HPV-16 positive without lesion confirmed by HPV genotyping assay,25,27,1 month,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3(B),21 March 2021,Cynthia Anderson,"Cynthia Anderson,Peace Sandy",Vaginal microbiome as HPV16-infection markers. (B) Histogram of the LDA scores computed for species differentially abundant between HPV16-positive women and controls. The LDA scores (log10) > 2 are listed,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia|s__Nocardia brevicatena,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus denitrificans,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter panaciterrae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces auratus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter oralis,k__Eukaryota|k__Fungi|p__Microsporidia|f__Enterocytozoonidae|g__Enterocytozoon|s__Enterocytozoon bieneusi,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae|g__Melampsora|s__Melampsora laricis-populina,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces boulardii (nom. inval.),k__Eukaryota|k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae|g__Kalmanozyma|s__Kalmanozyma brasiliensis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces mikatae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Thelebolaceae|g__Pseudogymnoascus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces kudriavzevii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Viruses|k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Alphapapillomavirus|s__Alphapapillomavirus 14",2|1239|1737404|1737405|1570339|165779|33036;2|201174|84998|84999|1643824|1380|1393034;2|204428|204429|51291|809|810|813;2|1239|909932|1843489|31977|39948|218538;2|1239|909932|1843489|31977|39948|309120;2|32066|203490|203491|203492|848|851;2|201174|1760|85004|31953|2701|2702;2|1239|91061|1385|539738|3076174|502393;2|201174|1760|85006|2805426|57499|1276;2|1239|186801|186802|216572|1637257|884684;2|201174|1760|2037|2049|2050|2051;2|201174|1760|85007|85025|1817|37327;2|201174|84998|84999|1643824|133925|133926;2|1224|28211|204455|31989|265|266;2|1239|1737404|1737405|1570339|543311|33033;2|976|117747|200666|84566|84567|363849;2|1239|1737404|1737405|1570339|162289|54005;2|1239|1737404|1737405|1570339|162289|33031;2|1239|186801|3082720|186804|1257|1261;2|976|200643|171549|171552|838|419005;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|28128;2|976|200643|171549|171552|838|28130;2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|2529408|131111;2|1239|526524|526525|128827|123375|102148;2|201174|1760|85011|2062|1883|114687;2|1224|1236|72274|135621|2901164|316;2|1239|909932|1843489|31977|29465|187328;2157|28890|183925|2158|2159|2172|66851;2759|4751|6029|27970|27971|31281;2759|4751|5204|162484|5258|5259|5260|203908;2759|4751|4890|4891|4892|4893|4930|252598;2759|4751|5204|5257|5267|5268|1804794|1392244;2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|4891|4892|4893|4930|114525;2759|4751|4890|147548|292491|46451|78156;2759|4751|4890|4891|4892|4893|4930|4932;2759|4751|4890|4891|4892|4893|4930|114524;2|1224|1236|91347|543;2|1239|91061|186826|33958|1578;10239|2732092|2732415|2732421|2732533|151340|2169595|333750|931244,Complete,Peace Sandy
bsdb:437/1/2,Study 437,"cross-sectional observational, not case-control",32656096,10.3389/fcimb.2020.00286,NA,"Yang Q, Wang Y, Wei X, Zhu J, Wang X, Xie X , Lu W",The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing,Frontiers in cellular and infection microbiology,2020,"HPV infection, cervical cancer, metabolism, shotgun metagenomic sequencing, vaginal microbiome",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,Healthy control,HPV-16+,Patients with HPV-16 positive without lesion confirmed by HPV genotyping assay,25,27,1 month,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3 (B),25 January 2024,Peace Sandy,Peace Sandy,Vaginal microbiome as HPV16-infection markers. (B) Histogram of the LDA scores computed for species differentially abundant between HPV16-positive women and controls. The LDA scores (log10) > 2 are listed,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. 1140_ESPC,k__Viruses|k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Alphapapillomavirus,k__Eukaryota|k__Fungi|p__Microsporidia|g__Mitosporidium|s__Mitosporidium daphniae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,k__Eukaryota|k__Fungi|p__Microsporidia|f__Nosematidae|g__Nosema|s__Nosema bombycis",2|1239|91061|186826|81852|1350|1579349;10239|2732092|2732415|2732421|2732533|151340|2169595|333750;2759|4751|6029|1633384|1485682;2759|4751|4890|4891|4892|4893|374468|5478;2759|4751|1913637|2212703|4827|34489|4830|91626;2759|4751|6029|27974|27977|27978,Complete,Peace Sandy
bsdb:438/1/1,Study 438,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, Murphy B, Ross RP, Fitzgerald GF, Stanton C , Cotter PD","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Untreated controls (week 4),Antibiotic treated (week 4),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,excluded if they required oral antibiotics (no time frame given),16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,Mmarin,"Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.

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

Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05).  Percentages are based on proportions of assignable reads.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543;2|1239|91061|186826|81850;2|1239|186801|3082720|186804;2|1224;2|1224|1236|91347|543,Complete,Chloe
bsdb:438/1/2,Study 438,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, Murphy B, Ross RP, Fitzgerald GF, Stanton C , Cotter PD","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Untreated controls (week 4),Antibiotic treated (week 4),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,excluded if they required oral antibiotics (no time frame given),16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,Mmarin,"Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.

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

Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,Chloe
bsdb:438/2/1,Study 438,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, Murphy B, Ross RP, Fitzgerald GF, Stanton C , Cotter PD","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Untreated controls (week 8),Antibiotic treated (week 8),Received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,excluded if they required oral antibiotics (no time frame given),16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,Mmarin,"Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. 
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. 
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. 

Statistically significant differences between treated infants and controls at week 8 are indicated by asterisks. Percentages are based on proportions of assignable tags.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543;2|1224;2|1224|1236|91347|543,Complete,Chloe
bsdb:438/3/1,Study 438,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, Murphy B, Ross RP, Fitzgerald GF, Stanton C , Cotter PD","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Week 4 (treated),Week 8 (treated),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,excluded if they required oral antibiotics (no time frame given),16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,Mmarin,"Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. 
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. 
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.

A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,Chloe
bsdb:438/3/2,Study 438,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, Murphy B, Ross RP, Fitzgerald GF, Stanton C , Cotter PD","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Week 4 (treated),Week 8 (treated),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,excluded if they required oral antibiotics (no time frame given),16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,Mmarin,"Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. 
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. 
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.

A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543;2|1239|186801|3082720|186804;2|1224;2|1224|1236|91347|543,Complete,Chloe
bsdb:439/1/1,Study 439,case-control,32158702,10.3389/fcimb.2020.00063,https://pubmed.ncbi.nlm.nih.gov/32158702/,"Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C , Rotimi CN",Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans,Frontiers in cellular and infection microbiology,2020,"16S V4 rRNA sequencing, gut microbiome, microbial composition, type 2 diabetes, urban Africans",Experiment 1,Nigeria,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus; The definition of T2D was based on the American Diabetes Association (ADA) criteria: a fasting plasma glucose concentration (FPG) ≥ 126 mg/dl (7.0 mmol/l) or a 2-h post-load value in the oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/l) on more than one occasion. Alternatively, a diagnosis of T2D was accepted if an individual was on pharmacological treatment for T2D, and a review of clinical records indicated adequate justification for that therapy.",193,98,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Table 3, Table 4",27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance between controls and individuals with Type 2 Diabetes,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum|s__Cellulosilyticum ruminicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|186801|3085636|3018741|698776|425254;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485|1492;2|1239|186801|186802|31979|1485|29363;2|1239;2|1239|186801|3082720|186804,Complete,Claregrieve1
bsdb:439/1/2,Study 439,case-control,32158702,10.3389/fcimb.2020.00063,https://pubmed.ncbi.nlm.nih.gov/32158702/,"Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C , Rotimi CN",Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans,Frontiers in cellular and infection microbiology,2020,"16S V4 rRNA sequencing, gut microbiome, microbial composition, type 2 diabetes, urban Africans",Experiment 1,Nigeria,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus; The definition of T2D was based on the American Diabetes Association (ADA) criteria: a fasting plasma glucose concentration (FPG) ≥ 126 mg/dl (7.0 mmol/l) or a 2-h post-load value in the oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/l) on more than one occasion. Alternatively, a diagnosis of T2D was accepted if an individual was on pharmacological treatment for T2D, and a review of clinical records indicated adequate justification for that therapy.",193,98,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Table 3, Table 4",15 August 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance between controls and individuals with Type 2 Diabetes,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter|s__Terrisporobacter glycolicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|976;2|200940|3031449|213115|194924|872|901;2157|28890;2|976|200643|171549|171552|838;2|1239|186801|3082720|186804|1505652|36841;2|1239|186801|3085636|186803|2316020|46228,Complete,Claregrieve1
bsdb:440/1/1,Study 440,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S , Chien AL",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,NA,Experiment 1,United States of America,Homo sapiens,"Nose,Skin of cheek","UBERON:0000004,UBERON:0008803",Rosacea,EFO:1000760,Healthy controls,Participants with papulopustular rosacea (PPR),Participants with rosacea included individuals with diagnosed papulopustular rosacea (PPR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,"4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents",16S,34,Illumina,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 1,30 May 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance between papulopustular rosacea (PPR) patients and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Gleimia|s__Gleimia europaea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",2|976|200643|171549|171552|1283313|76122;2|29547|3031852|213849|72294|194|827;2|201174|1760|85007|1653|1716|161879;2|201174|1760|2037|2049|2692113|66228;2|976|200643|171549|171552|838|28131,Complete,Claregrieve1
bsdb:440/1/2,Study 440,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S , Chien AL",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,NA,Experiment 1,United States of America,Homo sapiens,"Nose,Skin of cheek","UBERON:0000004,UBERON:0008803",Rosacea,EFO:1000760,Healthy controls,Participants with papulopustular rosacea (PPR),Participants with rosacea included individuals with diagnosed papulopustular rosacea (PPR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,"4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents",16S,34,Illumina,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Table 1,30 May 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance between papulopustular rosacea (PPR) patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus|s__Anoxybacillus kestanbolensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium|s__Azorhizobium doebereinerae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gadei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia stuartii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella algae",2|1239|91061|1385|186817|150247|227476;2|1224|28211|356|335928|6|281091;2|201174|1760|85009|31957|1912216|33011;2|976|200643|171549|2005520|156973|156974;2|1224|1236|91347|1903414|586|588;2|1224|1236|135622|267890|22|38313,Complete,Claregrieve1
bsdb:440/2/1,Study 440,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S , Chien AL",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,NA,Experiment 2,United States of America,Homo sapiens,"Nose,Skin of cheek","UBERON:0000004,UBERON:0008803",Rosacea,EFO:1000760,Healthy controls,Participants with erythematotelangiectatic rosacea,Participants with rosacea included individuals with diagnosed erythematotelangiectatic rosacea (ETR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,"4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents",16S,34,Illumina,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 1,3 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance in erythematotelangiectatic rosacea (ETR) patients compared to healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium|s__Azorhizobium doebereinerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia stuartii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas|s__Roseomonas mucosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella algae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1224|28211|356|335928|6|281091;2|976|200643|171549|171551|836|28124;2|1224|1236|91347|1903414|586|588;2|1224|28211|204441|433|125216|207340;2|1224|1236|135622|267890|22|38313;2|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:441/1/1,Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3a,3 June 2021,Claregrieve1,Claregrieve1,Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|2810280|1505663;2|201174|1760|2037|2049|1654,Complete,Fatima
bsdb:441/1/2,Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3a,3 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|3082720|186804|1505657;2|1224|1236|91347|543|570;2|1239|186801|3082720|186804|1501226;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|31979|1485,Complete,Fatima
bsdb:441/2/1,Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Influenza A (H1N1),EFO:1001488,Healthy controls,H1N1 cases,H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission,30,24,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure 2,3 June 2021,Claregrieve1,Claregrieve1,Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|1239|186801|3085636|186803|572511;2|1239|186801|3082720|186804|1501226;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|2569097|39488;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|1263|41978,Complete,NA
bsdb:441/2/2,Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Influenza A (H1N1),EFO:1001488,Healthy controls,H1N1 cases,H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission,30,24,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure 2,3 June 2021,Claregrieve1,Claregrieve1,Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1239|91061|186826|81852|1350;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289,Complete,NA
bsdb:441/3/1,Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,H1N1 patients,COVID-19 patients,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,24,30,subjects who received antibiotics and/or probiotics within 4 weeks of enrollment were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 4a,3 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differences in microbiota composition between COVID-19 patients and H1N1 patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|31979|1485,Complete,Fatima
bsdb:441/3/2,Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,H1N1 patients,COVID-19 patients,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,24,30,subjects who received antibiotics and/or probiotics within 4 weeks of enrollment were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 4a,3 June 2021,Claregrieve1,Claregrieve1,Differences in microbiota composition between COVID-19 patients and H1N1 patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|171552|838;2|1239|1737404|1582879;2|74201|203494|48461|1647988|239934;2|1239|1737404|1737405|1570339|1161127;2|976|200643|171549|171551|836,Complete,Fatima
bsdb:441/4/1,Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2A, 2B, 2C, 2D",30 June 2021,Fatima,Fatima,Taxonomic differences in fecal microbiota between patients with covid-19 and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061,Complete,NA
bsdb:442/1/1,Study 442,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han SH, Lee JS, Song KH, Choe YB, Ahn KJ , Lee YW",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,"Trichophyton rubrum, biodiversity, diabetes mellitus, microbiome",Experiment 1,South Korea,Homo sapiens,"Skin of sole of pes,Interdigital space","UBERON:0013778,UBERON:0036252",Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,unchanged,NA,decreased,Signature 1,Table 2,7 June 2021,Madhubani Dey,"Madhubani Dey,Atrayees",Decrease in the abundance of fungal species in Diabetes Mellitus patients,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Eukaryota|k__Fungi|p__Ascomycota,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Capnodiales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Omphalotaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Ascochyta,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Mycosphaerella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Stemphylium,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae|g__Stereum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium flabelliforme,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria alternata,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Ascochyta|s__Ascochyta herbicola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium herbarum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis",2759|4751|4890|147541;2759|4751|5204|155619;2759|4751|4890;2759|4751|4890|147548;2759|4751|4890|147541|92860;2759|4751|4890|147541|134362;2759|4751|5204|155619|5338;2759|4751|5204|155619|452342;2759|4751|4890|147541|92860|28556;2759|4751|4890|147541|2726946|452563;2759|4751|4890|147541|2726947|93133;2759|4751|5204|155619|452342|103376;2759|4751|5204|155619|5338|72117;2759|4751|4890|147541|92860|28556|5598;2759|4751|4890|147541|2726946|452563|5498;2759|4751|4890|147541|92860|683158|5453;2759|4751|4890|147541|2726947|93133|41254;2759|4751|4890|147541|92860|28556|95729;2759|4751|5204|155619|452342|103376|5644;2759|4751|4890|147541|2726946|452563|5498|887091;2759|4751|4890|147541|92860|28556|5598|5599;2759|4751|4890|147541|92860|683158|5453|749840;2759|4751|4890|147541|2726946|452563|5498|29918;2759|4751|4890|3239874|2916678|766764|5475|5480,Complete,Atrayees
bsdb:442/1/2,Study 442,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han SH, Lee JS, Song KH, Choe YB, Ahn KJ , Lee YW",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,"Trichophyton rubrum, biodiversity, diabetes mellitus, microbiome",Experiment 1,South Korea,Homo sapiens,"Skin of sole of pes,Interdigital space","UBERON:0013778,UBERON:0036252",Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,unchanged,NA,decreased,Signature 2,Table 2,7 June 2021,Madhubani Dey,"Madhubani Dey,Atrayees",Increase in the abundance of fungal species in Diabetes Mellitus patients,increased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Trichophyton|s__Trichophyton rubrum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta",2759|4751|5204|1538075;2759|4751|5204|1538075|162474;2759|4751|4890|147545|33183|34384|5550|5551;2759|4751|5204|1538075|162474|742845|55193|76775,Complete,Atrayees
bsdb:442/2/NA,Study 442,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han SH, Lee JS, Song KH, Choe YB, Ahn KJ , Lee YW",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,"Trichophyton rubrum, biodiversity, diabetes mellitus, microbiome",Experiment 2,South Korea,Homo sapiens,"Skin of sole of pes,Interdigital space","UBERON:0013778,UBERON:0036252",Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:443/1/1,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C), diarrhea predominant (IBS-D), and un-subtyped (IBS-U). All participants.",30,47,4 weeks,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3.,28 June 2021,Kwekuamoo,"Kwekuamoo,MyleeeA",Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511|1532;2|1239|186801|3085636|186803|572511|33035;2|1224|1236|72274|135621|286|287;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:443/1/2,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C), diarrhea predominant (IBS-D), and un-subtyped (IBS-U). All participants.",30,47,4 weeks,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Folakunmi
bsdb:443/2/1,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-C,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and healthy controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511|1532;2|1239|186801|3085636|186803|572511|33035;2|1239|91061|186826|33958|1578;2|1224|1236|72274|135621|286|287;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:443/2/2,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-C,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and healthy controls.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,2|201174|1760|85004|31953|1678|1686,Complete,Folakunmi
bsdb:443/3/1,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-D,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: diarrhea predominant IBS (IBS-D).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-D and healthy controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|976|200643|171549|815|816;2|1239|186801|186802|31979|49082|49118;2|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:443/3/2,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-D,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: diarrhea predominant IBS (IBS-D).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-D and healthy controls.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953|1678|1686;2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:443/4/NA,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-U,Patients with IBS diagnosed using Rome III. Patients were classified into sub-types: un-subtyped (IBS-U).,30,7,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:443/5/1,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,"Irritable Bowel Syndrome, diarrhea predominant (IBS-D)","Irritable Bowel Syndrome, constipation predominant (IBS-C)",Patients were classified into three sub-types using Rome III criteria: diarrhea predominant IBS (IBS-D).,20,20,4 weeks,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,16 November 2023,MyleeeA,"MyleeeA,Folakunmi",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and IBS-D,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:443/5/2,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,"Irritable Bowel Syndrome, diarrhea predominant (IBS-D)","Irritable Bowel Syndrome, constipation predominant (IBS-C)",Patients were classified into three sub-types using Rome III criteria: diarrhea predominant IBS (IBS-D).,20,20,4 weeks,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,9 February 2024,Folakunmi,Folakunmi,Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and IBS-D,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse",2|976|200643|171549|815|816;2|1239|186801|186802|31979|49082|49118,Complete,Folakunmi
bsdb:443/6/1,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,No Visible abdominal distension,Visible abdominal distension,Patients with IBS showing Visible abdominal distension as symptoms,13,34,4 weeks,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,16 November 2023,MyleeeA,MyleeeA,Association of IBS symptoms in relation to bacterial load,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",2|1239|186801|3085636|186803|572511|1532;2|1239|186801|186802|31979|49082|49118;2|1224|1236|72274|135621|286|287;2|976|200643|171549|815|816|818,Complete,Folakunmi
bsdb:443/7/1,Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 7,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,No Abdominal Bloating,Abdominal Bloating,Patients with IBS showing Abdominal Bloating/Abdominal discomfort as symptoms,25,22,4 Weeks,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,16 November 2023,MyleeeA,MyleeeA,Association of IBS symptoms in relation to bacterial load,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,2|1239|186801|3085636|186803|572511|1532,Complete,Folakunmi
bsdb:444/1/1,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 1,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Active patients,Inactive patients,Patients that are not engaged in any regular physical activity or exercise.,72,107,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Supplementary Table 2,14 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing",Differential abundance (mean normalized counts) at phylum level inactive group VS active group,increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Atrayees
bsdb:444/1/2,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 1,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Active patients,Inactive patients,Patients that are not engaged in any regular physical activity or exercise.,72,107,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 2,14 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing",Differential abundance (mean normalized counts) at genus level in inactive group VS active group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum",2|1224|1236|135624|83763|83770;2|1239|909932|1843488|909930|40840,Complete,Atrayees
bsdb:444/2/2,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 2,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Normal weight patients,Overweight patients,Patient with a BMI greater than or equal to 25 kg/m2 but not greater than 30 kg/m2.,59,76,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 2,16 March 2023,Deacme,"Deacme,Aiyshaaaa,Atrayees,ChiomaBlessing",Differential abundance (mean normalized counts) at genus level in overweight group VS normal weight group,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|201174|84998|84999|1643824|133925;2|1239|186801|3082720|3030910|86331;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|186806|1730;2|1239|186801|186802|31979|1485;2|1239|909932|1843488|909930|40840;2|1224|1236|135624|83763|83770,Complete,Atrayees
bsdb:444/3/1,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 3,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Normal weight patients,Obese patients,Patients with a BMI greater than 30 kg/m2,59,44,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 2,16 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing",Differential abundance (mean normalized counts) at genus level in obese group VS normal weight group,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Atrayees
bsdb:444/3/2,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 3,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Normal weight patients,Obese patients,Patients with a BMI greater than 30 kg/m2,59,44,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 2,16 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing",Differential abundance (mean normalized counts) at genus level in obese group VS normal weight group,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|31979|1485;2|1224|1236|135624|83763|83770,Complete,Atrayees
bsdb:444/4/1,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 4,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Normal weight/inactive patients,Patient that has a BMI greater than 18.5 kg/m2 but less than 25 kg/m2 and engaged in little to no physical activity on a regular basis.,26,33,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 3,4 February 2024,ChiomaBlessing,ChiomaBlessing,Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|1239|909932|1843488|909930|40840;2|1224|1236|135624|83763|83770,Complete,ChiomaBlessing
bsdb:444/4/2,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 4,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Normal weight/inactive patients,Patient that has a BMI greater than 18.5 kg/m2 but less than 25 kg/m2 and engaged in little to no physical activity on a regular basis.,26,33,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 3,4 February 2024,ChiomaBlessing,ChiomaBlessing,Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group,increased,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,2|508458|649775|649776|3029088|638847,Complete,NA
bsdb:444/5/1,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 5,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Overweight/Obese/active patients,Patient with a BMI greater than or equal to 25 kg/m2 but is also physically active.,26,46,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 3,16 March 2023,Deacme,"Atrayees,Aiyshaaaa,Deacme,ChiomaBlessing",Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in overweight/ obese active group compared to normal weight active group,increased,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,2|508458|649775|649776|3029088|638847,Complete,ChiomaBlessing
bsdb:444/5/2,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 5,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Overweight/Obese/active patients,Patient with a BMI greater than or equal to 25 kg/m2 but is also physically active.,26,46,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 3 & Supplementary Table 3,16 March 2023,Deacme,"Deacme,Aiyshaaaa,Atrayees,ChiomaBlessing",Differential abundance (mean normalized counts) at genus and phylum level (by individual BMI and physical activity groups) in overweight/ obese active group compared to normal weight active group,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|32066|203490;2|1239|1737404|1737405|1570339|162289;2|1239|909932|1843488|909930|40840;2|1224|1236|135624|83763|83770,Complete,ChiomaBlessing
bsdb:444/6/1,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 6,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Overweight/Obese/inactive patients,Patient with a BMI equal to or greater than 25 kg/m2 and is physically inactive.,26,74,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Supplementary Table 3,16 March 2023,Deacme,"Deacme,Aiyshaaaa,Atrayees,ChiomaBlessing",Differential abundances (mean normalized counts) at phylum level (by combined BMI and physical activity groups) in overweight/ obese/ inactive group VS normal weight/ active group,increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,ChiomaBlessing
bsdb:444/6/2,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 6,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Overweight/Obese/inactive patients,Patient with a BMI equal to or greater than 25 kg/m2 and is physically inactive.,26,74,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 3,4 February 2024,ChiomaBlessing,ChiomaBlessing,Differential abundances (mean normalized counts) at genus level (by combined BMI and physical activity groups) in overweight/ obese/ inactive group VS normal weight/ active group,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,2|1224|1236|135624|83763|83770,Complete,ChiomaBlessing
bsdb:444/7/1,Study 444,prospective cohort,36381318,NA,NA,"Himbert C, Stephens WZ, Gigic B, Hardikar S, Holowatyj AN, Lin T, Ose J, Swanson E, Ashworth A, Warby CA, Peoples AR, Nix D, Jedrzkiewicz J, Bronner M, Pickron B, Scaife C, Cohan JN, Schrotz-King P, Habermann N, Boehm J, Hullar M, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Ulrich AB, Shibata D, Boucher K, Huang LC, Schneider M, Round JL , Ulrich CM",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 7,"United States of America,Germany",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Overweight/Obese/active patients,Overweight/Obese/inactive patients,Patients with BMI greater than or equal to 25 kg/m2 and are not physically active.,46,74,4 weeks,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 3,4 February 2024,ChiomaBlessing,ChiomaBlessing,Differential abundances (mean normalized counts) at genus level by combined BMI and physical activity groups in overweight/ obese inactive group VS overweight/ obese active group,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|1239|909932|1843488|909930|40840;2|1224|1236|135624|83763|83770,Complete,ChiomaBlessing
bsdb:445/1/NA,Study 445,"cross-sectional observational, not case-control",32728349,10.1186/s12575-020-00131-7,https://doi.org/10.1186/s12575-020-00131-7,"De Maio F, Posteraro B, Ponziani FR, Cattani P, Gasbarrini A , Sanguinetti M",Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients,Biological procedures online,2020,"16S rRNA sequencing, Bacterial community, Nasopharynx, SARS-CoV-2 infection",Experiment 1,Italy,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients,COVID-19 cases,Diagnosis with COVID-19 based on SARS-CoV-2 RNA detection using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay,22,18,NA,16S,56,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:446/1/1,Study 446,"cross-sectional observational, not case-control",33219095,10.1128/mBio.01969-20,NA,"Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR , Simner PJ",Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients,mBio,2020,"COVID-19, SARS-CoV-2, metagenomic next-generation sequencing, metagenomics, nasopharyngeal",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 cases,Positive for SaRS-CoV-2 by diagnostic RT-PCR,10,40,NA,WMS,NA,Nanopore,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3,5 June 2021,Claregrieve1,"Claregrieve1,Aiyshaaaa,Atrayees",Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,2|201174|1760|85007|1653|1716|38284,Complete,Atrayees
bsdb:446/1/2,Study 446,"cross-sectional observational, not case-control",33219095,10.1128/mBio.01969-20,NA,"Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR , Simner PJ",Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients,mBio,2020,"COVID-19, SARS-CoV-2, metagenomic next-generation sequencing, metagenomics, nasopharyngeal",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 cases,Positive for SaRS-CoV-2 by diagnostic RT-PCR,10,40,NA,WMS,NA,Nanopore,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3,5 June 2021,Claregrieve1,"Claregrieve1,Aiyshaaaa,Atrayees",Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,2|201174|1760|85009|31957,Complete,Atrayees
bsdb:447/1/1,Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1 D,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,Davvve",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|1224|1236;2|1224|1236|135625|712|724;2|1224|1236|135625|712;2|1224|1236|135625,Complete,Claregrieve1
bsdb:447/1/2,Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1 D,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,Davvve",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|171550|239759;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171550,Complete,Claregrieve1
bsdb:447/2/1,Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 2D,9 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:447/2/2,Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Figure 2D,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls,decreased,"k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",2|32066;2|32066|203490|203491|203492;2|32066|203490;2|1239|186801|3085636|186803|1164882;2|1239|91061|186826|33958;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1239|91061|186826|33958|1243,Complete,Claregrieve1
bsdb:448/1/1,Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1a-c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|1239;2|1224;2|1239|91061|1385|186817;2|1224|1236|2887326|468;2|1224|1236|72274|135621;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286;2|1239|91061|1385|186817|1386,Complete,Fatima
bsdb:448/1/2,Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1a-c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:448/1/3,Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 1b,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1239|91061|1385|186817;2|1224|1236|2887326|468;2|1224|1236|72274|135621,Complete,Fatima
bsdb:448/1/4,Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 1b,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|28216|206351|481;2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,Fatima
bsdb:448/1/5,Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 5,Figure 1c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236|2887326|468|469;2|1239|91061|1385|186817|1386;2|1224|1236|72274|135621|286,Complete,Fatima
bsdb:448/1/6,Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 6,Figure 1c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:449/1/1,Study 449,"cross-sectional observational, not case-control",35411293,10.34172/bi.2021.23378,NA,"Han Y, Jia Z, Shi J, Wang W , He K",The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis,BioImpacts : BI,2022,"COVID-19, Faecalibacterium prausnitzii, Lactic acid bacteria, Microbiota, SARS-CoV-2",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,COVID-19 infected patients,23,19,NIL,WMS,NA,NA,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table 2,12 June 2021,Claregrieve1,"Claregrieve1,Davvve",Differential microbial abundance between the COVID-19 patients and the healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna sedimenticola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum propionicum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium cucumeris,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter braakii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii complex sp. CFNIH3,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium beijerinckii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium carboxidivorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas terrigena,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter oligotrophicus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter roggenkampii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. 638,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. E76,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. ODB01,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. T2,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Filimonas|s__Filimonas lacunae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus curvatus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia adecarboxylata,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. 29361,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. J807,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. LSNIH1,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. W17,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia amnigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia jeotgali,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia sp. WB101,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus sp. B2A1,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus sphaericus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium sp. DM1,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus graminis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus guangzhouensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea sp. SO10,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Peribacillus|s__Peribacillus frigoritolerans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium myrsinacearum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter|s__Pluralibacter gergoviae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas alkylphenolica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzihabitans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas rhodesiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. JY-Q,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. MRSN 12121,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. PONIH3,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. XWY-1,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella aquatilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter|s__Ruminobacter amylophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. B29,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. G1-14,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. FARSPH,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp. LM091,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Suicoccus|s__Suicoccus acidiformans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax boronicumulans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax paradoxus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PBL-H6,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PMC12,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio anguillarum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__uncultured Variovorax sp.",2|201174|1760|2037|2049|1654|1852377;2|1239|186801|3085636|186803|1843210|2696063;2|1239|186801|3085636|3118652|2039240|28446;2|1239|91061|1385|186817|1386|1396;2|976|117743|200644|2762318|59732|1813611;2|1224|1236|91347|543|544|57706;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|2077147;2|1239|186801|186802|1898207;2|1239|186801|186802|2109688;2|1239|186801|186802|31979|1485|1520;2|1239|186801|186802|31979|1485|217159;2|1224|28216|80840|80864|283|32013;2|1224|28216|80840|80864|283|285;2|1224|1236|91347|543|547|61645;2|1224|1236|91347|543|547|881260;2|1224|1236|91347|543|547|69218;2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|547|2027919;2|1224|1236|91347|543|547|158836;2|1224|1236|91347|543|547|208224;2|1224|1236|91347|543|547|2478464;2|1224|1236|91347|543|547|1812935;2|1224|1236|91347|543|547|885040;2|1224|1236|91347|543|547|399742;2|1224|1236|91347|543|547|2596949;2|1224|1236|91347|543|547|1827481;2|1224|1236|91347|543|547|2707174;2|1239|186801|186802|216572|216851|853;2|976|1853228|1853229|563835|649460|477680;2|1239|186801|186802|216572|946234|292800;2|1224|1236|91347|543|570|1134687;2|1224|1236|91347|543|570|571;2|1239|186801|3085636|186803|1506553|66219;2|1239|186801|3085636|186803|2719231|84030;2|1239|186801|3085636|186803|2719231|29370;2|1239|91061|186826|33958|2767842|1590;2|1239|91061|186826|33958|1578|1584;2|1239|91061|186826|33958|1578|33959;2|1239|91061|186826|33958|2767885|28038;2|1224|1236|91347|543|83654|83655;2|1224|1236|91347|543|83654|2714951;2|1224|1236|91347|543|83654|2681307;2|1224|1236|91347|543|83654|1920114;2|1224|1236|91347|543|83654|2282309;2|1224|1236|91347|543|1330545|61646;2|1224|1236|91347|543|1330545|1907578;2|1224|1236|91347|543|1330545|2153385;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|1598;2|1239|91061|1385|186817|400634|2081964;2|1239|91061|1385|186817|400634|1421;2|544448|2790996|2895623|2923352|2100;2|1224|28211|356|119045|407|2067957;2|1239|91061|1385|186822|44249|189425;2|1239|91061|1385|186822|44249|1473112;2|1224|1236|91347|1903409|53335|2575375;2|1239|91061|1385|186817|2675229|450367;2|1224|28211|356|69277|28100|28101;2|1224|1236|91347|543|1330546|61647;2|1224|1236|72274|135621|286|237609;2|1224|1236|72274|135621|286|47885;2|1224|1236|72274|135621|286|76760;2|1224|1236|72274|135621|286|306;2|1224|1236|72274|135621|286|1338689;2|1224|1236|72274|135621|286|1611770;2|1224|1236|72274|135621|286|1636610;2|1224|1236|72274|135621|286|2069256;2|1224|1236|91347|1903411|34037|34038;2|1224|28216|80840|119060|48736|329;2|201174|1760|85006|1268|32207|172042;2|201174|1760|85006|1268|32207|43675;2|1224|1236|135624|83763|866|867;2|201174|1760|2037|2049|2529408|52773;2|976|117747|200666|84566|28453|1933220;2|976|117747|200666|84566|28453|2003121;2|1224|28211|204457|41297|13687|2219696;2|1224|1236|135614|32033|40323|1904944;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|712624;2|1224|1236|135624|83763|83770|83771;2|1239|91061|186826|186827|2689587|2036206;2|1224|28216|80840|80864|34072|436515;2|1224|28216|80840|80864|34072|34073;2|1224|28216|80840|80864|34072|434009;2|1224|28216|80840|80864|34072|2126319;2|1224|1236|135623|641|662|55601;2|1239|186801|3085636|186803|2316020|33038;2|1224|28216|80840|80864|34072|114708,Complete,Peace Sandy
bsdb:449/1/2,Study 449,"cross-sectional observational, not case-control",35411293,10.34172/bi.2021.23378,NA,"Han Y, Jia Z, Shi J, Wang W , He K",The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis,BioImpacts : BI,2022,"COVID-19, Faecalibacterium prausnitzii, Lactic acid bacteria, Microbiota, SARS-CoV-2",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,COVID-19 infected patients,23,19,NIL,WMS,NA,NA,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 2,12 June 2021,Claregrieve1,"Claregrieve1,Davvve,Peace Sandy",Differential microbial abundance between the COVID-19 patients and the healthy controls,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema putidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans",2|29547|3031852|213849|72294|194|203;2|29547|3031852|213849|72294|194|204;2|203691|203692|136|2845253|157|221027;2|1239|186801|3085636|186803|1506553|66219,Complete,Peace Sandy
bsdb:450/1/1,Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 1,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Mice assessed 7 days after infection with respiratory syncytial virus (RSV),NA,NA,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",13 June 2021,Claregrieve1,"Claregrieve1,Folakunmi",Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239;2|1239|186801|3085636|186803;2|1239|91061|186826|33958,Complete,Folakunmi
bsdb:450/1/2,Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 1,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Mice assessed 7 days after infection with respiratory syncytial virus (RSV),NA,NA,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",13 June 2021,Claregrieve1,"Claregrieve1,Folakunmi",Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|976|200643|171549|815;2|976|200643;2|976|200643|171549|2005473,Complete,Folakunmi
bsdb:450/2/1,Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 2,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with influenza virus (H1N1),NA,NA,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 4C, 4D",16 June 2021,Claregrieve1,"Claregrieve1,Folakunmi",Differential abundance of gut microbiota of influenza virus (H1N1) infected mice between Day 0 and Day 7 of infection,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Folakunmi
bsdb:450/2/2,Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 2,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with influenza virus (H1N1),NA,NA,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 4C, 4D",16 June 2021,Claregrieve1,"Claregrieve1,Folakunmi",Differential abundance of gut microbiota of influenza virus (H1N1) infected mice between Day 0 and Day 7 of infection,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976;2|976|200643|171549|2005473;2|976|200643|171549|171551,Complete,Folakunmi
bsdb:450/3/1,Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 3,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with phosphate-buffered saline (PBS).,NA,NA,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",26 January 2024,Folakunmi,Folakunmi,Differential abundance of gut microbiota of phosphate-buffered saline (PBS) infected mice between Day 0 and Day 7 of infection,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239;2|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:450/3/2,Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 3,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with phosphate-buffered saline (PBS).,NA,NA,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",26 January 2024,Folakunmi,Folakunmi,Differential abundance of gut microbiota of phosphate-buffered saline (PBS) infected mice between Day 0 and Day 7 of infection,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia,2|976|200643,Complete,Folakunmi
bsdb:451/1/1,Study 451,case-control,33613481,10.3389/fmicb.2021.610370,https://pubmed.ncbi.nlm.nih.gov/33613481/,"Almeida-Santos A, Martins-Mendes D, Gayà-Vidal M, Pérez-Pardal L , Beja-Pereira A",Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients,Frontiers in microbiology,2021,"16S rRNA gene sequencing, Portugal, microbiota, next-generation sequencing, oral hygiene, type 2 diabetes mellitus",Experiment 1,Portugal,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Medicated Type II Diabetes individuals,Medicated Type II Diabetes individuals,24,22,2 months,16S,34,Illumina,"Mann-Whitney (Wilcoxon),ANCOM",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6,17 June 2021,Madhubani Dey,"Madhubani Dey,Chloe,Merit",Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (Mann-Whitney's U results),decreased,"k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",2|508458|649775;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775|649776|649777,Complete,Chloe
bsdb:451/1/2,Study 451,case-control,33613481,10.3389/fmicb.2021.610370,https://pubmed.ncbi.nlm.nih.gov/33613481/,"Almeida-Santos A, Martins-Mendes D, Gayà-Vidal M, Pérez-Pardal L , Beja-Pereira A",Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients,Frontiers in microbiology,2021,"16S rRNA gene sequencing, Portugal, microbiota, next-generation sequencing, oral hygiene, type 2 diabetes mellitus",Experiment 1,Portugal,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Medicated Type II Diabetes individuals,Medicated Type II Diabetes individuals,24,22,2 months,16S,34,Illumina,"Mann-Whitney (Wilcoxon),ANCOM",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S6,14 March 2022,Chloe,"Chloe,Merit",Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (ANCOM results),decreased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775;2|508458|649775|649776|649777,Complete,Chloe
bsdb:452/1/1,Study 452,"cross-sectional observational, not case-control",33193081,10.3389/fendo.2020.550319,https://pubmed.ncbi.nlm.nih.gov/33193081/,"Tang N, Luo ZC, Zhang L, Zheng T, Fan P, Tao Y , Ouyang F",The Association Between Gestational Diabetes and Microbiota in Placenta and Cord Blood,Frontiers in endocrinology,2020,"China, cord blood, gestational diabetes mellitus (GDM), microbiota, placenta",Experiment 1,China,Homo sapiens,Placenta,UBERON:0001987,Gestational diabetes,EFO:0004593,euglycemic (control) singleton pregnant women,Pregnant women with Gestational Diabetes Mellitus,"Pregnant women with Gestational Diabetes Mellitus (GDM) who had prenatal care at Xinhua Hospital, a tertiary hospital in Shanghai, and were admitted to the hospital for cesarean deliveries",7,8,Women who were treated with any antibiotics during pregnancy,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 3,14 June 2021,Madhubani Dey,"Madhubani Dey,Peace Sandy",Table 3: Relative abundances (%) of placental microbiota OTUs that differed between eight women with GDM and seven women without GDM (non-GDM).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|1185407;2|1239|186801|3085636|186803|189330;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|297314,Complete,Peace Sandy
bsdb:452/1/2,Study 452,"cross-sectional observational, not case-control",33193081,10.3389/fendo.2020.550319,https://pubmed.ncbi.nlm.nih.gov/33193081/,"Tang N, Luo ZC, Zhang L, Zheng T, Fan P, Tao Y , Ouyang F",The Association Between Gestational Diabetes and Microbiota in Placenta and Cord Blood,Frontiers in endocrinology,2020,"China, cord blood, gestational diabetes mellitus (GDM), microbiota, placenta",Experiment 1,China,Homo sapiens,Placenta,UBERON:0001987,Gestational diabetes,EFO:0004593,euglycemic (control) singleton pregnant women,Pregnant women with Gestational Diabetes Mellitus,"Pregnant women with Gestational Diabetes Mellitus (GDM) who had prenatal care at Xinhua Hospital, a tertiary hospital in Shanghai, and were admitted to the hospital for cesarean deliveries",7,8,Women who were treated with any antibiotics during pregnancy,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table 3,14 June 2021,Madhubani Dey,"Madhubani Dey,Peace Sandy",Table 3: Relative abundances (%) of placental microbiota OTUs that differed between eight women with GDM and seven women without GDM (non-GDM).,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:453/1/1,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,SARS-CoV-2 infected patients,">age 18, positive nasopharyngeal swab for SARS-CoV-2 by PCR, COVID-19 related symptoms present, weight > 110 pounds",34,50,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 infected cases and controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",2|201174|1760|85007|1653|1716;2|29547|3031852|213849|72294|194;2|1239|1737404|1737405|1570339|150022;2|201174|1760|2037|2049|2050;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1582879;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|1161127;2|1239|186801|186802|216572|236752;2|1239|91061|186826|186827|66831;2|1239|1737404|1737405|1570339|162290;2|1239|91061|1385|90964|1279;2|201174|84998|84999|1643824|1380;2|1239|186801|3082768|990719|990721;2|1239|909932|1843489|31977|39948;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|1392389,Complete,Lwaldron
bsdb:453/1/2,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,SARS-CoV-2 infected patients,">age 18, positive nasopharyngeal swab for SARS-CoV-2 by PCR, COVID-19 related symptoms present, weight > 110 pounds",34,50,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 infected cases and controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804|1505657;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|572511;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1224|1236|91347|543|561;2|1239|186801|3085656|3085657|2039302;2|1239|186801|186802|216572|292632;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|1766253;2|1224|1236|91347|543|570,Complete,Lwaldron
bsdb:453/2/1,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,SARS-CoV-2 infected patients,SARS-CoV-2 recovered individuals,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",50,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|29547|3031852|213849|72294|194;2|201174|1760|85007|1653|1716;2|201174|1760|2037|2049|2050;2|1239|186801|186802|1686313;2|1239|1737404|1582879;2|1239|1737404|1737405|1570339|1161127;2|1239|186801|186802|216572|236752;2|1239|91061|186826|186827|66831;2|1239|91061|1385|90964|1279;2|1239|1737404|1737405|1570339|162290;2|201174|1760|85007|2805586|1847725;2|1239|1737404|1737405|1570339|150022;2|1224|28216|80840|995019|40544;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|201174|84998|84999|1643824|1380;2|201174|1760|85006|85023|255204;2|508458|649775|649776|649777|508459;2|1239|186801|3085636|186803|1769710;2|1239|526524|526525|2810281|191303;2|1239|1737404|1737405|1570339|31983;2|1239|1737404|1737405|1570339|165779;2|201174|1760|85006|85020|36739;2|200940|3031449|213115|194924|872,Complete,Lwaldron
bsdb:453/2/2,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,SARS-CoV-2 infected patients,SARS-CoV-2 recovered individuals,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",50,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",2|1239|91061|186826|1300|1357;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|1926663;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|561;2|1239|186801|3082720|186804|1505657;2|1239|526524|526525|2810280|135858;2|1224|1236|91347|543|570;2|1239|186801|186802|216572|292632;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|1766253,Complete,Lwaldron
bsdb:453/3/1,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,Recovered COVID-19 patients,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",38,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between recovered COVID-19 patients and non-infected controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|s__rumen bacterium NK4A214",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|1926663;2|877428,Complete,Lwaldron
bsdb:453/3/2,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,Recovered COVID-19 patients,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",38,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial genera between recovered COVID-19 patients and non-infected controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803;2|1239|526524|526525|128827|1470349;2|200940|3031449|213115|194924|35832;2|976|200643|171549|171552|577309;2|1239|909932|1843489|31977|39948;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|1263,Complete,Lwaldron
bsdb:453/4/1,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Negative for COVID-19 viral RNA in feces,Positive for COVID-19 viral RNA in feces,COVID-19 viral RNA present in feces sample,26,24,NA,16S,123,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Dolosicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",2|1224|28216|80840|80864|283;2|203691|203692|136|2791015|399320;2|508458|649775|649776|649777|2753;2|1239|909932|909929|1843491|158846;2|1239|186801|3085636|186803|588605;2|1239|186801|3085636|1185407;2|1239|186801|3082720|186804|1505657;2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1485|1506;2|976|200643|171549|171552|577309;2|1239|91061|186826|186827|171413;2|1239|186801|3082720|186804|1870884;2|1224|1236|91347|1903414|583;2|32066|203490|203491|203492|848;2|1239|526524|526525|2810280|1505663;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|1769710;2|544448|2790996|2790998|2129;2|1239|186801|3085636|186803|1766253,Complete,Lwaldron
bsdb:453/4/2,Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Negative for COVID-19 viral RNA in feces,Positive for COVID-19 viral RNA in feces,COVID-19 viral RNA present in feces sample,26,24,NA,16S,123,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniferax,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Soonwooa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerosphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter",2|1239|91061|186826|186827|171412;2|201174|1760|85009|31957|53456;2|201174|84998|1643822|1643826|447020;2|201174|1760|85009|31957|72763;2|201174|1760|85006|1268|1269;2|1239|91061|186826|1300|1357;2|976|117743|200644|2762318|944321;2|1239|186801|186802|216572|1926663;2|976|200643|171549|2005520|156973;2|32066|203490|203491|1129771|168808;2|201174|1760|85006|85020|36739;2|1239|186801|3082720|186804|1501226;2|1224|1236|91347|543|547;2|1239|186801|3082720|186804|1505652;2|1239|186801|3085636|186803|1213720;2|1239|1737404|1737405|1570339|1273095;2|201174|1760|85006|85019|1696;2|201174|1760|85009|31957|1912216;2|201174|1760|85006|85023|255204,Complete,Lwaldron
bsdb:454/1/1,Study 454,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F , O'Toole PW",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 1,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (CRC),The patients undergoing surgery for CRC have confirmed CRC.,56,59,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File: Table S3 and Table S4,19 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Differential mucosal microbiota composition of patients with CRC compared to healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|201174|1760|2037|2049|1654;2|976|200643|171549|171550|239759;2|1239|909932|1843489|31977|209879;2|976|200643|171549|815|816;2|976;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|39948;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572|459786;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|909932|1843488|909930|33024;2|1224|1236|72274|135621|286;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|31979|1485;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1224|28216|80840|75682;2|1239|186801|186802|216572|258514;2|29547|3031852|213849|72294|194;2|1239|186801|186802|186806|1730;2|1239|186801|186802|404402;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171551,Complete,Chinelsy
bsdb:454/1/2,Study 454,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F , O'Toole PW",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 1,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (CRC),The patients undergoing surgery for CRC have confirmed CRC.,56,59,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File: Table S3,2 February 2024,ChiomaBlessing,ChiomaBlessing,Differential mucosal microbiota composition of patients with CRC compared to healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|526524|526525|128827|118966;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|1239|186801|186802|216572|216851;2|1239|186801|186802|204475;2|1239|526524|526525|128827|61170;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803;2|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:454/3/1,Study 454,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F , O'Toole PW",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 3,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,Distal (and rectal) cancer,Proximal cancer,Patients with proximal cancer,39,20,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File: Table S8,2 February 2024,ChiomaBlessing,ChiomaBlessing,Differential mucosal microbiota composition of proximal cancer compared to distal cancer,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:454/3/2,Study 454,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F , O'Toole PW",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 3,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,Distal (and rectal) cancer,Proximal cancer,Patients with proximal cancer,39,20,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File: Table S8,2 February 2024,ChiomaBlessing,ChiomaBlessing,Differential mucosal microbiota composition of proximal cancer compared to distal cancer,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella",2|1224|1236|135619|28256|2745;2|1224|1236|135622|267890|22,Complete,ChiomaBlessing
bsdb:455/1/1,Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 1,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women without gingivitis,pregnant women without gingivitis,Pregnant women sampled between 21 to 24 wk of gestation without gingivitis,10,10,6 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,decreased,increased,Signature 1,"Appendix Figure 1, 2, text",16 June 2021,Tislam,"Tislam,Fatima",Phylum and Genera showing significant differential abundance in subgingival samples.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Candidatus Saccharibacteria",2|976|200643|171549|815|816;2|32066|203490;2|32066|203490|203491|203492|848;2|203691;2|203691|203692|136|2845253|157;2|95818,Complete,Fatima
bsdb:455/1/2,Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 1,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women without gingivitis,pregnant women without gingivitis,Pregnant women sampled between 21 to 24 wk of gestation without gingivitis,10,10,6 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,decreased,increased,Signature 2,"Appendix Figure 2, text",16 June 2021,Tislam,"Tislam,Fatima",Phylum and Genera showing significant differential abundance in subgingival samples.,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus",2|976|117743|200644|2762318|59735;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|217201,Complete,Fatima
bsdb:455/2/1,Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 2,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Appendix Figure 1, 2, text",24 June 2021,Tislam,"Tislam,Fatima",Genera showing significant differential abundance in subgingival samples.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|815|816;2|29547|3031852|213849|72294|194;2|95818;2|1239|186801|3082720|3118655|44259;2|508458|649775|649776|3029087|1434006;2|203691;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Fatima
bsdb:455/3/1,Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 3,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Figure 3, text",24 June 2021,Tislam,Tislam,Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 349,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 346,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 258,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] saphenum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 238,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 304,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter actinomycetemcomitans,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 270,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.",2|1239|909932|1843489|31977;2|32066|203490|203491|1129771|32067;2|95818|713051;2|544448|2790996|2895623|2895509|56142;2|1239|186801|3085636|186803|712991;2|95818|713049;2|203691|203692|136|2845253|157|712739;2|1239|186801|186802|543314|51123;2|1239|186801|3085636|186803|43996|43997;2|203691|203692|136|2845253|157|51160;2|1239|186801|3082720|3118655|44259|143361;2|508458|649775|649776|3029087|1434006|651822;2|976|200643|171549|2005525|195950|28112;2|203691|203692|136|2845253|157|53418;2|203691|203692|136|2845253|157|712725;2|976|200643|171549|171552|838|712459;2|1224|1236|135625|712|416916|714;2|203691|203692|136|2845253|157|671227;2|203691|203692|136|2845253|157|158;2|508458|649775|649776|3029087|1434006|2699746,Complete,NA
bsdb:455/3/2,Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 3,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,"Figure 3, text",24 June 2021,Tislam,Tislam,Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 221,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 478,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium sp. oral taxon 194,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula",2|1239|909932|1843489|31977|29465|29466;2|201174|1760|2037|2049|1654|1655;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|186828|117563|46124;2|201174|1760|85006|1268|32207|2047;2|221235|1226342;2|201174|1760|2037|2049|1654|712124;2|201174|1760|2037|2049|1654|712118;2|1224|28216|206351|481|32257|505;2|1239|186801|3085636|186803|265975|712414;2|32066|203490|203491|1129771|32067|712362;2|1239|909932|909929|1843491|970|712538;2|201174|1760|85009|31957|1743|712503;2|201174|1760|2037|2049|1654|55565;2|201174|84998|84999|1643824|2767353|1382,Complete,NA
bsdb:455/4/1,Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 4,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women,pregnant women,pregnant women,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,decreased,NA,Signature 1,"Figure 3, text",7 July 2021,Tislam,Tislam,Linear discriminant analysis effect size. pregnant women without gingivitis versus nonpregnant women without gingivitis,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] saphenum",2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|1283313|1872471;2|976|200643|171549|171552|1283313|76122;2|976|117743|200644|2762318|59735;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016|45243;2|508458|649775|649776|3029087|1434006|651822;2|508458|649775|649776|3029087|1434006|2699746;2|32066|203490|203491|203492|848|860;2|32066|203490|203491|1129771|2755140|157692;2|32066|203490|203491|1129771|32067|157691;2|32066|203490|203491|1129771|32067|104608;2|1239|909932|1843489|31977|906|187326;2|544448|2790996|2895623|2895509|56142;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|2974251|305719;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|189723;2|976|200643|171549|171552|838|59823;2|201174|1760|85004|31953|196081|230143;2|1239|909932|909929|1843491|970|2053611;2|1239|909932|909929|1843491|970|69823;2|976|200643|171549|2005525|195950|28112;2|203691|203692|136|2845253|157|158;2|203691|203692|136|2845253|157|166;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|1926307;2|1239|186801|186802|543314|51123,Complete,NA
bsdb:455/4/2,Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 4,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women,pregnant women,pregnant women,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,decreased,NA,Signature 2,"Figure 3, text",7 July 2021,Tislam,Tislam,pregnant women without gingivitis versus nonpregnant women without gingivitis,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus|s__Terrahaemophilus aromaticivorans",2|976|117743|200644|2762318|59735|712187;2|1239|91061|1385|539738|1378|29391;2|1224|1236|135625|712|724|740;2|1224|28216|206351|481|482|267212;2|201174|1760|85006|1268|32207|172042;2|1239|91061|186826|1300|1301|1306;2|1224|1236|135625|712|217201|217202,Complete,NA
bsdb:456/1/1,Study 456,"cross-sectional observational, not case-control",33224990,10.1155/2020/8842651,https://pubmed.ncbi.nlm.nih.gov/33224990/,"Zhao X, Zhang Y, Guo R, Yu W, Zhang F, Wu F , Shang J",The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes,Journal of diabetes research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Patients with Type 2 Diabetes who were admitted to the First Affiliated Hospital of Zhengzhou University from October 2018 to October 2019;  The diagnostic criteria of diabetes mellitus were as follows: (1) twice fasting plasma glucose ðFPGÞ ≥ 7:0 mmol/L, (2) twice oral glucose tolerance test (OGTT ≥ 11:1 mmol/L), and (3) diabetic symptoms (polyuria, thirst, drinking more water, and unexplained weight loss) accompanied with twice random blood glucose ≥ 11:1 mmol/L.",179,137,long-term antibiotic application,16S,34,Illumina,"Mann-Whitney (Wilcoxon),LEfSe",0.05,NA,2,"age,sex",NA,NA,decreased,NA,unchanged,NA,NA,Signature 1,Figure 2,27 June 2021,Madhubani Dey,"Madhubani Dey,Aiyshaaaa,Peace Sandy","Figure 2: Composition of the gut microbiome in the DM or Con group. (a, b) Distribution of differential flora at the phylum and genus levels between the DM and Con groups.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|976;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|248744;2|976|200643|171549|1853231|283168;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|46205;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297|13687;2|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:456/1/2,Study 456,"cross-sectional observational, not case-control",33224990,10.1155/2020/8842651,https://pubmed.ncbi.nlm.nih.gov/33224990/,"Zhao X, Zhang Y, Guo R, Yu W, Zhang F, Wu F , Shang J",The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes,Journal of diabetes research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Patients with Type 2 Diabetes who were admitted to the First Affiliated Hospital of Zhengzhou University from October 2018 to October 2019;  The diagnostic criteria of diabetes mellitus were as follows: (1) twice fasting plasma glucose ðFPGÞ ≥ 7:0 mmol/L, (2) twice oral glucose tolerance test (OGTT ≥ 11:1 mmol/L), and (3) diabetic symptoms (polyuria, thirst, drinking more water, and unexplained weight loss) accompanied with twice random blood glucose ≥ 11:1 mmol/L.",179,137,long-term antibiotic application,16S,34,Illumina,"Mann-Whitney (Wilcoxon),LEfSe",0.05,NA,2,"age,sex",NA,NA,decreased,NA,unchanged,NA,NA,Signature 2,Figure 2,27 June 2021,Madhubani Dey,"Madhubani Dey,Lwaldron,Peace Sandy","Figure 2: Composition of the gut microbiome in the DM or Con group. (a, b) Distribution of differential flora at the phylum and genus levels between the DM and Con groups.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|201174|1760|2037|2049|1654;2|201174;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572|244127;2|201174|1760|85004|31953|1678;2|95818;2|1224|1236|91347|543|544;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|976|200643|171549|2005525|375288;2|1224;2|1224|1236|91347|543|160674;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|74201;2|1239|91061|186826|33958|46255,Complete,Peace Sandy
bsdb:457/1/1,Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls group,Individuals diagnosed with Periodontitis group,"Individuals with Peridontitis; Periodontal disease was assessed by determining the PD, CAL, BI, GI, and PLI, which were then measured at six sites (i.e., mesiobuccal, buccal, distobuccal, distolingual, lingual, and mesiolingual) according to the Community Periodontal Index by an experienced dentist. Periodontitis patients had a PD of ≥ 5 mm and CAL of ≥ 3 mm.",27,31,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,"Figure 3, text",22 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Increased abundance of bacterial species in individuals with Periodontitis as compared to healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|2974251|165179;2|203691|203692|136|2845253|157|58231;2|976|200643|171549|171552|1283313|671218;2|1224|28216|80840|995019|40544;2|203691|203692|136|2845253|157|59892;2|1239|186801|186802|216572|216851|853,Complete,Claregrieve1
bsdb:457/2/1,Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP); Patients were classified into the DAP group when both periodontitis and T2DM were present.,27,46,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Supplementary Fig 3a,27 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals in DAP group compared to healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis",2|976|200643|171549|171552|1283313|671218;2|976|200643|171549|171552|2974251|165179;2|1224|28216|80840|119060|48736|329;2|1224|28216|80840|995019|40544|234908,Complete,Claregrieve1
bsdb:457/3/NA,Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals with Type 2 Diabetes; Type 2 Diabetes determined by a fasting blood sugar of > 7.0 mmol/L and an HbA1c concentration of > 7%, as stated by the American Diabetes Association in 201834",27,9,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:457/4/1,Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls,Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",27,20,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Supplementary Fig 3b,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Increased abundance of microbial communities in individuals in Met group compared to the controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|1177574;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|2974251|228604;2|1239|526524|526525|128827|123375|102148;2|203691|203692|136|2845253|157|59892;2|203691|203692|136|2845253|157|58231,Complete,Claregrieve1
bsdb:457/5/1,Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",46,20,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5c, 5d",27 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in Met group compared to DAP group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium myrsinacearum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis",2|976|200643|171549|171552|1283313|671218;2|1224|28211|356|69277|28100|28101;2|976|200643|171549|171552|2974251|165179;2|1224|28216|80840|119060|48736|329;2|1224|28216|80840|995019|40544|234908,Complete,Claregrieve1
bsdb:457/5/2,Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",46,20,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5c, 5d",27 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals of Met group compared to DAP group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans",2|976|200643|171549|171552|838|1177574;2|32066|203490|203491|1129771|34104|34105;2|1239|91061|186826|1300|1301|1309,Complete,Claregrieve1
bsdb:458/1/1,Study 458,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q, Ma Y, Ling Y, Jin W, Su Y, Wang Q, Pan J, Zhang Y, Chen H, Yuan J, Wu H , Hu B","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,"Antimicrobials, COVID-19, Escalation, Metagenomic sequencing, Superinfection",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Non-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases,COVID-19 patients,Intubated patients with critically severe COVID-19 infection,54,50,NA,WMS,NA,BGISEQ-500 Sequencing,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,17 June 2021,Claregrieve1,Claregrieve1,Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|1236|2887326|468|469;2|1224|1236|91347|543|570;2|1224|28216|80840|2975441|93681|1909303;2|1224|28216|80840|119060|48736;2|1224|28211|204457|41297|13687,Complete,Fatima
bsdb:458/1/2,Study 458,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q, Ma Y, Ling Y, Jin W, Su Y, Wang Q, Pan J, Zhang Y, Chen H, Yuan J, Wu H , Hu B","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,"Antimicrobials, COVID-19, Escalation, Metagenomic sequencing, Superinfection",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Non-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases,COVID-19 patients,Intubated patients with critically severe COVID-19 infection,54,50,NA,WMS,NA,BGISEQ-500 Sequencing,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Text,17 June 2021,Claregrieve1,Claregrieve1,Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:458/2/NA,Study 458,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q, Ma Y, Ling Y, Jin W, Su Y, Wang Q, Pan J, Zhang Y, Chen H, Yuan J, Wu H , Hu B","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,"Antimicrobials, COVID-19, Escalation, Metagenomic sequencing, Superinfection",Experiment 2,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Inbutation non-covid,critically severe covid,Intubated patients with critically severe COVID-19 infection,20,50,NA,WMS,NA,BGISEQ-500 Sequencing,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:459/1/1,Study 459,"cross-sectional observational, not case-control",34058978,10.1186/s12575-021-00148-6,NA,"Engen PA, Naqib A, Jennings C, Green SJ, Landay A, Keshavarzian A , Voigt RM",Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients,Biological procedures online,2021,"COVID-19, Dysbiosis, Microbiota, Nasopharyngeal, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who are COVID-19 positive by RT-PCR,10,9,NA,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Tables 5 & 6,17 June 2021,Claregrieve1,"Claregrieve1,Chloe,WikiWorks,Merit",Differential abundance of nasopharyngeal bacteria between COVID-19-positive and COVID-19-negative samples,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacillota|c__Bacilli",2|976|200643|171549|171552|1283313;2|1239|1737404|1737405|1570339|165779;2|976;2|201174|1760|1643682|85030|38501;2|1239|186801|186802|3085642|580596;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|976|117743|200644|2762318|59732;2|1239|1737404|1737405|1570339|150022;2|976|117743|200644|49546|237;2|1239|91061|1385|539738|1378;2|201174|1760|85006|1268|57493;2|201174|1760|85006|1268|1269;2|1224|1236|2887326|468|475;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|29465;2|1224|1236|135623|641|662;2|1239|91061,Complete,Chloe
bsdb:459/1/2,Study 459,"cross-sectional observational, not case-control",34058978,10.1186/s12575-021-00148-6,NA,"Engen PA, Naqib A, Jennings C, Green SJ, Landay A, Keshavarzian A , Voigt RM",Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients,Biological procedures online,2021,"COVID-19, Dysbiosis, Microbiota, Nasopharyngeal, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who are COVID-19 positive by RT-PCR,10,9,NA,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Tables 5 & 6,17 June 2021,Claregrieve1,Claregrieve1,Differential abundance of nasopharyngeal bacteria between COVID-19-positive and COVID-19-negative samples,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania",2|1239|91061|1385|186823|432330;2|1224|28216|206351|1499392|397456,Complete,Chloe
bsdb:460/1/NA,Study 460,"cross-sectional observational, not case-control",33903709,10.1038/s41598-021-88536-6,NA,"Braun T, Halevi S, Hadar R, Efroni G, Glick Saar E, Keller N, Amir A, Amit S , Haberman Y",SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition,Scientific reports,2021,NA,Experiment 1,Israel,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients,COVID-19 positive patients,SARS-CoV-2 presence by RT-PCR,29,26,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:461/1/1,Study 461,"cross-sectional observational, not case-control",25012901,https://doi.org/10.1038/ismej.2014.114,https://pubmed.ncbi.nlm.nih.gov/25012901/,"Mason MR, Preshaw PM, Nagaraja HN, Dabdoub SM, Rahman A , Kumar PS",The subgingival microbiome of clinically healthy current and never smokers,The ISME journal,2015,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Never smokers,Healthy Current Smokers,people who are current smokers,100,100,3 months,16S,123456789,Roche454,T-Test,0.05,FALSE,NA,"age,education level,race,sex,socioeconomic status",NA,NA,increased,NA,NA,NA,NA,Signature 1,Text,14 March 2023,Kelvin Joseph,"Kelvin Joseph,Claregrieve1,WikiWorks",The relative abundance of selected species in current smokers and nonsmokers.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter haemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sueciensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oleovorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter|s__Pseudoramibacter alactolyticus",2|1224|1236|2887326|468|469|470;2|1224|1236|2887326|468|469|106649;2|1224|1236|2887326|468|469|29430;2|1224|1236|2887326|468|469|40214;2|1224|1236|2887326|468|469|108981;2|1239|909932|1843489|31977|156454|156456;2|200940|3031451|3024411|213121|893|895;2|1239|909932|1843489|31977|39948|309120;2|1239|186801|3082720|3118655|44259|143361;2|32066|203490|203491|203492|848|77917;2|32066|203490|203491|203492|848|851;2|1239|909932|1843489|31977|906|907;2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|906|349094;2|1224|1236|72274|135621|286|330;2|1239|186801|186802|186806|113286|113287,Complete,Claregrieve1
bsdb:461/1/2,Study 461,"cross-sectional observational, not case-control",25012901,https://doi.org/10.1038/ismej.2014.114,https://pubmed.ncbi.nlm.nih.gov/25012901/,"Mason MR, Preshaw PM, Nagaraja HN, Dabdoub SM, Rahman A , Kumar PS",The subgingival microbiome of clinically healthy current and never smokers,The ISME journal,2015,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Never smokers,Healthy Current Smokers,people who are current smokers,100,100,3 months,16S,123456789,Roche454,T-Test,0.05,FALSE,NA,"age,education level,race,sex,socioeconomic status",NA,NA,increased,NA,NA,NA,NA,Signature 2,Text,14 March 2023,Kelvin Joseph,"Kelvin Joseph,Claregrieve1,WikiWorks",The relative abundance of selected species in current smokers and nonsmokers.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis",2|201174|1760|2037|2049|1654|1659;2|201174|1760|2037|2049|1654|1656;2|1239|91061|186826|186828|117563|46124;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482|28449;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1305;2|201174|1760|2037|2049|1654|272548,Complete,Claregrieve1
bsdb:462/1/1,Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Healthy controls,Individuals diagnosed with Type 1 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance of fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Dioszegia,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces",2759|4751|5204|155616|5234|1884640|165440;2759|4751|4890|4891|4892|4893|4930,Complete,Claregrieve1
bsdb:462/1/2,Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Healthy controls,Individuals diagnosed with Type 1 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance of fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls,increased,"k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Schizoporaceae|g__Xylodon",2759|4751|1913637|2212732|214503|4854|4855;2759|4751|5204|155616|90883|1851551|42658;2759|4751|5204|155619|139380|574935|1124675,Complete,Claregrieve1
bsdb:462/2/1,Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,26,30 days,16S,NA,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance of the fungal genus in individuals diagnosed with Type 2 Diabetes compared to the healthy controls,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Ganoderma,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Eukaryota|k__Fungi|p__Ascomycota|g__Saitoella,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia",2759|4751|5204|155616|5234|1905116|4970;2759|4751|5204|155619|5303|5317|5314;2759|4751|5204|155616|90886|5408|1851509;2759|4751|4890|5605;2759|4751|5204|431957|431958|431959|148959,Complete,Claregrieve1
bsdb:462/2/2,Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,26,30 days,16S,NA,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance of the fungal genus in individuals diagnosed with Type 2 Diabetes compared to healthy controls,increased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Vishniacozyma",2759|4751|5204|452283|62914|1500560;2759|4751|5204|155616|90883|1851551|42658;2759|4751|5204|155616|5234|1884640|1891946,Complete,Claregrieve1
bsdb:462/3/1,Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Individuals diagnosed with Type 1 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Ganoderma,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces",2759|4751|5204|155616|5234|1905116|4970;2759|4751|5204|155619|5303|5317|5314;2759|4751|5204|155616|90886|5408|1851509;2759|4751|5204|155616|90883|1851551|42658,Complete,Claregrieve1
bsdb:462/3/2,Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Individuals diagnosed with Type 1 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4 and Figure 6,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients,increased,"k__Eukaryota|k__Fungi|p__Ascomycota,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis",2759|4751|4890;2759|4751|4890|4891|4892|4893|4930;2759|4751|5204|452283|62914|1500560,Complete,Claregrieve1
bsdb:463/1/NA,Study 463,time series / longitudinal observational,33833065,10.1136/gutjnl-2021-324090,NA,"Chen Y, Gu S, Chen Y, Lu H, Shi D, Guo J, Wu WR, Yang Y, Li Y, Xu KJ, Ding C, Luo R, Huang C, Yu L, Xu M, Yi P, Liu J, Tao JJ, Zhang H, Lv L, Wang B, Sheng J , Li L",Six-month follow-up of gut microbiota richness in patients with COVID-19,Gut,2021,"COVID-19, intestinal microbiology",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients 6 months post-COVID-19 infection,30,30,Any antibiotic or prebiotic use in previous months,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:463/2/NA,Study 463,time series / longitudinal observational,33833065,10.1136/gutjnl-2021-324090,NA,"Chen Y, Gu S, Chen Y, Lu H, Shi D, Guo J, Wu WR, Yang Y, Li Y, Xu KJ, Ding C, Luo R, Huang C, Yu L, Xu M, Yi P, Liu J, Tao JJ, Zhang H, Lv L, Wang B, Sheng J , Li L",Six-month follow-up of gut microbiota richness in patients with COVID-19,Gut,2021,"COVID-19, intestinal microbiology",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients in convalescence,Sample from COVID-19 convalescence period (from viral clearance to 2 weeks after hospital discharge),30,30,Any antibiotic or prebiotic use in previous months,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:464/1/1,Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Confirmed COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",100,48,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Supplementary Figures 1E and 1G,21 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Saccharibacteria|s__Candidatus Saccharibacteria genomosp. TM7-H1,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Candidatus Absconditabacteria|s__candidate division SR1 bacterium,k__Bacteria|p__Candidatus Saccharibacteria|s__candidate division TM7 genomosp. GTL1",2|976;2|363464;2|95818|2080739;2|95818|2093818|2093825|2171986|1331051;2|1224|1236|135615|868|2717;2|1239|186801|3085636|186803|43996;2|201174|1760|85007|1653|1716;2|1239|186801|186802|543314;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|265975;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1224;2|1239|526524|526525|128827|123375;2|1239|91061|186826|1300|1301;2|544448;2|221235|2044938;2|95818|443342,Complete,Claregrieve1
bsdb:464/1/2,Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Confirmed COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",100,48,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Supplementary Figures 1E and 1G,21 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|29547|3031852|213849|72294|194;2|1117;2|1239|91061|186826|186828|117563;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|1263|41978;2|1239|909932|909929|1843491|970;2|203691|203692|136|137|146;2|976|200643|171549|2005525|195950,Complete,Claregrieve1
bsdb:464/2/1,Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Confirmed COVID-19 patients who recovered,150,22,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4c,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls,decreased,"k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|95818|2093818|2093825|2171986|1331051;2|1239|186801|186802|543314;2|1224|1236|135625|712|724;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:464/2/2,Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Confirmed COVID-19 patients who recovered,150,22,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4c,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1239|909932|909929|1843491|82202;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:464/3/1,Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",48,24,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Figure 5c, S3E, S3G -Supp 05",25 June 2021,Claregrieve1,"Claregrieve1,Lwaldron",Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|s__bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|526524|526525|128827|61170;2|1239|186801|186802|1392389;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|28050;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|46205;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297|13687;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|1869227;2|1239|186801|186802|216572|707003,Complete,Claregrieve1
bsdb:464/3/2,Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",48,24,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 5c,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1224|1236|135619|28256|2745;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|265975;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827|123375;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|216572|946234;2|1224|28211|356|2831106|1082930;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563,Complete,Claregrieve1
bsdb:465/1/1,Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,"Diabetic peripheral neuropathy, bile acids, blood chemistry, gastrointestinal microbiota, insulin resistance, microbial diversity, richness, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Healthy controls,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes; The criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",14,45,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 5a, 5b",24 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance of bacterial communities in individuals with diabetic peripheral neuropathy compared with healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|201174;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|561;2|1224|1236|91347|543|1940338;2|1239;2|1239|186801|3085636|186803|1506553;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|2316020|33039,Complete,Claregrieve1
bsdb:465/1/2,Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,"Diabetic peripheral neuropathy, bile acids, blood chemistry, gastrointestinal microbiota, insulin resistance, microbial diversity, richness, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Healthy controls,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes; The criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",14,45,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 5a, 5b",24 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential abundance of bacterial communities in individuals with diabetic peripheral neuropathy compared with healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|815|816;2|976;2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:465/2/NA,Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,"Diabetic peripheral neuropathy, bile acids, blood chemistry, gastrointestinal microbiota, insulin resistance, microbial diversity, richness, type 2 diabetes",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Patients with peripheral neuropathy associated with type 2 diabetes; the criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",21,45,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:465/3/NA,Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,"Diabetic peripheral neuropathy, bile acids, blood chemistry, gastrointestinal microbiota, insulin resistance, microbial diversity, richness, type 2 diabetes",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; The diagnoses of type 2 diabetes mellitus were established according to the diagnostic criteria of the American Diabetes Association,14,21,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:466/1/1,Study 466,case-control,34436669,10.1007/s00784-021-04137-7,NA,"Gopinath D, Wie CC, Banerjee M, Thangavelu L, Kumar R P, Nallaswamy D, Botelho MG , Johnson NW",Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users,Clinical oral investigations,2022,"Microbiome, Microbiota, Oral microbiome, Smokeless tobacco, Smoking, Tobacco",Experiment 1,India,Homo sapiens,Buccal mucosa,UBERON:0006956,Chewing tobacco behavior,EFO:0004774,age-matched controls,smokeless tobacco users,Smokeless tobacco users with or without areca nut.,13,14,NA,16S,34,Illumina,DESeq2,0.01,NA,NA,"age,sex",NA,increased,increased,NA,increased,NA,NA,Signature 1,Figure 5,13 June 2023,Atrayees,"Atrayees,Lwaldron",Differentially abundant taxa identified in smokeless tobacco users and controls using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces plicatus",2|1239|186801|3085636|186803|43996;2|508458|649775|649776|3029087|1434006;2|201174|1760|85011|2062|1883|1922,Complete,Lwaldron
bsdb:466/2/1,Study 466,case-control,34436669,10.1007/s00784-021-04137-7,NA,"Gopinath D, Wie CC, Banerjee M, Thangavelu L, Kumar R P, Nallaswamy D, Botelho MG , Johnson NW",Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users,Clinical oral investigations,2022,"Microbiome, Microbiota, Oral microbiome, Smokeless tobacco, Smoking, Tobacco",Experiment 2,India,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behavior,EFO:0004318,age-matched controls,Smokers who were using either bidis or cigarettes,"Smokers who were using either bidis (thin, hand-rolled cigarettes composed of tobacco wrapped in a “tendu” or “temburni” leaf) or cigarettes",13,17,NA,16S,34,Illumina,DESeq2,0.01,NA,NA,"age,sex",NA,increased,increased,NA,increased,NA,NA,Signature 1,Figure 5,13 June 2023,Atrayees,"Atrayees,Lwaldron",Differentially abundant taxa identified in smokers and controls using DESeq2.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Candidatus Saccharibacteria",2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|177971;2|95818,Complete,Lwaldron
bsdb:466/3/1,Study 466,case-control,34436669,10.1007/s00784-021-04137-7,NA,"Gopinath D, Wie CC, Banerjee M, Thangavelu L, Kumar R P, Nallaswamy D, Botelho MG , Johnson NW",Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users,Clinical oral investigations,2022,"Microbiome, Microbiota, Oral microbiome, Smokeless tobacco, Smoking, Tobacco",Experiment 3,India,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behavior,EFO:0004318,Smokeless tobacco users,Smokers,Smokers who were using either bidis or cigarettes,14,17,NA,16S,34,Illumina,DESeq2,0.01,NA,NA,"age,sex",NA,increased,increased,NA,increased,NA,NA,Signature 1,Figure 5,13 June 2023,Atrayees,Atrayees,Differentially abundant taxa identified in smokeless tobacco users and smokers using DESeq2.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",2|32066|203490|203491|203492|848;2|29547|3031852|213849|72294|194,Complete,Lwaldron
bsdb:467/1/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HER2 Positive Breast Carcinoma,EFO:1000294,Her2 negative tumor,Her2 positive tumor,Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive),25,12,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,29 June 2021,Itslanapark,Itslanapark,Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by HER2 status,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,2|1239|909932|1843488|909930|904,Complete,Claregrieve1
bsdb:467/1/2,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HER2 Positive Breast Carcinoma,EFO:1000294,Her2 negative tumor,Her2 positive tumor,Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive),25,12,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,30 June 2021,Itslanapark,"Itslanapark,Claregrieve1","Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by ER, PR, and HER2 status",decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",2|200940|3031449|213115|194924|872;2|1239|186801|186802|216572|1263;2|1239|186801|3082768|424536,Complete,Claregrieve1
bsdb:467/2/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age at menarche,EFO:0004703,early age at menarche (≤11),later age at menarche (≥12),breast cancer patients with age at menarche being over 12 years old,11,26,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,increased,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,"Itslanapark,Claregrieve1","Mean estimate ratios gound using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,2|1224|1236|91347|543|561,Complete,Claregrieve1
bsdb:467/2/2,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age at menarche,EFO:0004703,early age at menarche (≤11),later age at menarche (≥12),breast cancer patients with age at menarche being over 12 years old,11,26,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,increased,NA,NA,NA,Signature 2,Table 5,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",decreased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:467/3/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Estrogen receptor status,EFO:0005512,ER+,ER-,breast cancer patients with negative Estrogen Receptor status,9,28,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,5 July 2021,Itslanapark,Itslanapark,"Mean ratio estimates obtained by zero-inflated negative binomial model of taxa abundances by estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 status.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:467/5/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Grade Low (I/II),Grade High (III),breast cancer patients with grade high level tumors (Grade III),14,23,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,increased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,2|201174|84998|1643822|1643826|84111,Complete,Claregrieve1
bsdb:467/5/2,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Grade Low (I/II),Grade High (III),breast cancer patients with grade high level tumors (Grade III),14,23,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|207244,Complete,Claregrieve1
bsdb:467/6/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer stage,EFO:0005607,Stage Low (I/II),Stage High (III),Breast cancer patients with high stage progression of breast cancer (Stage III).,22,15,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:467/6/2,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer stage,EFO:0005607,Stage Low (I/II),Stage High (III),Breast cancer patients with high stage progression of breast cancer (Stage III).,22,15,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2|1239|909932|1843488|909930|904;2|1239|526524|526525|2810280|135858,Complete,Claregrieve1
bsdb:467/7/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Age 50+,Age ≤50,Breast cancer patients whose age is ≤50 years old.,17,20,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Kruskall-Wallis,0.001,FALSE,NA,NA,"ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543;2|1239|91061|186826|1300|1357,Complete,Claregrieve1
bsdb:467/8/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Parous,EFO:0002947,Parous,Nulliparous,Breast cancer patients who are nulliparous (have had no live births.),29,8,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Kruskall-Wallis,0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",decreased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,2|1239|526524|526525|2810280|135858,Complete,Claregrieve1
bsdb:467/9/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 9,United States of America,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,BMI<25,BMI≥25,Breast cancer patients with a high body mass index (BMI≥25),9,28,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 6,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",increased,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,Claregrieve1
bsdb:467/10/1,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,TBF≤46%,TBF>46%,Breast cancer patients with a total body fat percentage ≥46%.,25,12,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 6,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:467/10/2,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,TBF≤46%,TBF>46%,Breast cancer patients with a total body fat percentage ≥46%.,25,12,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 6,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",decreased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,2|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:467/11/NA,Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 11,United States of America,Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Yes Physical Activity,No Physical Activity,Breast cancer patients who do not have regular physical activity.,24,13,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:468/1/1,Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,NA,Experiment 1,Turkey,Homo sapiens,"Vaginal fluid,Feces,Endocervix","UBERON:0036243,UBERON:0001988,UBERON:0000458",Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women with histology-proven stage 3/4 endometriosis,14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,24 June 2021,Samara.Khan,"Samara.Khan,Peace Sandy",Diferences between microbiota in women with endometriosis and healthy controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",2|201174|1760|85004|31953|2701;2|1224|1236|91347|543|1940338;2|976|200643|171549|171552|1283313;2|1239|91061|186826|1300|1301;2|544448|2790996|2790998|2129,Complete,Peace Sandy
bsdb:468/1/2,Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,NA,Experiment 1,Turkey,Homo sapiens,"Vaginal fluid,Feces,Endocervix","UBERON:0036243,UBERON:0001988,UBERON:0000458",Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women with histology-proven stage 3/4 endometriosis,14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,5 February 2024,Peace Sandy,Peace Sandy,Diferences between microbiota in women with endometriosis and healthy controls.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",2|32066|203490|203491|1129771|168808;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|906;2|201174|1760|85004|31953|2701;2|976|200643|171549|2005519|397864,Complete,Peace Sandy
bsdb:469/1/1,Study 469,"cross-sectional observational, not case-control",34151035,10.1016/j.synbio.2021.06.002,NA,"Liu J, Liu S, Zhang Z, Lee X, Wu W, Huang Z, Lei Z, Xu W, Chen D, Wu X, Guo Y, Peng L, Lin B, Chong Y, Mou X, Shi M, Lan P, Chen T, Zhao W , Gao Z",Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19,Synthetic and systems biotechnology,2021,"COVID-19, Metabolome, Nasopharyngeal microbiome, SARS-CoV-2, Susceptibility",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID-19 controls,COVID-19 patients,Positive for infection with SARS-CoV-2 by nucleic acid testing,3,6,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figures 3c-d,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in nasopharyngeal samples between COVID-19 cases and controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",2|1239|91061|1385|539738|1378|1379;2|29547|3031852|213849|72294|194|824;2|32066|203490|203491|1129771|32067|157688;2|1239|91061|1385|539738|1378|29391;2|1224|1236|135614|32033|40323|40324,Complete,Fatima
bsdb:470/1/1,Study 470,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P , Zeller G",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,NA,Experiment 1,"France,Austria,China,United States of America,Germany,Italy,Japan",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1 (species) and extended data fig. 4 (genera),26 June 2021,Lwaldron,Lwaldron,Species and genera enriched in CRC vs controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|186801|186802|216572|244127|1872531;2|1239|186801|186802|1898207;2|1239|909932|1843489|31977|39948|1955814;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|851;2|32066|203490|203491|203492|848|76859;2|32066|203490|203491|203492|848|155615;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539738|1378|29391;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1649459|154046;2|1239|186801|3085636|186803|1506553;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|3082720|186804|1904861;2|1239|186801|3082720|186804|1257;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28133;2|1239|526524|526525|128827|123375;2|1239|526524|526525|128827|123375|102148;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|292632|2053618;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33039,Complete,NA
bsdb:470/1/2,Study 470,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P , Zeller G",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,NA,Experiment 1,"France,Austria,China,United States of America,Germany,Italy,Japan",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Extended Data Fig. 4,5 July 2021,Lwaldron,Lwaldron,Genera enriched in CRC vs controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506553;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1239|526524|526525|128827|123375;2|1239|186801|186802|216572|292632,Complete,NA
bsdb:470/1/3,Study 470,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P , Zeller G",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,NA,Experiment 1,"France,Austria,China,United States of America,Germany,Italy,Japan",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 3,Fig. 1,5 July 2021,Lwaldron,Lwaldron,Species enriched in CRC vs controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium",2|1239|1737404|1737405|1570339|165779|1287640;2|1239|186801|186802|216572|244127|1872531;2|1239|909932|1843489|31977|39948|1955814;2|1239|186801|3085636|186803|2719313|208479;2|32066|203490|203491|203492|848|851;2|32066|203490|203491|203492|848|76859;2|32066|203490|203491|203492|848|155615;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378|29391;2|1239|186801|3085636|186803|1649459|154046;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28133;2|1239|526524|526525|128827|123375|102148;2|1239|186801|186802|216572|292632|2053618;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|1898207;2|1239|186801|3082720|186804|1904861,Complete,NA
bsdb:471/1/1,Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"France,China,Austria,United States of America,Canada,Italy",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Extended Data Fig. 4,26 June 2021,Lwaldron,Lwaldron,taxonomic meta-analysis of CRC cases vs controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila sp.,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171552|1283313|76122;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1737405|1570339|165779|33037;2|1239|186801|186802|216572|244127|1872531;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|291644;2|200940|3031449|213115|194924|35832|1929485;2|200940|3031449|213115|194924|35832|35833;2|29547|3031852|213849|72294|194|824;2|29547|3031852|213849|72294|194|204;2|29547|3031852|213849|72294|194|827;2|200940|3031449|213115|194924|872|876;2|1224|28216|206351|481|538|539;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806|1730|1736;2|1239|186801|186802|216572|946234|292800;2|32066|203490|203491|203492|848|850;2|32066|203490|203491|203492|848|859;2|32066|203490|203491|203492|848|851;2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|186828|117563|46124;2|1239|186801|3085636|186803|658086;2|201174|84998|84999|1643824|2767353|1383;2|32066|203490|203491|1129771|32067|104608;2157|28890|183925|2158|2159|2172|2173;2157|28890|183925|2158|2159|2172|66852;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|1737404|1737405|1570339|162289|54005;2|1239|186801|3082720|186804|1257|1261;2|1239|186801|3082720|186804|1257|1262;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|201174|1760|2037|2049|2529408|181487;2|1239|909932|909929|1843491|970|69823;2|201174|84998|1643822|1643826|84108|84109;2|201174|84998|1643822|1643826|84108|2049041;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|1300|1301|1334;2|1239|91061|186826|1300|1301|315405;2|1239|91061|186826|1300|1301|1303|1077464;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|186802|543314|56774;2|1239|186801|3085636|186803|2316020|33039,Complete,Lwaldron
bsdb:471/1/2,Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"France,China,Austria,United States of America,Canada,Italy",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Extended Data Fig. 4,26 June 2021,Lwaldron,Lwaldron,taxonomic meta-analysis of CRC cases vs controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",2|1239|186801|3085636|186803|658081;2|1239|186801|186802|216572|1263|457412;2|1224|1236|72274|135621|286|306;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|3085636|186803|2569097|39488;2|201174|84998|1643822|1643826|447020|446660;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|841|166486;2|201174|84998|1643822|1643826|644652|471189;2|201174|1760|85004|31953|1678|1686,Complete,Lwaldron
bsdb:471/1/3,Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"France,China,Austria,United States of America,Canada,Italy",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 3,Extended Data Fig. 5,26 June 2021,Lwaldron,Lwaldron,putative oral species in CRC cases vs controls,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus",2|32066|203490|203491|203492|848|851;2|1239|1737404|1737405|1570339|543311|33033;2|1239|91061|1385|539738|1378|29391;2|1239|186801|3082720|186804|1257|341694;2|1239|526524|526525|128827|123375|102148;2|976|200643|171549|171552|838|28131;2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|186828|117563|46124;2|1224|28216|206351|481|538|539;2|29547|3031852|213849|72294|194|204;2|976|200643|171549|171552|1283313|76122;2|1239|186801|186802|543314|56774;2|29547|3031852|213849|72294|194|824;2|976|200643|171549|171552|838|28133;2|1239|91061|186826|1300|1301|1303|1077464,Complete,Lwaldron
bsdb:471/1/4,Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"France,China,Austria,United States of America,Canada,Italy",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 4,Extended Data Fig. 5,26 June 2021,Lwaldron,Lwaldron,putative oral species in CRC cases vs controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis",2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|113107,Complete,Lwaldron
bsdb:472/1/1,Study 472,case-control,34302684,10.1007/s40618-021-01595-4,https://pubmed.ncbi.nlm.nih.gov/34302684/,"Wei J, Qing Y, Zhou H, Liu J, Qi C , Gao J",16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors,Journal of endocrinological investigation,2021,"16S rRNA gene amplicon sequencing, Gestational diabetes mellitus, Gut microbiota, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant individuals who are normal glucose tolerance (NGT)],Pregnant individuals with gestational diabetes,Pregnant individuals with gestational diabetes,18,15,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3b, 3c, Table S1",16 August 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in GDM individuals as compared to NGT controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica|s__Salmonella enterica subsp. enterica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum",2|1239|186801;2|1239|186801|186802|1898207;2|1239;2|1239|186801|186802|216572|1263|40518;2|1224|1236|91347|543|590|28901|59201;2|1239|186801|3085636|186803|1506577|36835,Complete,Claregrieve1
bsdb:472/1/2,Study 472,case-control,34302684,10.1007/s40618-021-01595-4,https://pubmed.ncbi.nlm.nih.gov/34302684/,"Wei J, Qing Y, Zhou H, Liu J, Qi C , Gao J",16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors,Journal of endocrinological investigation,2021,"16S rRNA gene amplicon sequencing, Gestational diabetes mellitus, Gut microbiota, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant individuals who are normal glucose tolerance (NGT)],Pregnant individuals with gestational diabetes,Pregnant individuals with gestational diabetes,18,15,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3b, 3c, Table S1",16 August 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in GDM individuals as compared to NGT controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium",2|976|200643|171549;2|976;2|976|200643;2|1239|186801|3085636|186803|140625,Complete,Claregrieve1
bsdb:473/1/1,Study 473,"cross-sectional observational, not case-control",33659220,10.3389/fcimb.2021.625581,NA,"Nardelli C, Gentile I, Setaro M, Di Domenico C, Pinchera B, Buonomo AR, Zappulo E, Scotto R, Scaglione GL, Castaldo G , Capoluongo E",Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to <i>Fusobacterium periodonticum</i>?,Frontiers in cellular and infection microbiology,2021,"Fusobacterium periodonticum, SARS-CoV-2, microbiota, nasopharyngeal swab, next generation sequencing",Experiment 1,Italy,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Symptomatic COVID-19 positive patients,12,18,NA,16S,123,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3A-F,28 June 2021,Claregrieve1,"Claregrieve1,Peace Sandy","Nasopaheryngeal microbiome composition in COVID-19 patients and Control group. The graphs show the percentage of relative abundance (%) of the all taxonomic levels from Phylum to Species, obtained by using the MicrobAT Suite - SmartSeq. Each column in the plot represents a group, and each color in the column represents the relative abundance (%) for each taxon. In panel (A) we show the phyla with average relative abundance greater than 1% in all studied groups; we found two phyla significantly less abundant in COVID-19 patients respect to Controls, Proteobacteria, and Fusobacteria. Not statistically significant difference in taxa abundance was observed when T0 and T1 COVID-19 patients were compared. The other panels (B–F) show the taxa abundance from class to up species level significantly different between groups by Kruskal Wallis test. (B) class (C) order, (D) family, (E) genus (F) species. *p < 0.05; **p < 0.001.",decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|32066|203490|203491|203492;2|32066|203490|203491;2|32066;2|32066|203490|203491|203492|848;2|1224|1236;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1224|1236|135625|712;2|1224|1236|135625,Complete,Peace Sandy
bsdb:474/1/1,Study 474,case-control,33977168,10.1016/j.genrep.2021.101200,NA,"Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA , Siddiki AZ",Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases,Gene reports,2021,"COPD, COVID-19, Diversity, Microbiome, Non-COVID, SARS-CoV-2, URTI",Experiment 1,"Bangladesh,China,United Kingdom,United States of America",Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID patients with URTI or COPD,COVID-19 patients,Confirmed COVID-19 diagnosis by RT-qPCR,10,11,NA,WMS,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Text/Figure 3,28 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differential abundance of bacteria between non-COVID-19 patients and COVID-19 patients,increased,"k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Fusobacteriota",2|1117;2|1224;2|544448;2|32066,Complete,Fatima
bsdb:474/1/2,Study 474,case-control,33977168,10.1016/j.genrep.2021.101200,NA,"Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA , Siddiki AZ",Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases,Gene reports,2021,"COPD, COVID-19, Diversity, Microbiome, Non-COVID, SARS-CoV-2, URTI",Experiment 1,"Bangladesh,China,United Kingdom,United States of America",Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID patients with URTI or COPD,COVID-19 patients,Confirmed COVID-19 diagnosis by RT-qPCR,10,11,NA,WMS,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Text/Figure 3,28 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differential bacterial abundance between non-COVID-19 patients and COVID-19 patients,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota",2|201174;2|976;2|1239,Complete,Fatima
bsdb:475/1/NA,Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Non-COVID-19 patients (Group NP),"6 COVID-19 patients, 10 non-COVID-19 patients, 2 healthy controls",13,18,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:475/2/NA,Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 2,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type I Patients,"16 COVID-19 patients, 2 healthy controls",13,18,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,increased,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:475/3/NA,Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type II patients,"47 COVID-19 patients, 1 healthy control",13,48,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,increased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:475/4/NA,Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 4,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type III patients,"10 COVID-19 patients, 1 healthy control",13,11,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:475/5/NA,Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 5,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type IV patients,4 COVID-19 patients,13,4,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:475/6/NA,Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 6,China,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Group I - High Diversity COVID-19 patients,Group II - Medium Diversity COVID-19 patients,Patients with medium microbial diversity in rectal samples,15,24,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:475/7/NA,Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 7,China,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Group I - High Diversity COVID-19 patients,Group III - Low Diversity COVID-19 patients,Patients with low microbial diversity in rectal swab samples,15,24,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:476/1/1,Study 476,case-control,34055851,10.3389/fnut.2021.638825,NA,"Tian Y, Sun KY, Meng TQ, Ye Z, Guo SM, Li ZM, Xiong CL, Yin Y, Li HG , Zhou LQ",Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery,Frontiers in nutrition,2021,"16S sequence, SARS-CoV-2, gut microbiota, recovered COVID-19 patient, short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,"Patients between 25-45 years of age with documented recovery from COVID-19, detailed medical records during hospitalization and discharge certificate",7,7,Participants instructed to avoid any drugs affecting gastrointestinal function before sampling,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,decreased,decreased,NA,NA,Signature 1,Figure 4b,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between controls and recovered COVID-19 patients,increased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lycidae|s__Metriorrhynchinae|g__Microtrichalus,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae|g__Candidatus Microthrix,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",2|201174|84992;2759|33208|6656|50557|7041|71195|2043424|343821;2|201174|84992|84993|1798913|41949;2|201174|84992|84993|1798913;2|201174|1760|85006|1268|32207;2|201174|1760|85006;2|1239|526524|526525|2810280|1505663;2|201174|1760|85006|1268,Complete,Fatima
bsdb:476/1/2,Study 476,case-control,34055851,10.3389/fnut.2021.638825,NA,"Tian Y, Sun KY, Meng TQ, Ye Z, Guo SM, Li ZM, Xiong CL, Yin Y, Li HG , Zhou LQ",Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery,Frontiers in nutrition,2021,"16S sequence, SARS-CoV-2, gut microbiota, recovered COVID-19 patient, short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,"Patients between 25-45 years of age with documented recovery from COVID-19, detailed medical records during hospitalization and discharge certificate",7,7,Participants instructed to avoid any drugs affecting gastrointestinal function before sampling,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,decreased,decreased,NA,NA,Signature 2,Figure 4b,29 June 2021,Claregrieve1,"Claregrieve1,Merit",Differential abundance of microbial taxa between controls and recovered COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|2569097|39488;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263|41978;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572;2|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:477/1/1,Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 1,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients,Patients with confirmed COVID-19 infection and severe symptoms; required hospital admission,18,18,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552|1283313;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|1239|526524|526525|128827,Complete,Fatima
bsdb:477/2/1,Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 2,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients requiring ICU,Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit,18,19,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care,increased,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,2|203691|203692|136|2845253|157,Complete,Fatima
bsdb:477/2/2,Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 2,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients requiring ICU,Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit,18,19,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S5,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care,decreased,k__Eukaryota|s__uncultured phototrophic eukaryote,2759|172788,Complete,Fatima
bsdb:477/3/1,Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 3,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with confirmed COVID-19 infection and severe symptoms who were hospitalized,19,18,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacterial taxa between mild and severe COVID-19 cases,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Fatima
bsdb:478/1/1,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,13 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",2|201174|1760|85009|31957|2801844;2|201174|1760|2037|2049|2050;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|265975|712414;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2419515;2|201174|84998|1643822|1643826|84108;2|201174|1760|85009|31957|2801844|1750,Complete,Atrayees
bsdb:478/1/2,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus nagelii",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|2767888|82688,Complete,Atrayees
bsdb:478/2/1,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 2,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Flu patients,COVID-19 patients,Confirmed COVID-19 cases,29,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and other flu patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",2|201174|1760|85009|31957|2801844;2|1239|91061|186826|33958|2742598|1613;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|265975|712414;2|976|200643|171549|171552|838|419005;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2419515;2|201174|84998|1643822|1643826|84108;2|201174|1760|85009|31957|2801844|1750,Complete,Atrayees
bsdb:478/3/1,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,29,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus nagelii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|2767888|82688;2|1239|91061|186826|33958|2742598|1613;2|976|200643|171549|171552|838|419005,Complete,Atrayees
bsdb:478/3/2,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,29,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",2|1239|186801|3085636|186803|265975;2|201174|1760|85009|31957|2801844;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|2050;2|201174|1760|85006|1268|32207|2419515;2|1239|186801|3085636|186803|265975|712414;2|201174|1760|85009|31957|2801844|1750,Complete,Atrayees
bsdb:478/4/1,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 4,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a-b,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls by LefSe,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",2|201174|1760|2037|2049|76833;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|201174|1760|85006|85016|1707;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84162;2|1239|186801|3082720|3118655|44259;2|201174|1760|85006|2805426|57499;2|1239|186801|3085636|186803|1164882;2|1239|186801|3082720|3030910|86331;2|1239|1737404|1737405|1570339|543311;2|201174|1760|85009|31957|1743;2|201174|1760|2037|2049|2529408;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|186801|3085636|186803|265975;2|201174|1760|85006|85017|186188;2|201174|1760|85009|31957|2801844;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|184869;2|201174|1760|2037|2049|2050,Complete,Atrayees
bsdb:478/4/2,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 4,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a-b,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls by LefSe,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|186827|46123,Complete,Atrayees
bsdb:478/5/1,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 5,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,28,29,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls by LefSe,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|186801|3085636|186803|265975;2|201174|1760|85006|85017|186188;2|201174|1760|85009|31957|2801844;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|184869,Complete,Atrayees
bsdb:478/5/2,Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 5,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,28,29,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls by LefSe,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:479/1/1,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 1,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Healthy controls,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,10,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Table S1,30 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and ICU COVID-19 patients,decreased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Deinococcota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Tepidiphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Thermosinus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Tissierellia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",2|95818;2|1297;2|1224|1236|135624|84642;2|1239|91061|1385|186823;2|1224|28211|204458|76892;2|1224|28216|206351|1499392;2|1297|188787|118964|183710;2|29547|3031852|213849|72293;2|1224|2008785|119069|206349;2|201174|1760|85006|85021;2|1224|28216|80840|75682;2|201174|84995|84996|84997;2|1239|909932|909929|1843490;2|1239|186801|68295|186814;2|1239|186801|68295|543371;2|1224|1236|2887326|468|469;2|1224|1236|135624|84642|642;2|201174|1760|85006|1268|1663;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1224|28216|80840|119060|32008;2|1239|186801|3085636|186803|830;2|1239|186801|186802|31979|1485;2|1297|188787|118964|183710|1298;2|1239|186801|3082720|3118655|44259;2|1224|28216|206351|1499392|397456;2|1239|186801|3085636|186803|43994;2|201174|1760|85006|85023|33882;2|1224|1236|135625|712|745;2|1224|28216|80840|2975441|335058;2|1224|28216|80840|119060|48736;2|201174|84995|84996|84997|42255;2|1224|28216|206351|481|1193515;2|1224|2008785|119069|206349|203470;2|1239|186801|68295|186814|1754;2|1239|186801|68295|186814|28895;2|1239|909932|909929|1843490|261684;2|976|117743|200644|49546;2|544448|31969;2|1224|28216|206351;2|976|200643|171549|171551;2|1239|909932|909929|1843491;2|1239|1737404;2|1224|28216|80840|80864|34072,Complete,Atrayees
bsdb:479/1/2,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 1,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Healthy controls,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,10,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Table S1,30 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and ICU COVID-19 patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|201174|1760|85006|85020;2|1224|1236|91347|1903409;2|201174|1760|85007|85025;2|1224|1236|91347|1903410;2|29547|3031852|213849;2|1224|1236|135614|32033;2|1224|1236|91347|1903411;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|1506553;2|201174|1760|85007|2805586|1847725;2|201174|1760|85006|1268|1269;2|201174|84998|84999|1643824|133925;2|1239|91061|1385|186822|44249;2|1224|1236|91347|1903409|53335;2|201174|1760|85007|85025|1827;2|1224|1236|91347|543|590;2|201174|1760|85004|31953|196081;2|1224|1236|91347|1903411|613;2|1224|1236|135614|32033|40323;2|1239|186801|186802|543314;2|201174|1760|85007;2|1239|91061|186826|81852;2|1224|1236|72274|135621;2|1239|91061|1385|90964,Complete,Atrayees
bsdb:479/2/1,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 2,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Healthy controls,Mild-moderate COVID-19 patients,COVID-19 patients with mild to moderate symptoms that were not admitted to an intensive care unit,10,11,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases,decreased,"k__Bacteria|p__Deinococcota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Okadaella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Tepidiphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Thermosinus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",2|1297;2|1239|91061|1385|186823;2|1224|28211|204458|76892;2|1224|28216|206351|1499392;2|1224|2008785|119069|206349;2|201174|1760|85006|85021;2|201174|1760|85006|85023;2|1224|28216|80840|75682;2|201174|84995|84996|84997;2|1239|909932|909929|1843490;2|1239|186801|68295|186814;2|1239|186801|68295|543371;2|1224|28216|80840;2|201174|1760|85006|1268|1663;2|1239|526524|526525|128827|118747;2|1224|28216|80840|119060|32008;2|1297|188787|118964|183710|1298;2|1224|28216|206351|1499392|397456;2|1239|186801|3085636|186803|43994;2|201174|1760|85006|1268|57493;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|948104;2|1224|28216|80840|2975441|335058;2|1224|28216|80840|119060|48736;2|201174|84995|84996|84997|42255;2|1224|28216|206351|481|1193515;2|1224|2008785|119069|206349|203470;2|1239|186801|68295|186814|1754;2|1239|186801|68295|186814|28895;2|1239|909932|909929|1843490|261684;2|1224|28216|80840|119060;2|1239|186801|186802|31979;2|201174|1760|85007;2|1224|1236|91347|543;2|29547;2|201174|1760|85009|31957;2|1239|909932|909929|1843491;2|1224|28216|80840|80864|34072,Complete,Atrayees
bsdb:479/2/2,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 2,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Healthy controls,Mild-moderate COVID-19 patients,COVID-19 patients with mild to moderate symptoms that were not admitted to an intensive care unit,10,11,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases,increased,"k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1297|188787|118964|183710;2|1224|28211|356|119045;2|1224|28211;2|29547|3031852|213849;2|29547;2|976|117743|200644;2|544448;2|1239|186801|53433|972|2330;2|1224|28211|356|119045|407;2|32066|203490|203491|1129771|34104;2|1239|186801|186802|543314;2|1239|91061|186826|81852;2|1239|186801|186802|186806;2|1224|1236|2887326|468;2|544448|31969|2085|2092;2|1239|91061|1385|90964,Complete,Atrayees
bsdb:479/3/1,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 3,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Mild-Moderate COVID-19 patients,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,11,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Tissierellia",2|1224|1236|2887326|468|469;2|1224|1236|135624|84642;2|1224|1236|135624|84642|642;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|1239|186801|3085636|186803|830;2|95818;2|1239|186801|186802|31979|1485;2|1239|186801|3082720|3118655|44259;2|976|117743|200644;2|1239|186801|53433|972;2|1239|186801|53433|972|2330;2|29547|3031852|213849|72293;2|1224|28211|356|119045|407;2|544448|31969|2085|2092;2|1224|1236|135625|712|745;2|544448|31969|2085|2092;2|544448|31969;2|1224|1236|2887326|468;2|201174|1760|85006|1268;2|32066|203490|203491;2|32066|203490|203491|203492;2|976|117743|200644|49546;2|1239|186801|186802|186806;2|29547;2|1224|28211;2|201174|1760|85004|31953;2|1224|28216|206351;2|976|200643|171549|171551;2|544448;2|1239|1737404,Complete,Atrayees
bsdb:479/3/2,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 3,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Mild-Moderate COVID-19 patients,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,11,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Okadaella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1224|1236|91347|543|547;2|1224|1236|91347|1903409;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|201174|1760|85006|1268|57493;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|1300|1357;2|201174|1760|85007|2805586|1847725;2|201174|1760|85006|85023;2|201174|1760|85006|1268|1269;2|201174|1760|85007|85025;2|1239|91061|186826|1300|948104;2|201174|84998|84999|1643824|133925;2|1239|91061|1385|186822|44249;2|1224|1236|91347|1903409|53335;2|1224|1236|91347|1903410;2|201174|1760|85007|85025|1827;2|1224|1236|91347|543|590;2|201174|1760|85004|31953|196081;2|1224|1236|91347|1903411|613;2|1224|1236|135614|32033|40323;2|1224|1236|135614|32033;2|1224|1236|91347|1903411;2|201174|1760|85007|1653;2|201174|1760|85007;2|1224|1236|91347|543;2|201174|1760|85009|31957;2|1224|1236|72274|135621|286;2|1224|1236|135614|32033,Complete,Atrayees
bsdb:479/4/1,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 4,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Patients infected with other human coronaviruses,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,8,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,"Claregrieve1,Atrayees",Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Arsenophonus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Casaltella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Demequinaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacillota|c__Tissierellia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|28211|204441|433;2|1224|1236|2887326|468|469;2|201174|1760|2037|2049|1654|29317;2|1224|1236|135624|84642;2|1224|1236|135624|84642|642;2|1224|28216|80840|506;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1224|1236|91347|1903414|637;2|201174|1760|85006|1268|1663;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|201174|1760|1643682|85030|38501;2|1239|186801|3085636|186803|572511;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696;2|1224|28211|204458|76892|41275;2|1224|28216|80840|119060|32008;2|1239|186801|186802|543314|1715793;2|1224|28211|204458|76892|75;2|1224|28211|204458|76892;2|1224|1236|1706369|1706371;2|976|1853228|1853229|563835;2|1239|186801|3082768|424536;2|976|117743|200644|2762318|59732;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107;2|1224|28216|80840|119060|106589;2|201174|1760|85006|1042322;2|200940|3031449|213115|194924;2|1239|186801|3085636|186803|189330;2|1239|91061|186826|186827|66831;2|1239|186801|3082720|3118655|44259;2|201174|1760|1643682|85030;2|1239|526524|526525|128827|1573535;2|201174|1760|85006|85021;2|201174|1760|85006|85021|53457;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045;2|1224|28211|356|119045|407;2|201174|1760|85006|85023|33882;2|1224|1236|91347|1903414;2|201174|1760|85007|1762;2|201174|1760|85007|1762|1763;2|1239|909932|1843489|31977|909928;2|201174|1760|85009|85015;2|201174|1760|85009|85015|1839;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231;2|1224|28216|80840|75682;2|976|200643|171549|2005525|375288;2|1224|28211|204455|31989|265;2|976|117747|200666|84566|84567;2|1224|28216|80840|2975441|335058;2|1239|91061|1385|186818;2|201174|1760|85010|2070;2|1224|28216|80840|119060|48736;2|1224|28211|356|82115;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|201174|84995|84996|84997|42255;2|201174|84995|84996|84997;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263;2|201174|1760|85010|2070|1835;2|1224|28216|206351|481|1193515;2|976|117747|200666|84566;2|1224|28211|204457|41297;2|1224|28211|204457|41297|13687;2|1239|186801|3085636|186803|1506577;2|1224|1236|135614|32033|338;2|201174|1760|2037;2|1224|28211;2|1239|91061|1385|186817;2|1224|28216|80840|119060;2|1224|28216|80840;2|1239|186801|186802|31979;2|201174|1760|85006|85020;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|186806;2|976|117743|200644|49546;2|201174|1760|85006|85021;2|201174|1760|85006|85023;2|201174|1760|85006|1268;2|1224|28216|206351;2|201174|1760|85007|85025;2|1224|28211|204455|31989;2|1239|1737404|1737405|1570339;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297;2|1239|1737404;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:479/4/2,Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 4,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001729,UBERON:0001728",COVID-19,MONDO:0100096,Patients infected with other human coronaviruses,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,8,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1239|91061|186826|1300|1357;2|1224|1236|91347|543|590;2|201174|1760|85004|31953|196081;2|1224|1236|91347|1903411|613;2|29547|3031852|213849;2|1239|186801|186802|543314|2137877;2|1239|91061|186826|81852;2|1224|1236|72274|135621,Complete,Atrayees
bsdb:480/1/1,Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 1,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Control group,Vaginal Fluid,"Vaginal samples were collected and processed for the evaluation of
their bacterial profile:",11,21,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,There was increased abundance of gemella and streptococcus when comparing the vaginal fluid of endometriosis patients to healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:480/1/2,Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 1,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Control group,Vaginal Fluid,"Vaginal samples were collected and processed for the evaluation of
their bacterial profile:",11,21,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"There was decreased abundance of aerococcus in vaginal fluid of endometriosis patients compared to healthy controls. Atopobium, which is normally found in the lower female reproductive tract, was completely absent in vaginal fluid of endometriosis patients.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",2|1239|91061|186826|186827|1375;2|201174|84998|84999|1643824|1380,Complete,Peace Sandy
bsdb:480/2/1,Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 2,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Control group,Eutopic Endometrium Samples,"Eutopic Endometrium samples were collected and processed for the evaluation of
their bacterial profile:",11,18,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,There was increased abundance of bifidobacterium when comparing the endometrial lining of endometriosis patients to healthy controls,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:480/2/2,Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 2,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Control group,Eutopic Endometrium Samples,"Eutopic Endometrium samples were collected and processed for the evaluation of
their bacterial profile:",11,18,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"There was decreased abundance of atopobium, mobiluncus, campylobacter, chromohalobacter, and alcanivorax when comparing the endometrial lining of endometriosis patients to healthy controls",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Chromohalobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",2|1224|1236|135619|224372|59753;2|201174|84998|84999|1643824|1380;2|29547|3031852|213849|72294|194;2|1224|1236|135619|28256|42054;2|201174|1760|2037|2049|2050,Complete,Peace Sandy
bsdb:480/3/1,Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 3,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Controls group,endometriotic lesion samples,"endometriotic lesion samples  collected and processed for the evaluation of
their bacterial profile:",11,8,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were increased: aerococcus, staphylococcus, sphingomonas, alishewanella, pseudomonas, and enterococcus",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|91061|186826|186827|1375;2|1239|91061|1385|90964|1279;2|1224|28211|204457|41297|13687;2|1224|1236|135622|72275|111142;2|1224|1236|72274|135621|286;2|1239|91061|186826|81852|1350,Complete,Peace Sandy
bsdb:480/3/2,Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 3,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Controls group,endometriotic lesion samples,"endometriotic lesion samples  collected and processed for the evaluation of
their bacterial profile:",11,8,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were decreased: prevotella, atopobium, afipia, mobiluncus, campylobacter, and facklamia",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia",2|976|200643|171549|171552|838;2|201174|84998|84999|1643824|1380;2|1224|28211|356|41294|1033;2|201174|1760|2037|2049|2050;2|29547|3031852|213849|72294|194;2|1239|91061|186826|186827|66831,Complete,Peace Sandy
bsdb:481/1/1,Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,5,13,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3d,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between healthy controls and COVID-19 patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA",2|1239|186801|3085636|186803|2316020|33038;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|2810280|3025755|1547;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|658082;2|1239|186801|3085636|186803|658655,Complete,Atrayees
bsdb:481/1/2,Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,5,13,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3d,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between healthy controls and COVID-19 patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis",2|976|200643|171549|171550|239759|1470347;2|1239|186801|3085636|186803|841|166486;2|1224|28216|80840|469610;2|1239|186801|3085636|186803|2569097|39488;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|171550|239759|626932;2|976|200643|171549|2005519|1348911|1099853;2|1239|186801|3085636|186803|28050|39485;2|976|200643|171549|2030927;2|976|200643|171549|815|816|291644;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|216572|1263|40518;2|976|200643|171549|815|909656|204516,Complete,Atrayees
bsdb:481/2/1,Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Antibiotic-naive COVID-19 patients,Antibiotic-treated COVID-19 patients,Patients with COVID-19 treated with antibiotics,8,5,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",2|1239|909932|1843489|31977|29465|29466;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|2810280|3025755|1547,Complete,Atrayees
bsdb:481/2/2,Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Antibiotic-naive COVID-19 patients,Antibiotic-treated COVID-19 patients,Patients with COVID-19 treated with antibiotics,8,5,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3g,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2 1 46FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|1239|186801|186802|216572|292632|2053618;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|841|301301;2|1224|28216|80840|995019|577310|487175;2|1239|186801|3085636|186803|2683689;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|33042|116085;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|909656|821,Complete,Atrayees
bsdb:481/3/1,Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with severe COVID-19,3,3,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild and severe COVID-19 patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glucuronolyticum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella glucosivorans,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis",2|201174|1760|85007|1653|1716|61592;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|81852|1350|1352;2|29547|3031852|213849|72294|194|824;2|201174|1760|85007|1653|1716|39791;2|201174|1760|85006|1268|32207|172042;2|201174|1760|85004|31953|419014|419015;2|1239|91061|186826|81852|1350|33945;2|1239|91061|186826|81852|1350|37734;2|1239|91061|186826|33958|1243|1246;2|1239|91061|186826|33958|46255|1583;2|1224|28216|80840|80864|80865;2|1224|28216|206351|481|538|2766967;2|29547|3031852|213849|72294|194|199;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|570|548;2|1239|91061|186826|1300|1301|68892;2|1239|909932|1843489|31977|906|187326,Complete,Atrayees
bsdb:481/3/2,Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with severe COVID-19,3,3,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild and severe COVID-19 patients,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,2|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:482/1/1,Study 482,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J , Zhao J",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,NA,Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,8,15,NA,WMS,NA,DNBSEQ-T7,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2c,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between mild and severe COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838,Complete,Fatima
bsdb:482/1/2,Study 482,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J , Zhao J",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,NA,Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,8,15,NA,WMS,NA,DNBSEQ-T7,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2c,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between mild and severe COVID-19 patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1239|91061|1385|90964|1279;2|1224|1236|91347|543|561,Complete,Fatima
bsdb:482/2/1,Study 482,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J , Zhao J",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,NA,Experiment 2,China,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,7,15,NA,WMS,NA,DNBSEQ-T7,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S6b,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between mild and severe COVID-19 patients,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,Fatima
bsdb:483/1/1,Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, pneumonia patients, antibiotics treated COVID-19 patients",Antibiotic-naive COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, not treated with antibiotics",29,7,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii",2|201174|1760|2037|2049|1654|1656;2|1239|186801|3085636|186803|1649459|154046;2|976|200643|171549|815|816|291645,Complete,Chloe
bsdb:483/1/2,Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, pneumonia patients, antibiotics treated COVID-19 patients",Antibiotic-naive COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, not treated with antibiotics",29,7,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 August 2021,Chloe,Chloe,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and healthy controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,2|1239|186801|186802|186806|1730|39496,Complete,Chloe
bsdb:483/2/1,Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Antibiotic-naive COVID-19 patients, pneumonia patients, uninfected controls",Antibiotic-treated COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, treated with antibiotics",28,8,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive and antibiotic-treated COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|216572;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|658089;2|1239|186801|186802|186806|1730|39496,Complete,Chloe
bsdb:483/3/1,Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, COVID-19 patients",Pneumonia controls,Patients hospitalized with community-acquired pneumonia,30,6,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,"Claregrieve1,Chloe",Differential abundance of microbial taxa between healthy controls and pneumonia controls,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",2|1239|526524|526525|2810280|100883;2|1239|91061|186826|81852|1350|1352;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|3085636|186803|658089;2|1239|186801|186802|186806|1730|39496,Complete,Chloe
bsdb:484/1/1,Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,"ACE2, COVID-19, Campylobacter, Metagenome sequencing, Prevotella, Streptococcus",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients with fever and cough,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,11,11,NA,WMS,NA,MGISEQ-2000,ANOVA,0.05,FALSE,NA,NA,NA,decreased,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and non-COVID-19 patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1239|91061|186826|1300|1301|1759399;2|1239|91061|186826|1300|1301|1311;2|1239|91061|186826|1300|1301|1307;2|29547|3031852|213849|72294|194|197;2|976|200643|171549|171552|558436|839;2|976|200643|171549|171552|838|59823,Complete,Fatima
bsdb:484/2/1,Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,"ACE2, COVID-19, Campylobacter, Metagenome sequencing, Prevotella, Streptococcus",Experiment 2,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Healthy controls,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,7,11,NA,WMS,NA,MGISEQ-2000,ANOVA,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 3,9 April 2023,Aiyshaaaa,Aiyshaaaa,Analysis of species with differential abundance among the COVID-19 and healthy cohorts.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus sanguinicola,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus koreensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus uberis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rodentium",2|1239|91061|186826|186827|1375|119206;2|29547|3031852|213849|72294|194|199;2|29547|3031852|213849|72294|194|204;2|1239|186801|186802|31979|1485|1491;2|32066|203490|203491|203492|848|2663009;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|1164882|617123;2|32066|203490|203491|1129771|32067|157687;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|1177574;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|2974251|28135;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|2382163;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1307;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|1349;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|248315,Complete,NA
bsdb:484/3/NA,Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,"ACE2, COVID-19, Campylobacter, Metagenome sequencing, Prevotella, Streptococcus",Experiment 3,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Healthy controls,COVID-19 negative patients with fever and cough,COVID-19 negative patients with fever and cough,7,11,NA,WMS,NA,MGISEQ-2000,ANOVA,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:484/4/1,Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,"ACE2, COVID-19, Campylobacter, Metagenome sequencing, Prevotella, Streptococcus",Experiment 4,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients with fever and cough,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,11,11,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,NA,NA,NA,decreased,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S5,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and symptomatic non-COVID-19 patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus sanguinicola,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 299,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix|s__Erysipelothrix sp. HDW6B,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema phagedenis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus troglodytae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix|s__Erysipelothrix larvae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HSISM1,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus teuberi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus koreensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ruminicola,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema brennaborense,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella cardium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium camelliae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix|s__Brochothrix thermosphacta,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus marmotae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium divergens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Fermentimonas|s__Fermentimonas caenicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus uberis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",2|1239|91061|186826|1300|1301|1759399;2|1239|186801|3085636|186803|28050|39485;2|1239|91061|186826|186827|1375|119206;2|29547|3031852|213849|72294|194|197;2|1239|186801|3085636|186803|1164882|617123;2|976|200643|171549|171551|836|837;2|29547|3031852|213849|72294|194|199;2|1239|91061|186826|1300|1301|1156431;2|976|200643|171549|171552|558436|839;2|1239|91061|186826|1300|1301|113107;2|1239|91061|1385|539738|1378|1379;2|976|200643|171549|171552|838|652716;2|1239|909932|1843489|31977|29465|39777;2|32066|203490|203491|203492|848|2663009;2|29547|3031852|213849|72294|194|204;2|1239|526524|526525|128827|1647|2714929;2|203691|203692|136|2845253|157|162;2|976|117743|200644|49546|1016|1019;2|1239|91061|186826|1300|1301|1111760;2|1239|526524|526525|128827|1647|1514105;2|1239|91061|186826|1300|1301|1316408;2|1239|91061|186826|1300|1301|1307;2|1239|91061|186826|1300|1301|1156433;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|81852|2737|519472;2|1239|91061|186826|1300|1301|2382163;2|1239|91061|186826|1300|1301|2698804;2|203691|203692|136|2845253|157|81028;2|976|117743|200644|2762318|59735|1585976;2|976|200643|171549|171552|838|28129;2|1239|91061|186826|1300|1301|1305;2|976|117743|200644|2762318|59732|1265445;2|1239|91061|1385|186820|2755|2756;2|976|200643|171549|171551|836|36874;2|1239|91061|186826|1300|1301|1825069;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|186828|2747|2748;2|976|200643|171549|2005520|1784836|1562970;2|976|200643|171549|171552|2974251|28135;2|1239|91061|186826|186828|2747|2751;2|1239|91061|186826|1300|1301|45634;2|1239|186801|3085636|186803|1506553|66219;2|32066|203490|203491|1129771|32067|712357;2|976|200643|171549|171551|836|28123;2|976|200643|171549|815|816|28113;2|29547|3031852|213849|72294|194|827;2|1239|91061|186826|1300|1301|1349;2|1239|91061|186826|1300|1301|1311,Complete,Fatima
bsdb:485/1/1,Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2759|4751|4890|4891|4892|4893|4930;2|1239|91061|186826|81852|1350,Complete,Fatima
bsdb:485/1/2,Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|1239|186801|3085636|186803|207244;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|201174|84998|1643822|1643826|84111,Complete,Fatima
bsdb:485/2/1,Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S5-7,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,increased,"k__Eukaryota|k__Fungi|p__Ascomycota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis",2759|4751|4890;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|544;2759|4751|4890|4891|4892|4893|4930;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|2719313|208479;2759|4751|4890|4891|4892|4893|4930|4932;2|1224|1236|135625|712|724|729;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|1896336;2|1239|91061|186826|81852|1350|1351,Complete,Fatima
bsdb:485/2/2,Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Tables S5-7,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA",2|1224|28216|80840|995019|577310;2|201174|84998|1643822|1643826|644652;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|658087;2|1239|526524|526525|128827|469614;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|371601;2|1239|186801|3085636|186803|658086;2|1239|186801|186802|186806|1730|39490;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|207244|649756;2|1224|28216|80840|469610;2|1239|186801|3085636|186803|658089;2|1239|186801|3085636|186803|658082,Complete,Fatima
bsdb:486/1/1,Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,Asymptomatic COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with no symptoms,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,3 July 2021,Claregrieve1,"Claregrieve1,Merit",Differential microbial abundance between healthy volunteers and asymptomatic COVID-19 patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Diptera|f__Micropezidae|s__Calobatinae|g__Compsobata|s__Compsobata cibaria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Hemiptera|f__Aphididae|s__Aphidinae|g__Ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.",2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106|74426;2759|33208|6656|50557|7147|115293|115294|286452|1262234;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|547;2|1239|186801|3085636|186803|2719313|358743;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578|1587;2759|33208|6656|50557|7524|27482|133076|666060;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171551;2|1239|186801|186802|216572|1263;2|1224|1236|91347|543|620;2|1224|1236|91347|543|620|622;2|1239|91061|186826|33958|46255;2|1239|186801|3085636|186803|2316020|33038;2|1224|1236|91347|543;2|1239|186801;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|216572|1263|41978;2|1239|186801|186802|216572|1263;2|1239|91061|186826|81852|1350|35783,Complete,Fatima
bsdb:486/1/2,Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,Asymptomatic COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with no symptoms,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,3 July 2021,Claregrieve1,"Claregrieve1,Fatima",Differential microbial abundance between healthy volunteers and asymptomatic COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|1843488|909930|904;2|1224|1236|135624;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678|1680;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|1239|186801|3085636|186803|2719313|1531;2|29547;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|81850;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1239|909932|909929|1843491|52225|52226;2|201174|84998|84999|1643824|133925;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171552|2974251|165179;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|301302;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40519;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|1239|909932|1843489|31977;2|1239|91061|186826|33958;2|1224|1236|135625|712;2|1239|909932|1843489|31977,Complete,Fatima
bsdb:486/2/1,Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with mild symptoms and no requirement of oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,3 July 2021,Claregrieve1,"Claregrieve1,Merit",Differential microbial abundance between healthy volunteers and mild COVID-19 patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus|s__Melissococcus plutonius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|106649;2|1239|186801|3085636|186803|2719313|358743;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578|1587;2|1239|91061|186826|81852|33969;2|1239|91061|186826|81852|33969|33970;2|201174|1760|85006|1268;2|1224|1236|2887326|468;2|1224|1236|72274;2|1224|1236|91347|543|620;2|1224|1236|91347|543|620|624;2759|33090|35493;2|1239|91061|186826|33958|46255;2|1224|1236|91347|543;2759|33090|35493;2|1239|91061|186826|81852|1350|35783;2|1239|91061|186826|33958|1578;2|1239|91061|186826;2|1239|91061|186826|33958|1578|1591,Complete,Fatima
bsdb:486/2/2,Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with mild symptoms and no requirement of oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,4 July 2021,Claregrieve1,"Claregrieve1,Fatima",Differential microbial abundance between healthy volunteers and mild COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|1843488|909930|904;2|1224|1236|135624;2|1239|186801|3085636|186803|207244;2|29547|3031852|213849;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|543|547;2|1239|186801|3085636|186803|2719313|1531;2|29547;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|29547|3031852|213849|72293;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|28052;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|201174|84998|84999|1643824|133925;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|909932|909929|1843491|970;2|1239|186801|186802|216572|292632;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|1239|909932|1843489|31977;2|74201;2|1239|186801;2|1239|91061|186826|33958;2|1224|1236|135625|712;2|1239|909932|1843489|31977,Complete,Fatima
bsdb:486/3/1,Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Severe COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with severe disease and requiring oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,4 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and severe COVID-19 patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae",2|976|200643|171549|815|816;2|976|200643;2|976|200643|171549;2|976;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|543;2|201174;2|201174|1760|85004;2|201174|1760|85004|31953;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81850;2;2|1224|1236|91347|543|620;2|1224|1236|91347|543|620|624;2|1239|91061|186826;2|1239|91061|186826|33958|1578|1587;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|81852|33969;2|1239|186801|3085636|186803|2719313|358743;2|1239|91061|186826|81852;2|1224|1236|91347|543|620|622,Complete,Claregrieve1
bsdb:486/3/2,Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Severe COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with severe disease and requiring oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3c,4 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and severe COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|1843488|909930|904;2|1224|1236|135624;2|1239|186801|186802|3085642|580596;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1224|28216|80840|80864;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|543|547;2|1239|186801|3085636|186803|2719313|1531;2|29547;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|28052;2|1239|186801|3085636|186803;2|1239|91061|186826|81850;2|1239|909932|1843489|31977|906;2|544448|31969;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|541000;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3085636|186803|841;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|544448;2|74201;2;2|1239|186801;2|1224|28216|80840|80864;2|201174|84998|84999|84107;2|1239|186801|186802;2|1239;2|1239|186801|3085636|186803;2|1239|91061|186826|33958;2|1239|186801|186802|216572;2|1224|1236|135625|712;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:487/1/1,Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Infected COVID-19 samples (respiratory positive),Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,12,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,increased,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S1,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643;2|976|200643|171549,Complete,NA
bsdb:487/1/2,Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Infected COVID-19 samples (respiratory positive),Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,12,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,increased,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S1,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,2|201174|1760|2037,Complete,NA
bsdb:487/2/1,Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 1,Supplementary Table S2,4 July 2021,Claregrieve1,"Claregrieve1,Merit",Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|877420;2|1239|186801|3085656|3085657|2039302;2|1239|909932;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|1239|186801|3085636|186803|841;2|1239|909932|909929;2|877428;2|1239|186801|186802|216572,Complete,NA
bsdb:487/2/2,Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 2,Supplementary Table S2,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|201174;2|1224;2|201174|84998;2|1239|91061;2|1224|1236;2|201174|84998|84999;2|1239|91061|186826;2|1224|1236|91347;2|201174|84998|84999|84107;2|1239|91061|186826|81852;2|1239|91061|186826|81850;2|201174|84998|1643822|1643826;2|1239|91061|186826|1300;2|1239|186801|3082720|186804;2|201174|1760|85004|31953;2|1224|1236|91347|543;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|216851|1946507;2|1239|91061|186826|33958|1253;2|1224|1236|91347|543|544,Complete,NA
bsdb:487/3/1,Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Infected COVID-19 samples (respiratory positive),Samples from symptomatic/mild COVID-19 patients collected on or before positive detection of SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,unchanged,Signature 1,Supplementary Table S2,4 July 2021,Claregrieve1,"Claregrieve1,Merit",Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__uncultured Oscillospira sp.",2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976;2|976|200643|171549|2005519|397864;2|976|200643|171549|2005519;2|1239|186801|186802|3085642|580596;2|976|200643|171549|1853231|574697;2|1239|186801|186802|1980681;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|877420;2|976|200643|1970189|1573805;2|1239|186801|3085656|3085657|2039302;2|1239|909932;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|909932|909929;2|1224|28216|80840|995019|40544;2|976|200643|171549|2005525;2|1239|909932|1843489|31977;2|877428;2|1239|186801|186802|216572|119852|512316,Complete,NA
bsdb:487/3/2,Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Infected COVID-19 samples (respiratory positive),Samples from symptomatic/mild COVID-19 patients collected on or before positive detection of SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,unchanged,Signature 2,Supplementary Table S2,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",2|201174;2|1224;2|201174|84998;2|1239|91061;2|1224|1236;2|201174|84998|84999;2|1239|91061|186826;2|1239|1737404|1737405;2|201174|1760|85004;2|1224|1236|91347;2|1239|186801|186802;2|201174|84998|84999|84107;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|201174|84998|1643822|1643826;2|1239|91061|186826|1300;2|1239|186801|3082720|186804;2|201174|1760|85004|31953;2|1224|1236|91347|543;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|1239|186801|3082720|186804|1501226;2|1239|91061|186826|33958|1253;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|2569097|39488;2|1224|1236|91347|543|620;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|186801|3082720|186804|1505657,Complete,NA
bsdb:488/1/1,Study 488,case-control,33663411,10.1186/s12876-021-01693-w,NA,"Mei L, Zhou J, Su Y, Mao K, Wu J, Zhu C, He L , Cui Y",Gut microbiota composition and functional prediction in diarrhea-predominant irritable bowel syndrome,BMC gastroenterology,2021,"Diarrhea-predominant irritable bowel syndrome, Functional prediction, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Individuals aged from 20 to 64 meeting the Rome IV diagnostic criteria [19] for IBS-D,30,30,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,4 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1",Differential microbial abundance between IBS-D patients and controls by LefSe,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|201174;2|976|200643|171549|171552|1283313;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|28026;2|1239|186801;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|186802|216572|1263;2|1239|186801|186802|1898207;2|976|200643|171549|171552|1926672|1852370;2|976|200643|171549|815|909656|310297,Complete,Claregrieve1
bsdb:488/1/2,Study 488,case-control,33663411,10.1186/s12876-021-01693-w,NA,"Mei L, Zhou J, Su Y, Mao K, Wu J, Zhu C, He L , Cui Y",Gut microbiota composition and functional prediction in diarrhea-predominant irritable bowel syndrome,BMC gastroenterology,2021,"Diarrhea-predominant irritable bowel syndrome, Functional prediction, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Individuals aged from 20 to 64 meeting the Rome IV diagnostic criteria [19] for IBS-D,30,30,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,4 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1",Differential microbial abundance between IBS-D patients and controls by LefSe,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1239|91061;2|976|200643|171549|815|816|817;2|1224|1236|91347|543;2|1224|1236|91347|543|561|562;2|1224|1236;2|1239|91061|186826;2|1224;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|91347,Complete,Claregrieve1
bsdb:489/1/1,Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 1,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia control patients (COVID-negative),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",8,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Table S5, Table S8, Table S11",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between controls and ICU-admitted COVID-19 patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Ihubacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus rivorum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Candidatus Anaerococcus phoceensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuscaniense,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. IrT-R5M2-141,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S362,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sundsvallense,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S4-8,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Gorbachella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TM-40,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fusiformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.",2|201174|1760|85006|85020;2|201174|1760|85006;2|201174|1760|85007|85025;2|1224|28211;2|201174;2|201174|1760|85010|2070;2|201174|1760|85011|2062;2|1239|526524|526525;2|201174|1760|85007|1762;2|1224|28211|356;2|1239|909932|1843489;2|1239|526524;2|1224|28211|204441|41295;2|201174|1760|85006|85019;2|1239|91061|1385|90964;2|201174|1760|85006|1268;2|1239|526524|526525|128827;2|1224|28216|80840;2|201174|1760|85006|85023;2|201174|1760|85007|1653;2|1239|91061|186826|186827;2|1239|909932;2|1239|91061|1385|186822;2|1239|91061;2|1239|91061|1385|186817;2|1239|91061|186826|81852;2|201174|1760|85006|1268|1663;2|1239|909932|1843489|31977|909928;2|201174|1760|85006|85020;2|1239|91061|186826|81852|2737;2|201174|84998|1643822|1643826|84108;2|201174|1760|85006;2|201174|1760|85006|1268|1269;2|201174|1760|85007|85025|1827;2|201174|1760|85006|1268|57493;2|976|117743|200644|49546;2|201174|1760|85011|2062|1883;2|1239|526524|526525|128827;2|544448|31969|186329|2146|33926;2|201174|1760|85007|1762|1763;2|1224|28216|80840|995019;2|1239|186801|3082720|3030910|86331;2|1239|526524;2|1239|186801|186802|216572|1935176;2|1239|186801|186802|404402;2|1239|186801|186802|31979|1434004;2|1224|1236|135625|712|724;2|1239|186801|186802|543314|1926667;2|201174|1760|85006|85019|1696;2|1239|91061|186826|81852|1350;2|201174|1760|85007|1653|1716;2|1239|91061|186826|186827|66831;2|1224|28216|80840;2|201174|1760|85007;2|1239|91061|1385|186822|44249;2|1239|91061|1385|186817|1386;2|1239|91061|186826|81852|1350|1352;2|201174|1760|85007|1653|1716|43765;2|1239|1737404|1737405|1570339|165779|54007;2|201174|1760|85007|1653|1716|156978;2|1239|91061|186826|186827|66831|178214;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|81852|1350|1354;2|1239|91061|186826|81852|1350|762845;2|976|200643|171549|171552|2974257|28127;2|1239|1737404|1737405|1570339|165779|337317;2|1239|91061|186826|81852|2737;2|201174|1760|85007|1653|1716|302449;2|1239|91061|186826|33958|1578|1587;2|201174|1760|85007|1653|1716|146482;2|1239|1737404|1737405|1570339|162289|1647712;2|201174|84998|1643822|1643826|84108|2049041;2|201174|1760|85006|1268|1269|1270;2|1239|1737404|1737405|1570339|165779|938293;2|201174|1760|85007|1653|1716|161902;2|201174|1760|85007|1653|1716|38286;2|976|200643|171549|171552|838|1219629;2|1239|186801|3085636|186803|3342669|45851;2|1239|186801|186802|216572|1935176;2|201174|1760|85004|31953;2|201174|1760|85007|85025|1827|1831;2|1239|186801|186802|216572|1935461;2|1224|28211|356;2|201174|84998|84999|84107|1473205|1473216;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|404402|404403;2|1239|91061|186826|81852|1350|37734;2|1224|1236|91347|543|570|571;2|1239|186801|186802|31979|1434004;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|31979|1485|371143;2|1224|28216|80840|995019|577310;2|1239|186801|186802|31979|1485|69833;2|1239|91061|186826|81852|1350|35783;2|201174|1760|85007|1653|1716|1720,Complete,Fatima
bsdb:489/1/2,Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 1,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia control patients (COVID-negative),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",8,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Table S5, S8, S11",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between controls and ICU-admitted COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus gorbachii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MC_18,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. DJF_RP53,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. NML96-0085,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S470,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. gpac007,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. BI-42,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobium|s__Anaerobium acetethylicum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans acetigenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. A9,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp. 992a,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture clone 7-14,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 14505,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. FSAA-17,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BPY5,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon G70,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|1239|186801|186802|216572|35829;2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|244127|169435;2|201174|84998|84999|1643824|1380|1393034;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|816|291644;2|976|200643|171549|815|816|29523;2|976|200643|171549|815|816|46506;2|1239|186801|186802|3085642|580596|2049021;2|1239|91061|186826|186828;2|1239|186801|3082768|990719;2|1224|1236|91347|543|544;2|1239|186801|186802|543314;2|1239|186801|186802|31979|1485|1506;2|201174|84998|84999|84107|102106;2|976|200643|171549|2005519|1348911;2|976|200643|171549|2005519|1348911|1099853;2|201174|84998|84999|84107;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|1432051;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|3085636|186803|2719313|460384;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|1686313;2|1239|186801|186802|1686313|938288;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|1407607;2|1239|91061|186826|186828|117563;2|1239|186801|53433|972|2330;2|1239|91061|186826|33958|1243;2|544448|31969|2085|2092|2093;2|544448|31969|2085|2092;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|265975|1969407;2|1239|186801|186802|216572|119852|119853;2|1239|186801|186802|186807|2740;2|976|200643|171549|815|909656|204516;2|976|200643|171549|171552|838|28125;2|1239|186801|186802|216572|1017280;2|508458|649775|649776|3029088|638847;2|508458|649775|649776|3029088|638847|638849;2|1239|186801|3085636|186803|588605;2|1224|1236|91347|543|590;2|1239|186801|186802|216572|292632;2|1224|1236|135623|641|662;2|1239|526524|526525|2810280|3025755|29348;2|201174|84998|84999|84107;2|1239|186801|186802|216572;2|201174|84998;2|201174|1760|2037|2049|1653174;2|976|200643|171549|171552|1980689;2|976|200643|171549|171550;2|1239|186801|3085636|186803|2005359;2|1239|186801|186802|3082771|1738645;2|1239|1737404|1737405|1570339|162289|411567;2|976|200643|171549|171552|838|1755609;2|976|200643|171549|171552|838|537298;2|201174|1760|85007|1653|1716|598660;2|201174|1760|85007|1653|1716|702963;2|976|200643|171549|171552|1980689|1870999;2|1239|1737404|1737405|1570339|162289|1647714;2|1239|1737404|1737405|1570339|162289|361492;2|976|200643|171549|171552|838|243905;2|1239|186801|3085636|186803|1855714|1619234;2|201174|1760|2037|2049|1653174|59505;2|1239|186801|186802|216572|1200657|319644;2|1239|186801|3085636|186803|1649459;2|201174|84998|84999|84107|102106;2|976|200643|171549|1853231|574697;2|1239|186801|186802|31979|1485|397283;2|1239|186801|3085636|186803|207244|1261637;2|1239|186801|186802|31979|1485|598552;2|200940|3031449|213115|194924|872;2|201174|1760|2037|2049|184869|184870;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|31979|1485|169136;2|1239|186801|186802|1392389|1640371;2|1239|186801|3085636|186803|1506577;2|976|200643|171549|815|816|338188;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|31979|1485|1572655;2|976|200643|171549|171552|838|712495;2|1239|186801|186802|3082771|1738645;2|1224|1236|91347|543|570,Complete,Fatima
bsdb:489/2/1,Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 2,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,COVID-positive patients admitted to infectious disease ward (w-COVID-19),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",9,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Table S6, S9, S12",6 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19),increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Ihubacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. DJF_SLA47,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fusiformis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S362,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuscaniense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S4-8,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. MANG,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Gorbachella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TM-40,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2|1224|28216|80840;2|201174|1760|85007|85025;2|1224|28211;2|201174|1760|85010|2070;2|1239|526524|526525;2|201174|1760|85007|1762;2|1224|28211|356;2|1239|526524;2|1224|1236|135624|84642;2|1224|28211|204441|41295;2|201174|1760|85006|1268;2|201174|1760|85006|85019;2|201174|1760|85007|1653;2|1239|91061|1385|90964;2|201174|1760|85006|85023;2|1239|91061|1385|186822;2|201174|1760|85006|1268|1663;2|201174|1760|85006|1268;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827;2|1239|91061|186826|81852|2737;2|201174|1760|85006|85023|33882;2|1239|91061|1385|186822|44249;2|201174|1760|85006|1268|1269;2|201174|1760|85007|85025|1827;2|201174|1760|85007|1653;2|201174|1760|85006|1268|57493;2|201174|1760|85011|2062|1883;2|544448|31969|186329|2146|33926;2|976|117743|200644|49546;2|201174|1760|85007|1762|1763;2|1224|1236|135624|84642|642;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|404402;2|1239|186801|186802|31979|1434004;2|1224|1236|135625|712|724;2|1239|186801|186802|543314|1926667;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2|201174|1760|85006|85019|1696;2|201174|1760|85007|1653|1716|156978;2|1239|91061|186826|81852|1350|537280;2|201174|84998|1643822|1643826|84108|2049041;2|32066|203490|203491|203492|848|68766;2|1239|91061|186826|33958|1578|1596;2|1239|186801|186802|31979|1485|69833;2|1239|1737404|1737405|1570339|162289|1647712;2|201174|1760|85007|1653|1716|169292;2|1239|1737404|1737405|1570339|165779|938293;2|1239|91061|1385|90964|1279|1280;2|201174|1760|85007|1653|1716|38286;2|1239|91061|186826|81852|1350|53345;2|201174|1760|85007|85025|1827|1831;2|201174|1760|85007|1653|1716|302449;2|1239|186801|3085636|186803|2316020|46228;2|976|200643|171549|171552|838|1219629;2|976|200643|171549|815|816|298389;2|201174|1760|85004|31953;2|1239|186801|3085636|186803|3342669|45851;2|201174|84998|84999|84107|1473205|1473216;2|1239|91061|186826|81852|2737;2|1239|186801|186802|216572|1935461;2|1239|186801|186802|404402|404403;2|1239|91061|186826|81852|1350|37734;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|31979|1434004;2|1239|186801|186802|31979|1485|371143;2|1224|28216|80840|995019|577310;2|1239|91061|1385|90964|1279|29387;2|1239|91061|1385|90964|1279|1282,Complete,Fatima
bsdb:489/2/2,Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 2,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,COVID-positive patients admitted to infectious disease ward (w-COVID-19),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",9,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Table S6, S9, S12",6 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19),decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Alterileibacterium|s__Alterileibacterium massiliense,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus degeneri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|g__Kallipyga|s__Kallipyga massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Lagierella|s__Lagierella massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. DJF_RP53,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum anthropi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. DJF_B097,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. 1120,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S8 F8,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. C71,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp. 992a,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. Marseille-P328,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BPY5,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. enrichment culture clone,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella|s__Moritella abyssi,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture clone 7-14,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. Marseille-P2398,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. Marseille-P3260,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae",2|1239|91061|186826|186827|1375;2|1224|1236|135619|224372;2|1224|1236|135619|224372|59753;2|1239|186801|3082720|3030910|1980680|1870997;2|1239|1737404|1737405|1570339|165779|361500;2|1239|186801|3085636|186803|207244|649756;2|29547|3031852|213849|72294|194|76517;2|1239|91061|186826|186828;2|1224|1236|91347|543|544;2|1239|186801|186802|543314;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|2810280|100883|100884;2|976|200643|171549|2005519|1348911;2|976|200643|171549|2005519|1348911|1099853;2|201174|84998|84999|84107;2|201174|84998;2|1224|1236|91347|543|413496;2|200940|3031449|213115|194924|872;2|1239|909932|1843489|31977|39948|309120;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|1686313;2|1239|186801|186802|1686313|938288;2|1239|186801|186802|216572|946234;2|1239|91061|186826|186828|117563;2|1239|526524|526525|128827|1937007;2|1239|1737404|1472763|1472764;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|28052;2|1239|91061|186826|1300|1357;2|1239|1737404|1737405|1570339|1945592|1689303;2|976|200643|171549|171552|1980689;2|976|200643|171549|171552|1980689|1870999;2|201174|1760|85008|28056;2|1224|1236|135622|267891;2|1239|1737404|1737405|1570339|1161127;2|201174|84998|84999|1643824|133925;2|976|200643|171549|2005525|375288|387661;2|1224|1236|91347|1903410;2|976|200643|171549|815|909656|204516;2|976|200643|171549|171552|52228|1703337;2|976|200643|171549|171552|838|28130;2|976|200643|171549|171552|838|537298;2|1239|186801|3085636|186803|841|301302;2|1224|1236|91347|543|590;2|1239|909932|909929|1843491;2|1239|909932|909929|1843491|970;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|201174|1760|2037|2049|184869|1177728;2|1224|1236|135623|641|662;2|1239|186801|186802|216572|39492;2|1239|909932|1843488|909930;2|201174|84998|84999|84107;2|201174|84998;2|28221;2|1239|186801|186802|1686313;2|1239|186801|3082720|186804;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|816|537274;2|1239|186801|3085636|186803|28050|706562;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|838|28125;2|1239|186801|3085636|186803|841|2049040;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|590|28901;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|841|1227508;2|976|200643|171549|171552|52228|242750;2|1239|91061|186826|1300|1301|1308;2|976|200643|171549|1853231|574697;2|1224|1236|91347|543|547;2|201174|84998|84999|84107|102106;2|1224|1236|91347|543|561;2|976|200643|171549|171552|838|1330241;2|1224|1236|91347|543|561|1299485;2|1239|186801|3085636|186803|207244|1261637;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|216572|1263|1816688;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|31979|1485|1572655;2|976|200643|171549|171550|239759|1648956;2|1224|1236|91347|1903409|53335|549;2|1224|1236|91347|543|620|624;2|1239|186801|186802|216572|1930587|1852369;2|1239|186801|3085636|186803|33042|2049024;2|200940|3031449|213115|194924|872;2|1224|1236|135622|267891|58050|111292;2|1239|186801|186802|31979|1485|598552;2|1239|91061|186826|186828|117563|2049028;2|1239|186801|3085636|186803|572511|1805476;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|459786|1871036;2|1224|1236|91347|543|547|550,Complete,Fatima
bsdb:489/3/1,Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 3,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia controls (COVID-negative),COVID-positive patients admitted to infectious disease ward (w-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in infectious disease ward",8,9,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S1, S4, S7, S10",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between non-COVID-19 patients and non-ICU COVID-19 patients,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Syntrophobotulus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Candidatus Syntrophonatronum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pacaella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacteria|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella asaccharolytica,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Alterileibacterium|s__Alterileibacterium massiliense,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. oral taxon 375,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S276,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. DNF00912,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. DJF_B097,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Bacillota|c__Tissierellia|g__Kallipyga|s__Kallipyga massiliensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S8 F8,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. C71,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. Marseille-P328,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Syntrophobotulus|s__Syntrophobotulus glycolicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. Marseille-P2398,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Candidatus Syntrophonatronum|s__Candidatus Syntrophonatronum acetioxidans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera massiliensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. S7D,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pacaella|s__Pacaella massiliensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Candidatus Peptoniphilus massiliensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. Marseille-P3260,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas phoceensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. enrichment culture clone,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. IrT-R5M2-141,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.",2|1224;2|1224|1236|135619|224372;2|201174;2|201174|1760|85006;2|28221;2|1239|909932|1843488|909930;2|1239|909932|1843489|31977;2|1224|1236|91347|1903410;2|1239|186801|186802|68298;2|201174|1760|85011|2062;2|1239|909932|909929|1843491;2|201174|1760|85006|85020;2|976|117747;2|1224|1807140|225057|225058;2|1239|186801|3082720|186804;2|1224|1236|91347|543;2|1239|909932;2|1239|91061|186826|186827;2|1239|91061|1385|90964;2|201174|84998|84999|1643824;2|1224|1236|135623|641;2|1224|1236|135619|224372|59753;2|1239|91061|186826|186827|1375;2|1224|28216|80840|995019|40544;2|1239|186801|186802|2937909|51196;2|1239|526524|526525|2810280|100883;2|1239|186801|3082720|186804;2|201174|84998|84999|1643824|133925;2|201174;2|1224|28216|80840|995019;2|1239|909932|1843489|31977|909928;2|1239|91061|186826|1300|1357;2|1239|186801|186802|68298|1795789;2|1239|186801|186802|216572|1935176;2|1239|909932|1843488|909930|904;2|508458|649775|649776|649777|1931105;2|1239|909932|909929|1843491|970;2|1239|91061|186826|81852;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|241189;2|1224|1807140|225057|225058|119977;2|1239|909932|1843489|31977|906;2|200940|3031449|213115|194924|35832;2|1224|1236|91347|543|561;2|1224|1236|91347|543;2|1239|91061|186826|1300;2|1224|1236|135623|641|662;2|976|200643|171549|171552|838|28130;2|976|200643|171549|171552|52228|1703337;2|1239|909932|1843489|31977|39948|309120;2|1239|186801|3082720|186804|1257|1261;2|1239|1737404|1737405|1570339|165779|54007;2|976|200643|171549|2005525|375288|387661;2|1239|1737404|1737405|1570339|1161127|507844;2|1239|186801|3082720|3030910|1980680|1870997;2|976|200643|171549|171550|239759|1288121;2|1239|1737404|1737405|1570339|162289|712430;2|1239|1737404|1737405|1570339|162289|1647711;2|1239|909932|1843489|31977|906|1285934;2|976|200643|171549|815|816|537274;2|1239|526524|526525|2810280|100883|100884;2|1239|526524|526525|128827|1573535|1735;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1472763|1472764;2|1239|909932|1843489|31977|906|2023260;2|1239|91061|186826|81852|1350|1352;2|201174|84998|84999|1643824|1380|1872650;2|976|200643|171549|171552|2974257|28127;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|186827|66831|178214;2|1239|91061|186826|81852|1350|1354;2|976|200643|171549|171552|838|1330241;2|976|200643|171549|171551|836|28123;2|1224|1236|91347|543|561|1299485;2|1239|186801|186802|216572|1263|1816688;2|201174|1760|85007|1653|1716|43765;2|1224|1236|91347|543|620|624;2|1224|1236|91347|1903409|53335|549;2|1239|91061|186826|186827|66831;2|1239|186801|186802|2937909|51196|51197;2|1239|186801|3085636|186803|572511|1805476;2|1239|91061|1385|90964|1279|1290;2|1239|186801|186802|68298|1795789|1795816;2|1239|186801|186802|216572|1935176;2|1239|909932|1843489|31977|906|1232428;2|1239|909932|1843489|31977|39948|487173;2|1224|1236|91347|1903411|613|615;2|1239|909932|1843488|909930|904|187327;2|1239|909932|1843489|31977|39948|1577797;2|508458|649775|649776|649777|1931105|1871009;2|1239|1737404|1737405|1570339|162289|337315;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|459786|1871036;2|1224|1236|91347|543|570|571;2|976|200643|171549|1853231|574697|1720203;2|976|200643|171549|171550|239759|1648956;2|976|200643|171549|171552|577309|454154;2|1239|909932|909929|1843491|970|971;2|201174|1760|85007|1653|1716|146482;2|1239|91061|186826|1300|1301|1328;2|1224|1236|91347|543|561;2|1224|1236|91347|543|547;2|1224|1236|91347|543|413496|28141;2|1239|186801|3085636|186803|841|2049040;2|1239|186801|186802|186806|1730|290054;2|1239|91061|1385|90964|1279|29387,Complete,Fatima
bsdb:489/3/2,Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 3,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia controls (COVID-negative),COVID-positive patients admitted to infectious disease ward (w-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in infectious disease ward",8,9,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S1, S4, S7, S10",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between non-COVID-19 patients and non-ICU COVID-19 patients,decreased,"k__Bacteria|p__Spirochaetota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S470,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. NML96-0085,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio cellulolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobium|s__Anaerobium acetethylicum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. A9,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. MANG,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. FSAA-17,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 14505,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Candidatus Dorea massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas sp. S479,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon G70,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 653,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans acetigenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. ID5,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",2|203691;2|32066;2|1224|1236|135624|84642;2|544448|31969|2085|2092;2|1239|186801|186802|543314;2|1224|28216|80840|119060;2|1224|1236|2887326|468;2|1224|28216|80840;2|1224|28211|204458|76892;2|201174|1760|85009|31957;2|1224|1236|91347|1903414|583;2|1224|1236|91347|1903414;2|201174|1760|85009|31957;2|201174|1760|2037|2049|1653174;2|201174|1760|85007|1653;2|1239|186801|3085636|186803|1432051;2|201174|1760|85006|85023|33882;2|1239|186801|3085636|186803|2005359;2|1239|186801|186802|216572|244127;2|1239|186801|186802|3082771|1738645;2|1239|186801|186802|186807|2740;2|1239|186801|3085636|186803|1407607;2|1239|526524|526525|128827;2|1239|186801|186802|216572|1017280;2|1239|91061|1385|186822|44249;2|1224|1236|135624|84642|642;2|1239|186801|3085636|186803|588605;2|1239|186801|186802|216572|35829;2|1239|91061|186826|33958|1243;2|1239|186801|186802|216572|1905344;2|976|200643|171549|171550;2|1239|186801|3082768|990719;2|1239|91061|186826|33958;2|544448|31969|2085|2092|2093;2|1239|91061|1385|539738|1378;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|291644;2|201174|1760|85007|1653|1716|598660;2|976|200643|171549|171550|239759|28117;2|1239|1737404|1737405|1570339|162289|1647714;2|1224|1236|91347|1903414|583|584;2|1224|1236|91347|1903414|583;2|201174|1760|85007|1653|1716|702963;2|1239|186801|186802|216572|1200657;2|1239|186801|186802|216572|35829|35830;2|976|200643|171549|815|816|46506;2|1239|186801|3085636|186803|1855714|1619234;2|201174|1760|2037|2049|1653174|59505;2|1239|186801|186802|216572|1263|438033;2|976|200643|171549|815|816|817;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|31979|1485|397283;2|976|200643|171549|815|816|298389;2|201174|1760|85006|85023|33882;2|1239|186801|186802|1392389|1640371;2|1239|186801|186802|31979|1485|169136;2|1239|186801|3085636|186803|189330|1470355;2|1239|186801|3085636|186803|1506553|29347;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|2316020|342942;2|1239|186801|3085636|186803|1506577;2|976|200643|171549|815|816|338188;2|1239|526524|526525|128827;2|1239|186801|186802|3082771|1738645;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|3085642|580596;2|976|200643|171549|1853231|574697|1647678;2|976|200643|171549|171552|838|712495;2|1239|186801|3085636|186803|2719313|460384;2|32066|203490|203491|203492|848|68766;2|976|200643|171549|815|816|29523;2|1239|186801|186802|216572|1905344|1550024;2|976|200643|171549|815|816|291645;2|1239|186801|186802|216572|1263|1227507;2|1239|186801|186802|31979|1485|1569942;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|186802|216572|1200657|319644;2|1239|91061|1385|186822|44249;2|1239|186801|3085636|186803|1432051|1924109;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|3085636|186803|1432051|1720294;2|1239|186801|186802|216572|47246;2|1239|186801|3085636|186803|2005359|1544;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|31979|1485|320882;2|1239|909932|1843489|31977|39948|39950;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|816|818,Complete,Lwaldron
bsdb:490/1/1,Study 490,case-control,19903265,10.1111/j.1365-2982.2009.01427.x,NA,"Tana C, Umesaki Y, Imaoka A, Handa T, Kanazawa M , Fukudo S",Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2010,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"All patients were diagnosed with IBS after conducting a medical interview based on Rome II criteria and positive judgment by a Rome II modular questionnaire retrospectively and positively fulfilling Rome III criteria. According to Rome II criteria related to bowel habits, 11 subjects had constipation-predominant IBS (IBS-C), eight had diarrhoea-predominant IBS (IBS-D) and seven had mixed IBS (IBS-M).",26,26,"In the previous study, agents containing probiotics were administered to humans and stopped thereafter. On day 10 after stopping the administration of probiotics, levels of these bacteria returned to the levels before administration of probiotics. No subject received antibiotics during the abstention period.",WMS,NA,RT-qPCR,Spearman Correlation,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,4 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees","Comparison of GI microbiota between IBS patients and the
controls",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:490/1/2,Study 490,case-control,19903265,10.1111/j.1365-2982.2009.01427.x,NA,"Tana C, Umesaki Y, Imaoka A, Handa T, Kanazawa M , Fukudo S",Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2010,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"All patients were diagnosed with IBS after conducting a medical interview based on Rome II criteria and positive judgment by a Rome II modular questionnaire retrospectively and positively fulfilling Rome III criteria. According to Rome II criteria related to bowel habits, 11 subjects had constipation-predominant IBS (IBS-C), eight had diarrhoea-predominant IBS (IBS-D) and seven had mixed IBS (IBS-M).",26,26,"In the previous study, agents containing probiotics were administered to humans and stopped thereafter. On day 10 after stopping the administration of probiotics, levels of these bacteria returned to the levels before administration of probiotics. No subject received antibiotics during the abstention period.",WMS,NA,RT-qPCR,Spearman Correlation,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,text,19 July 2023,Atrayees,Atrayees,"Comparison of GI microbiota between IBS patients and the controls

Abundance in",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:491/1/1,Study 491,case-control,21741921,10.1053/j.gastro.2011.06.072,NA,"Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ , Versalovic J",Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Children ages 7-12 who met the Pediatric Rome III criteria for IBS (Table 1). Subtyping of IBS was based on previous recommendations for IBS in adults because no Pediatric Rome subtype criteria exist for children.,27,28,6 months,16S,123,PhyloChip,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2; Supplementary Table 1A,8 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1",Differential microbial abundance between IBS patients and controls,increased,"k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Myxococcota|o__Polyangiales|f__Polyangiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae",2|57723|204432|204433|204434;2|1224|1236|135624|84642;2|1224|1236|135622|72275;2|1239|91061|1385|186817;2|201174|1760|85006|85016;2|1239|186801|186802|31979;2|1224|1236|118969|118968;2|200940|3024418|213118|213119;2|200940|3031449|213115|194924;2|1224|1236|91347|543;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806;2|1239|186801|3085636|186803;2|40117|203693|189778|189779;2|1224|1236|135625|712;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804;2|2818505|3031712|49;2|976|200643|171549|171552;2|201174|1760|85006|85017;2|1239|91061|186826|1300;2|200940|3024408|213462|213465;2|1224|1236|72273|135617,Complete,Claregrieve1
bsdb:491/1/2,Study 491,case-control,21741921,10.1053/j.gastro.2011.06.072,NA,"Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ , Versalovic J",Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Children ages 7-12 who met the Pediatric Rome III criteria for IBS (Table 1). Subtyping of IBS was based on previous recommendations for IBS in adults because no Pediatric Rome subtype criteria exist for children.,27,28,6 months,16S,123,PhyloChip,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2; Supplementary Table 1B,8 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1",Differential microbial abundance between IBS patients and controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|976|200643|171549|815;2|201174|1760|85006|85016;2|1239|186801|3085636|186803;2|1239|91061|1385|186822;2|976|200643|171549|171551;2|1239|91061|186826|1300;2|976;2|976|200643|171549|815|909656|821,Complete,Claregrieve1
bsdb:492/1/1,Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy,"Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy (T2D group); the T2DM cohort included subjects (a) positive for at least one of the three biochemical tests (HbA1c > 7%, fasting blood sugar > 120 mg% and post-prandial blood sugar > 200 mg%); (b) had history of taking anti-diabetic medications (Metformin or combinations of Metformin and / or Insulin) and (c) had no clinical signs of DR",30,24,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,increased,unchanged,NA,increased,Signature 1,"Table 2, Table 3",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Decreased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Archaea|p__Thermoproteota,k__Bacteria|p__Elusimicrobiota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1224|28216|80840|80864|283;2|1239|186801|3085636|186803|33042;2157|28889;2|74152;2|32066;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:492/1/2,Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy,"Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy (T2D group); the T2DM cohort included subjects (a) positive for at least one of the three biochemical tests (HbA1c > 7%, fasting blood sugar > 120 mg% and post-prandial blood sugar > 200 mg%); (b) had history of taking anti-diabetic medications (Metformin or combinations of Metformin and / or Insulin) and (c) had no clinical signs of DR",30,24,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,increased,unchanged,NA,increased,Signature 2,"Table 2, Table 3",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Increased abundance of microbial communities in individuals with Type 2 Diabetes compared to healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Lentisphaerota,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Synergistota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1239|909932|1843488|909930|904;2|976|200643|171549|1853231|574697;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2157|28890;2|1239|186801|3085636|186803|140625;2|256845;2157|28890|183925|2158|2159|2172;2|203691;2|508458;2|203691|203692|136|2845253|157;2|1239|91061|186826|33958|46255,Complete,Claregrieve1
bsdb:492/2/1,Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Healthy controls,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,30,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Table 4",5 July 2021,Madhubani Dey,"Madhubani Dey,Fatima,Claregrieve1",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Archaea|p__Thermoproteota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174;2|1239|909932|909929|1843491|82373;2|544448|31969|186332|186333|2152;2|976;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|128827|118747;2|1239|186801|3085636|186803|830;2|95818;2|1239|186801|186802|31979|1485;2|1224|28216|80840|80864|283;2157|28889;2|200940|3031449|213115|194924|872;2|1224|1236|91347|1903409|551;2|1239|186801|186802|216572|216851;2|32066;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|52225;2|1239|186801|3085636|186803|841;2|201174|1760|85006|1268|32207;2|203691;2|1239|91061|186826|1300|1301;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:492/2/2,Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Healthy controls,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,30,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Table 4",5 July 2021,Madhubani Dey,"Madhubani Dey,Fatima,Claregrieve1",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Synergistota,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Verrucomicrobiota",2|1239|909932|1843488|909930|904;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|508458|649775|649776|649777|508459;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2157|28890;2|256845;2|1239|909932|909929|1843491|158846;2|1224|28216|80840|75682|846;2|976|200643|171549|2005525|375288;2|1224|1236|91347|543|620;2|508458;2|544448;2|74201,Complete,Claregrieve1
bsdb:492/3/1,Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,24,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Table 5",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Lentisphaerota,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|201174;2|1239|909932|909929|1843491|82373;2|544448|31969|186332|186333|2152;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|872;2|1224|1236|91347|1903409|551;2157|28890;2|32066;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|140625;2|256845;2157|28890|183925|2158|2159|2172;2|1239|909932|909929|1843491|52225;2|203691;2|1239|91061|186826|1300|1301;2|203691|203692|136|2845253|157;2|1239|91061|186826|33958|46255,Complete,Claregrieve1
bsdb:492/3/2,Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,24,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Table 5",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Elusimicrobiota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Synergistota,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|508458|649775|649776|649777|508459;2|74152;2|1239|91061|186826|81852|1350;2|1239|909932|1843488|909930|33024;2|1224|1236|91347|543|620;2|508458;2|74201,Complete,Claregrieve1
bsdb:493/1/1,Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Vitiligo patients before narrowband UV (NBUVB) light irradiation in normal skin (NF group),Vitiligo patients after NBUVB irradiation on normal skin (NB group),"Vitiligo patients after NBUVB irradiation on normal skin (NB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 7-9)",24 April 2023,Atrayees,"Atrayees,Folakunmi",Relative abundance of predominant bacteria at phylum and genus level in the NF and NB groups.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Cyanobacteriota",2|976|200643;2|1117,Complete,Folakunmi
bsdb:493/1/2,Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Vitiligo patients before narrowband UV (NBUVB) light irradiation in normal skin (NF group),Vitiligo patients after NBUVB irradiation on normal skin (NB group),"Vitiligo patients after NBUVB irradiation on normal skin (NB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 7-9)",2 February 2024,Folakunmi,Folakunmi,Relative abundance of predominant bacteria at phylum and genus level in the NF and NB groups.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota",2|201174;2|1224,Complete,Folakunmi
bsdb:493/2/1,Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 2,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Normal skin of Vitiligo patients before narrowband UV (NBUVB) light irradiation (NF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 9-11)",2 February 2024,Folakunmi,Folakunmi,Relative abundance of predominant bacteria at phylum and genus level in the NF and DB groups.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota",2|976|200643;2|1224,Complete,Folakunmi
bsdb:493/2/2,Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 2,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Normal skin of Vitiligo patients before narrowband UV (NBUVB) light irradiation (NF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 9-11)",2 February 2024,Folakunmi,Folakunmi,Relative abundance of predominant bacteria at phylum and genus level in the NF and DB groups.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota",2|1239;2|201174,Complete,Folakunmi
bsdb:493/3/1,Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 3,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Lesional skin of Vitiligo patients before irradiation (DF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,decreased,Signature 1,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 12-14)",2 February 2024,Folakunmi,Folakunmi,Relative abundance of predominant bacteria at phylum and genus level in the DF and DB groups.,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota",2|1224;2|201174,Complete,Folakunmi
bsdb:493/3/2,Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 3,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Lesional skin of Vitiligo patients before irradiation (DF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,decreased,Signature 2,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 12-14)",2 February 2024,Folakunmi,Folakunmi,Relative abundance of predominant bacteria at phylum and genus level in the DF and DB groups.,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Folakunmi
bsdb:494/1/1,Study 494,case-control,32214153,10.1038/s41598-020-62224-3,https://pubmed.ncbi.nlm.nih.gov/32214153/,"Li Q, Chang Y, Zhang K, Chen H, Tao S , Zhang Z",Implication of the gut microbiome composition of type 2 diabetic patients from northern China,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; T2D subjects were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) 7 mmol/L or greater and/or 2-h fasting oral glucose tolerance test (OGTT) 11.1 mmol/L or greater35; (ii) no previously received pharmacologic treatment; and (iii) body mass index (BMI) > 18.0 kg/m2.,40,20,2 months,16S,45,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 2b,5 July 2021,Madhubani Dey,"Madhubani Dey,Atrayees",Decreased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:494/1/2,Study 494,case-control,32214153,10.1038/s41598-020-62224-3,https://pubmed.ncbi.nlm.nih.gov/32214153/,"Li Q, Chang Y, Zhang K, Chen H, Tao S , Zhang Z",Implication of the gut microbiome composition of type 2 diabetic patients from northern China,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; T2D subjects were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) 7 mmol/L or greater and/or 2-h fasting oral glucose tolerance test (OGTT) 11.1 mmol/L or greater35; (ii) no previously received pharmacologic treatment; and (iii) body mass index (BMI) > 18.0 kg/m2.,40,20,2 months,16S,45,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Figure 2b,5 July 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803|189330;2|32066|203490|203491|203492|848;2|1239;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:495/1/1,Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance in individuals with type 2 diabetes compared to healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|906;2|1239|909932;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:495/1/2,Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 3,5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance in individuals with type 2 diabetes compared to healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|577309,Complete,Claregrieve1
bsdb:495/2/1,Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Healthy controls,Individuals with Prediabetes (PreDM),Individuals with Prediabetes (PreDM); PreDM was defined as FBG of 6.1–7.0 mmol/L or HbA1c levels of 6.0%–6.5%.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1",Differential microbial abundance in individuals with prediabetes compared to healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|909932|1843489|31977|906;2|1224;2|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:495/2/2,Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Healthy controls,Individuals with Prediabetes (PreDM),Individuals with Prediabetes (PreDM); PreDM was defined as FBG of 6.1–7.0 mmol/L or HbA1c levels of 6.0%–6.5%.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 3,22 July 2022,Claregrieve1,Claregrieve1,Differential microbial abundance in individuals with prediabetes compared to healthy controls,decreased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|29547|3031852|213849|72293|209,Complete,Claregrieve1
bsdb:496/1/1,Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,40,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 1E,7 July 2021,Claregrieve1,"Claregrieve1,Fatima,LGeistlinger",Differential microbial abundance between healthy controls and COVID-19 patients (LDA>2),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|1239|526524|526525|128827|174708;2|1239|1737404|1737405|1570339|165779;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|1239|186801|186802|31979|1485;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|29547|3031852|213849|72293|209;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|437755;2|1239|186801|3085636|186803|265975;2|1224|1236|91347|1903414|583;2|201174|1760|85006|1268|32207;2|201174|1760|85004|31953|196081;2|1239|186801|3085636|186803|177971;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:496/1/2,Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,40,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 1E,7 July 2021,Claregrieve1,"Claregrieve1,Fatima",Differential microbial abundance between healthy controls and COVID-19 patients (LDA>2),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1224|28216|80840|119060|32008;2|976|200643|171549|1853231|574697;2|1239|186801|186802|31979|1485;2|1224|28216|80840|80864|283;2|1239|186801|3085636|186803|33042;2|1224|28216|80840|119060|106589;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|28050;2|1224|28216|206351|481|482;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1224|28216|80840|119060|48736;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|256845|1313211|278082|255528|172900;2|1224|1236|91347|1903411|629,Complete,Fatima
bsdb:496/2/1,Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Seasonal flu patients,COVID-19 patients,Patients with COVID-19,33,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 1G,7 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between seasonal flu patients and COVID-19 patients (LDA>2),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1224|1236|91347|543|561;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|375288;2|1239|909932|1843489|31977|29465;2|1224|28216|80840|995019|40544;2|32066|203490|203491|203492|848,Complete,Fatima
bsdb:496/2/2,Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Seasonal flu patients,COVID-19 patients,Patients with COVID-19,33,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 1G,7 July 2021,Claregrieve1,"Claregrieve1,Merit",Differential microbial abundance between seasonal flu patients and COVID-19 patients (LDA>2),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|416916;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|128827|118747;2|1224|28216|80840|119060|32008;2|1239|186801|186802|31979|1485;2|1224|28216|80840|119060|106589;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|1224|1236|135625|712|724;2|29547|3031852|213849|72293|209;2|1239|91061|186826|33958|1243;2|1239|186801|3085636|186803|437755;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572|119852;2|1239|909932|1843488|909930|33024;2|508458|649775|649776|3029088|638847;2|1224|28216|80840|119060|48736;2|1239|186801|3085636|186803|177971;2|1224|1236|135614|32033|40323;2|1239|186801;2|1239|186801|186802|31979,Complete,Fatima
bsdb:497/1/1,Study 497,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T, Tuitemwong P, Thiennimitr P, Sarichai P, Na Pombejra S, Piriyakhuntorn P, Hantrakool S, Chai-Adisaksopha C, Rattarittamrong E, Tantiworawit A , Norasetthada L",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pretreatment,Febrile neutropenia,patients with neutropenic fever during intensive chemotherapy,10,10,3 months.,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,S1 table.,14 March 2023,Cyberian,"Cyberian,Chloe,Aiyshaaaa,Folakunmi",The taxa that increased in relative abundance from pretreatment to febrile neutropenia.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:497/1/2,Study 497,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T, Tuitemwong P, Thiennimitr P, Sarichai P, Na Pombejra S, Piriyakhuntorn P, Hantrakool S, Chai-Adisaksopha C, Rattarittamrong E, Tantiworawit A , Norasetthada L",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pretreatment,Febrile neutropenia,patients with neutropenic fever during intensive chemotherapy,10,10,3 months.,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,S1 table.,14 March 2023,Cyberian,"Cyberian,Chloe,Folakunmi",Taxa that decreased in relative abundance from pretreatment to febrile neutropenia,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,2|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:497/2/NA,Study 497,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T, Tuitemwong P, Thiennimitr P, Sarichai P, Na Pombejra S, Piriyakhuntorn P, Hantrakool S, Chai-Adisaksopha C, Rattarittamrong E, Tantiworawit A , Norasetthada L",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,febrile neutropenia,Bone marrow recovery,After initiation of induction chemotherapy,10,10,3 months.,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:497/3/1,Study 497,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T, Tuitemwong P, Thiennimitr P, Sarichai P, Na Pombejra S, Piriyakhuntorn P, Hantrakool S, Chai-Adisaksopha C, Rattarittamrong E, Tantiworawit A , Norasetthada L",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pre-treatment,Bone marrow recovery,After initiation of  induction chemotherapy treatment,10,10,3 months.,16S,345,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,S1 table.,25 March 2023,Cyberian,"Cyberian,Folakunmi",taxa that increased in relative abundance from pretreatment to bone marrow recovery.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:497/3/2,Study 497,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T, Tuitemwong P, Thiennimitr P, Sarichai P, Na Pombejra S, Piriyakhuntorn P, Hantrakool S, Chai-Adisaksopha C, Rattarittamrong E, Tantiworawit A , Norasetthada L",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pre-treatment,Bone marrow recovery,After initiation of  induction chemotherapy treatment,10,10,3 months.,16S,345,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,S1 table.,25 March 2023,Cyberian,"Cyberian,Folakunmi",The taxa that decreased in relative abundance from pretreatment to bone marrow recovery,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,2|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:498/1/1,Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Asymptomatic uninfected controls,"Symptomatic, mild to moderate COVID-19 patients","Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized",21,38,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 1,Figure 3B,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy","Differences in the abundance of taxa of the URT microbiome between adults with and without SARS�CoV-2 infection. Differential abundance testing was conducted using DESeq2 models at the ASV level
including age and sex as covariates B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly
different between groups.",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas sp.,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium spiritivorum",2|1239|1737404|1737405|1570339|165779|1872515;2|1224|28211|204458|76892|41275|1871086;2|29547|3031852|213849|72294|194|76517;2|201174|1760|85007|1653|1716|156978;2|201174|1760|85007|1653|1716|1720;2|1239|1737404|1582879;2|1239|91061|186826|186828|117563|2049028;2|1239|1737404|1737405|1570339|162289|33031;2|1239|1737404|1737405|1570339|162289|1971214;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|2974251|165179;2|976|117747|200666|84566|28453|258,Complete,Peace Sandy
bsdb:498/1/2,Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Asymptomatic uninfected controls,"Symptomatic, mild to moderate COVID-19 patients","Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized",21,38,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 2,Figure 3B,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy","Differences in the abundance of taxa of the URT microbiome between adults with and without SARS�CoV-2 infection. Differential abundance testing was conducted using DESeq2 models at the ASV level including age and sex as covariates B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between groups.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|207244|649756;2|201174|1760|85007|1653|1716|1720;2|1224|28216|206351|481|482|192066;2|976|200643|171549|171552|838|28130;2|1239|91061|1385|90964|1279|1283;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:498/2/1,Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 patients with low viral load,COVID-19 patients with high viral load,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized,  with high viral load (quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1)",21,38,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 1,Figure 4b,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy","Differences in the abundance of taxa of the URT microbiome between SARS-CoV-2–infected adults
with and without high viral load (defined as a quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1 [N1]). Differential
abundance testing was conducted using DESeq2 models at the ASV level including age and sex as
covariates. B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between
groups. The asterisks indicate ASVs that were significantly different between groups and had a consistent
direction of association in similar DESeq2 analyses that used a definition of high viral load based on a quan�titative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 2 (N2). The striped bars indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses comparing adults with andwithout SARS-CoV-2 infection.",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1239|1737404|1737405|1570339|165779|1872515;2|29547|3031852|213849|72294|194|76517;2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|81852|1350|35783;2|1239|186801|186802|216572|216851|853;2|1239|1737404|1737405|1570339|162289|1971214;2|976|200643|171549|171552|2974251|165179;2|1224|1236|91347|543;2|1224|28216|206351|481,Complete,Peace Sandy
bsdb:498/2/2,Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 patients with low viral load,COVID-19 patients with high viral load,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized,  with high viral load (quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1)",21,38,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 2,Figure 4b,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy","Differences in the abundance of taxa of the URT microbiome between SARS-CoV-2–infected adults
with and without high viral load (defined as a quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1 [N1]). Differential
abundance testing was conducted using DESeq2 models at the ASV level including age and sex as
covariates. B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between
groups. The asterisks indicate ASVs that were significantly different between groups and had a consistent
direction of association in similar DESeq2 analyses that used a definition of high viral load based on a quan�titative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 2 (N2). The striped bars indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses comparing adults with andwithout SARS-CoV-2 infection.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|186828|29393|29394;2|1239|91061|186826|186828|117563|137732;2|1224|28216|206351|481|482|192066;2|976|200643|171549|171552|838|28130;2|1239|91061|1385|90964|1279|1283;2|1239|91061|186826|1300|1301|1306;2|1224|1236|2887326|468|469;2|1224|1236|135614|32033|40323,Complete,Peace Sandy
bsdb:499/1/1,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients fulfilled the Rome II criteria. Alternating IBS (IBS-A),46,19,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,"Differences Between Intestinal Microbiota in Healthy and IBS.
NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|820;2|1239|186801|186802|216572|216851;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|195950,Complete,Lwaldron
bsdb:499/1/2,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients fulfilled the Rome II criteria. Alternating IBS (IBS-A),46,19,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,"Differences Between Intestinal Microbiota in Healthy and IBS.
NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",2|1239|186801|3085636|186803|572511;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3085636|186803|33042|33043;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|2719231|29370;2|1239|186801|3085636|186803|248744;2|1239|186801|186802|216572|100175;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40519;2|1239|91061|186826|1300|1301|1338;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|244328,Complete,Lwaldron
bsdb:499/2/1,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients fulfilled the Rome II criteria. Constipation-predominant IBS (IBS-C),46,18,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|s__uncultured Bacteroidetes bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|2974257|28134;2|976|200643|171549|171552|558436|839;2|976|200643|171549|2005525|195950;2|976|152509,Complete,Lwaldron
bsdb:499/2/2,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients fulfilled the Rome II criteria. Constipation-predominant IBS (IBS-C),46,18,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1239|186801|186802|216572|244127;2|1239|186801|3082720|3030910|109326;2|1239|91061|1385|186822|55079;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3085636|186803|33042|33043;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|248744;2|1239|186801|186802|216572|100175;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|44748;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|186802|216572|29343;2|1239|186801|186802|216572|1535;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33038,Complete,Lwaldron
bsdb:499/3/1,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients fulfilled the Rome II criteria. Diarrhea-predominant IBS (IBS-D),46,25,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|329854;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|2974257|28134;2|976|200643|171549|2005525|195950,Complete,Lwaldron
bsdb:499/3/2,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients fulfilled the Rome II criteria. Diarrhea-predominant IBS (IBS-D),46,25,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|1239|186801|3085636|186803|830;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|186807|2740;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|46228,Complete,Lwaldron
bsdb:499/4/1,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS (All patients),IBS patients fulfilled the Rome II criteria. All IBS patients.,46,62,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|s__uncultured Bacteroidetes bacterium,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",2|201174|1760|85004|31953|1678;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|820;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|2974257|28134;2|976|200643|171549|171552|558436|839;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|2005525|195950;2|976|152509;2|1239|186801|244328,Complete,Lwaldron
bsdb:499/4/2,Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS (All patients),IBS patients fulfilled the Rome II criteria. All IBS patients.,46,62,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|1239|91061|1385|186822|55079;2|1239|91061|186826|1300|1301|1338;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|216572|100175;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|3030910|109326;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|33042|33043;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|46228,Complete,Lwaldron
bsdb:500/1/1,Study 500,case-control,33980943,10.1038/s41598-021-89516-6,NA,"Gaibani P, Viciani E, Bartoletti M, Lewis RE, Tonetti T, Lombardo D, Castagnetti A, Bovo F, Horna CS, Ranieri M, Viale P, Re MC , Ambretti S",The lower respiratory tract microbiome of critically ill patients with COVID-19,Scientific reports,2021,NA,Experiment 1,Italy,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,COVID-19 negative patients with pneumonia,COVID-19 patients,COVID-19 Critically Ill Subjects,24,24,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,Figure 3,14 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy",The figure shows the microbial taxa with significant differences between the COVID-19 positive (red) and negative patients (green) (LDA score>2) with their original identification codes.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas alcaligenes,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|108981;2|1224|1236|91347|543;2|1239|186801|3082720|186804|2743582|89152;2|1224|1236|72274|135621|286|43263;2|976|117747|200666|84566|28453,Complete,Peace Sandy
bsdb:500/1/2,Study 500,case-control,33980943,10.1038/s41598-021-89516-6,NA,"Gaibani P, Viciani E, Bartoletti M, Lewis RE, Tonetti T, Lombardo D, Castagnetti A, Bovo F, Horna CS, Ranieri M, Viale P, Re MC , Ambretti S",The lower respiratory tract microbiome of critically ill patients with COVID-19,Scientific reports,2021,NA,Experiment 1,Italy,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,COVID-19 negative patients with pneumonia,COVID-19 patients,COVID-19 Critically Ill Subjects,24,24,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,Figure 3,14 July 2021,Claregrieve1,"Claregrieve1,Aleru002,Peace Sandy","The figure shows the microbial taxa with significant differences between the COVID-19-positive (red) and negative patients 
(green) (LDA score>2) with their original identification codes.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|s__Streptococcaceae bacterium RF32,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral clone CW040,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Candidatus Absconditabacteria|s__candidate division SR1 bacterium",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|29547|3031852|213849|72294|194;2|95818|2093818|2093819|2093822|2093823|1476577;2|976|117743|200644|49546|1016;2|1239|186801|3085636|186803|43996;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|2974257|425941;2|1239|91061|186826|33958|2759736|57037;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|437755;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552;2|201174|1760|85006|1268|32207|43675;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300|423432;2|1239|91061|186826|1300|1301;2|95818|163601;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2|221235|2044938,Complete,Peace Sandy
bsdb:501/1/1,Study 501,"cross-sectional observational, not case-control",NA,https://doi.org/10.21767/2476-1974.100036,https://reproductive-immunology.imedpub.com/reproductive-microbiomes-using-the-microbiome-as-a-novel-diagnostic-tool-for-endometriosis.php?aid=20437,NA,NA,NA,NA,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Endometriosis,EFO:0001065,Women scheduled for laparoscopic surgery for benign uterine/ ovarian conditions as well as women with Stage I or Stage II endometriosis,One (1) Stage III Endometriosis patient,One (1) Stage III Endometriosis patient was diagnosed via laparoscopic surgery and categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,17,1,None,16S,345,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,8 August 2021,Samara.Khan,Samara.Khan,"In this experiment, 9 patients had stage I, II or III endometriosis. The nine patients in the control group were undergoing laparoscopic surgery for other gynecological reasons, for a total of 18 patients.

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

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

It should also be noted that multiple unidentified species of Barnesiella were reported to be significantly different, but researchers did not specify which species so these were excluded from curation. There were also multiple unidentified species of Ruminococcus and Clostridium.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkalitalea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|186802|216572|35829;2|1224|28216|80840|506|222;2|976|200643|1970189|558415|1193324;2|1239|526524|526525|128827|174708;2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816;2|1239|186801|186802|3085642|580596;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|946234;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|201174|1760|85009|31957|1743;2|32066|203490|203491|1129771|168808;2|1239|91061|1385|90964|1279;2|1239|526524|526525|2810281|191303,Complete,NA
bsdb:502/1/1,Study 502,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Fulfilled the Rome III criteria for the diagnosis of IBS.,24,19,2 months,16S,23,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus buchneri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|91061|1385|186817|2893057|79880;2|1239|91061|1385|186817|1386|1396;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|29547|3031852|213849|72294|194;2|1239|186801|3082720|186804|1870884|1496;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958;2|1239|91061|186826|33958|2767893|1581;2|1239|91061|186826|33958|2767887|1624;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:502/1/2,Study 502,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Fulfilled the Rome III criteria for the diagnosis of IBS.,24,19,2 months,16S,23,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:502/2/1,Study 502,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C),24,4,2 months,16S,23,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",2|1239|91061|1385|186817|2893057|79880;2|201174|1760|85004|31953,Complete,Atrayees
bsdb:502/2/2,Study 502,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C),24,4,2 months,16S,23,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:502/3/1,Study 502,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).,24,10,2 months,16S,23,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|91061|1385|186817|2893057|79880;2|1239|91061|1385|186817|1386|1396;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|1239|186801|3082720|186804|1870884|1496;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958;2|1239|91061|186826|33958|2767887|1624;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:502/3/2,Study 502,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).,24,10,2 months,16S,23,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:502/4/1,Study 502,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-M,Fulfilled the Rome III criteria for the diagnosis of IBS. Mixed IBS (IBS-M).,24,5,2 months,16S,23,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus buchneri",2|1239|91061|1385|186817|2893057|79880;2|201174|1760|85004|31953;2|29547|3031852|213849|72294|194;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958|2767893|1581,Complete,Atrayees
bsdb:503/1/1,Study 503,prospective cohort,23565884,10.1111/1469-0691.12213,NA,"Lazarevic V, Manzano S, Gaïa N, Girard M, Whiteson K, Hibbs J, François P, Gervaix A , Schrenzel J",Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Antibiotics, metagenomics, microbiota, otitis media, saliva",Experiment 1,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Amoxicillin,CHEBI:2676,Control(Unexposed to Amoxicillin),Amoxicillin-exposed,This is the group of children who were exposed to amoxicillin treatment for acute otitis media (AOM). They received amoxicillin as part of their treatment.,15,18,6 months.,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,"age,sex",NA,increased,NA,NA,NA,increased,Signature 1,Supplementary file: Table 2.,15 October 2023,Chinelsy,Chinelsy,Changes in taxa abundance at different visits (A2 vs. A1),increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota",2|1224|28216|80840;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1224,Complete,Chinelsy
bsdb:503/2/1,Study 503,prospective cohort,23565884,10.1111/1469-0691.12213,NA,"Lazarevic V, Manzano S, Gaïa N, Girard M, Whiteson K, Hibbs J, François P, Gervaix A , Schrenzel J",Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Antibiotics, metagenomics, microbiota, otitis media, saliva",Experiment 2,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Amoxicillin,CHEBI:2676,Control(Unexposed to Amoxicillin),Amoxicillin-exposed,This is the group of children who were exposed to amoxicillin treatment for acute otitis media (AOM). They received amoxicillin as part of their treatment.,15,18,6 months.,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,"age,sex",NA,increased,NA,NA,NA,increased,Signature 1,Supplementary file: Table 2.,20 July 2021,Chloe,"Chloe,Lwaldron,Chinelsy",Changes in taxa abundance at different visits (A3 vs. A1),increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota",2|1224|28216|80840;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1224,Complete,Chinelsy
bsdb:504/1/1,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,BNH with TNBC normal tissue,BNH with TNBC tumor tissue,Tumor tissue from black non-hispanic patients with triple negative breast cancer,7,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 6a,26 July 2021,Itslanapark,"Itslanapark,Chloe","Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae",2|201174;2|1224|28211|356|41294,Complete,Chloe
bsdb:504/2/1,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,WNH with TNBC normal tissue,WNH with TNBC normal tissue,Tumor tissue from white non-hispanic patients with triple negative breast cancer,6,6,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 6,26 July 2021,Itslanapark,Itslanapark,"Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Chloe
bsdb:504/3/NA,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,WNH with TNBC normal tissue (second set),WNH with TNBC normal tissue (second set),Tumor tissue from white non-hispanic patients with triple negative breast cancer,10,10,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:504/4/1,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 4,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,TPBC normal tissue,TPBC tumor tissue,Tumor tissue from patients with triple positive breast cancer,10,10,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Table 6,26 July 2021,Itslanapark,Itslanapark,"Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",increased,"k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|32066;2|1239|91061|186826|1300|1301,Complete,Chloe
bsdb:504/5/1,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 5,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Normal tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 8,26 July 2021,Itslanapark,Itslanapark,"Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,2|1239|91061|1385|186818,Complete,Chloe
bsdb:504/5/2,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 5,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Normal tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 8,26 July 2021,Itslanapark,Itslanapark,"Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,2|1224|28211|204458|76892|20,Complete,Chloe
bsdb:504/6/1,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 6,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Tumor tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 8,27 July 2021,Itslanapark,Itslanapark,"Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium",2|1239|909932|1843489|31977|29465;2|1224|28211|356|69277|28100,Complete,Chloe
bsdb:504/6/2,Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 6,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Tumor tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 8,27 July 2021,Itslanapark,"Itslanapark,Atrayees","Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae",2|1239|91061|186826|33958|1578;2|1224|28211|204458|76892|20;2|1224|28211|356|41294;2|1224|28211|204458|76892,Complete,Chloe
bsdb:505/1/2,Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 1,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001988,UBERON:0001204",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"Twelve male and 29 female IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as diarrhea predominant (IBS-D), constipation predominant (IBS-C) or alternating IBS subgroup (IBS-A)",26,41,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Tables 2 and 3,19 July 2021,Kwekuamoo,"Chloe,Kwekuamoo","Real time PCR analysis of fecal bifidobacteria in HS, IBS patients and IBS subgroups",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia lituseburensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953|1678|1686;2|1239|186801|3082720|186804|1501226|1537;2|201174|1760|85004|31953|1678,Complete,Chloe
bsdb:505/2/NA,Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 2,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001988,UBERON:0001204",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as diarrhea predominant (IBS-D),26,14,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:505/3/NA,Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 3,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001988,UBERON:0001204",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as  alternating IBS subgroup (IBS-A),26,16,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:505/4/NA,Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 4,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001988,UBERON:0001204",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as  constipation predominant (IBS-C),26,11,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:506/1/1,Study 506,case-control,22356587,10.1111/j.1365-2982.2012.01893.x,NA,"Duboc H, Rainteau D, Rajca S, Humbert L, Farabos D, Maubert M, Grondin V, Jouet P, Bouhassira D, Seksik P, Sokol H, Coffin B , Sabaté JM",Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,The diagnosis of IBS-D was defined by the Rome 3 criteria,18,14,3 months,16S,NA,RT-qPCR,"Mann-Whitney (Wilcoxon),T-Test",0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,19 July 2021,Kwekuamoo,Kwekuamoo,"Comparison of fecal counts (A) in all bacteria, Faecalibacterium prausnitzii, lactobacillus and bifidobacterium and (B) of the main fecal bacterial groups that transform bile acid (coccoides, bacteroides, Escherichia coli, and leptum) in feces of healthy subjects (white bar) and diarrhea predominant IBS patients (gray bar) by quantitative polymerase chain reaction. All results are expressed in log10 bacteria per gram of stool.",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,2|1224|1236|91347|543|561|562,Complete,Atrayees
bsdb:506/1/2,Study 506,case-control,22356587,10.1111/j.1365-2982.2012.01893.x,NA,"Duboc H, Rainteau D, Rajca S, Humbert L, Farabos D, Maubert M, Grondin V, Jouet P, Bouhassira D, Seksik P, Sokol H, Coffin B , Sabaté JM",Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,The diagnosis of IBS-D was defined by the Rome 3 criteria,18,14,3 months,16S,NA,RT-qPCR,"Mann-Whitney (Wilcoxon),T-Test",0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,19 July 2021,Kwekuamoo,"Kwekuamoo,Aiyshaaaa","Comparison of fecal counts (A) in all bacteria, Faecalibacterium prausnitzii, lactobacillus and bifidobacterium and (B) of the main fecal bacterial groups that transform bile acid (coccoides, bacteroides, Escherichia coli, and leptum) in feces of healthy subjects (white bar) and diarrhea predominant IBS patients (gray bar) by quantitative polymerase chain reaction. All results are expressed in log10 bacteria per gram of stool.",decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:507/1/1,Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients after Rifaximin treatment,"Patients affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively treated with 1,200 mg of Rifaximin daily for 10 days.",20,20,1 month,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977|29465,Complete,Chloe
bsdb:507/1/2,Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients after Rifaximin treatment,"Patients affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively treated with 1,200 mg of Rifaximin daily for 10 days.",20,20,1 month,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.,increased,NA,NA,Complete,Chloe
bsdb:507/2/1,Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients 1 month after Rifaximin treatment,"Patients 1 month after Rifaximin treatment affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively.",20,20,1 month prior to Rifaximin treatment.,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by Rifaximin treatment time a versus time c.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Chloe
bsdb:507/2/2,Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients 1 month after Rifaximin treatment,"Patients 1 month after Rifaximin treatment affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively.",20,20,1 month prior to Rifaximin treatment.,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by rifaximin treatment at time a versus time c,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,2|1239|186801|3085636|186803|841,Complete,Chloe
bsdb:508/1/1,Study 508,case-control,33099131,10.1016/j.parkreldis.2020.10.034,https://pubmed.ncbi.nlm.nih.gov/33099131/,"Zhang F, Yue L, Fang X, Wang G, Li C, Sun X, Jia X, Yang J, Song J, Zhang Y, Guo C, Ma G, Sang M, Chen F , Wang P",Altered gut microbiota in Parkinson's disease patients/healthy spouses and its association with clinical features,Parkinsonism & related disorders,2020,"Clinical features/classifications, Gut microbiota dysbiosis, Metagenomics, Neurodegenerative disease, Parkinson's disease (PD)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"The patients were diagnosed with primary Parkinson's disease according to the Movement Disorder Society Clinical Diagnostic Criteria for Parkinson’s disease (MDS-PD Criteria, 2015) of Xiangyang NO.1 People’s Hospital.",137,63,90 days.,16S,4,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table S2,22 February 2023,Jacquelynshevin,Jacquelynshevin,33 significantly differential gut bacterial markers identified by LEfSe analysis.,increased,"k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia,k__Bacteria|p__Actinomycetota|c__Actinomycetes",2|28221;2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551;2|1239|909932|1843489|31977;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201;2|1239|186801|186802|216572;2|1239|186801|186802;2|1239;2|1224;2|201174|84992;2|201174|1760,Complete,Fatima
bsdb:508/1/2,Study 508,case-control,33099131,10.1016/j.parkreldis.2020.10.034,https://pubmed.ncbi.nlm.nih.gov/33099131/,"Zhang F, Yue L, Fang X, Wang G, Li C, Sun X, Jia X, Yang J, Song J, Zhang Y, Guo C, Ma G, Sang M, Chen F , Wang P",Altered gut microbiota in Parkinson's disease patients/healthy spouses and its association with clinical features,Parkinsonism & related disorders,2020,"Clinical features/classifications, Gut microbiota dysbiosis, Metagenomics, Neurodegenerative disease, Parkinson's disease (PD)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"The patients were diagnosed with primary Parkinson's disease according to the Movement Disorder Society Clinical Diagnostic Criteria for Parkinson’s disease (MDS-PD Criteria, 2015) of Xiangyang NO.1 People’s Hospital.",137,63,90 days.,16S,4,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Table S2,22 February 2023,Jacquelynshevin,Jacquelynshevin,33 significantly differential gut bacterial markers identified by LEfSe analysis.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacteroidota",2|976|200643|171549;2|976|200643;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|32066;2|976,Complete,Fatima
bsdb:509/1/1,Study 509,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R, Chen L, Cao L, Li KJ, Huang Y, Luan XQ , Li G",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 1,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 10,14 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1",Differential microbial abundance between the smoking and non-smoking mice,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales|f__Blastocatellaceae|g__Blastocatella,k__Bacteria|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Chloroflexota|c__Ktedonobacteria|o__Ktedonobacterales|f__Ktedonobacteraceae,k__Bacteria|p__Chloroflexota|c__Ktedonobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae|g__Pullulanibacillus,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus",2|976|200643|171549|171552|1283313;2|57723|1562566|1748771|1748772|1281902;2|57723|1562566|1748771;2|976|768503|768507|2896860|120831;2|1224|1236|91347|543|1940338;2|200795|388447|388448|388449;2|200795|388447;2|1239|91061|186826|1300|1357;2|544448|31969;2|544448;2|1224|28216|32003|206379;2|1224|28216|32003;2|1224|28216|80840|75682;2|976|117747|200666|84566|84567;2|1239|91061|1385|186818|162291;2|976|200643|171549|171551|836;2|1224|1236|91347|1903414|583;2|1239|91061|1385|186821|475230;2|976|117747|200666|84566;2|1239|91061|1385|186821;2|1239|186801|186802|216572|292632;2|1239|91061|186826|186828|82802,Complete,Claregrieve1
bsdb:509/1/2,Study 509,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R, Chen L, Cao L, Li KJ, Huang Y, Luan XQ , Li G",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 1,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 10,23 April 2023,Sophy,"Sophy,Claregrieve1",Differential microbial abundance between the smoking and non-smoking mice,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella",2|201174|1760|85006|85020|43668;2|1239|91061|1385|186822|55080;2|1224|28216|80840|119060;2|200940|3031651|69541;2|1224|28216|80840|80864|238749;2|1224|1236|91347|543|547;2|1224|1236|91347;2|1224|1236|91347|543;2|200940|3031651|3031668|213422|28231;2|1224|1236|91347|543|579;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|1224|28211|356|69277|68287;2|201174|1760|85006|1268|57494;2|1224|1236|135619;2|1239|909932|1843488|909930|33024;2|1224|28211|356|69277;2|1224|28216|80840|119060|48736;2|1224|1236|91347|543|160674,Complete,Claregrieve1
bsdb:509/2/1,Study 509,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R, Chen L, Cao L, Li KJ, Huang Y, Luan XQ , Li G",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 2,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),NA,NA,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,29 May 2023,Atrayees,"Atrayees,ChiomaBlessing",Differentially abundant taxon in the smoking and the non-smoking groups.,increased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Candidatus Thermoprofundales,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Jatrophihabitantales|f__Jatrophihabitantaceae|g__Jatrophihabitans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae|g__Pullulanibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|s__uncultured Planctomycetaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|201174|84992|84993;2|976|200643|171549|171552|1283313;2157|2283796|183967|347538;2|976|768503|768507|2896860|120831;2|201174|1760|2805415|2805416|1434010;2|1239|91061|186826|1300|1357;2|1239|91061|1385|90964|69965;2|1239|186801|3085636|186803|248744;2|976|200643|171549|2005523|346096;2|976|117747|200666|84566|84567;2|1239|91061|1385|186818|162291;2|976|200643|171549|171551|836;2|1224|1236|91347|1903414|583;2|1224|28211|356|118882|354349;2|1239|91061|1385|186821|475230;2|1239|186801|186802|216572|292632;2|1239|91061|186826|186828|82802;2|1224|28211|204458|76892;2|203682|203683|112|126|100233;2|1224|1236|91347|543|1940338,Complete,Atrayees
bsdb:509/2/2,Study 509,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R, Chen L, Cao L, Li KJ, Huang Y, Luan XQ , Li G",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 2,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),NA,NA,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,29 May 2023,Atrayees,"Atrayees,ChiomaBlessing,Chinelsy",Differentially abundant taxon in the smoking and the non-smoking groups.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paucimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Variibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|s__uncultured Phyllobacteriaceae bacterium",2|201174|1760|85006|85020|43668;2|1239|91061|1385|186822|55080;2|1239|526524|526525|128827|1774107;2|201174|1760|85007|1653|1716;2|1224|28216|80840|80864|238749;2|1224|1236|91347|543|547;2|200940|3031651|3031668|213422|28231;2|1239|91061|1385|90964|227979;2|1224|1236|91347|543|579;2|1239|91061|186826|33958|1578;2|1224|28211|356|69277|68287;2|200930|68337|191393|2945020|248038;2|201174|1760|85006|1268|57494;2|1224|1236|135625|712|745;2|1224|28216|80840|119060|157932;2|1224|1236|91347|543|160674;2|1224|28211|356|41294|1649510;2|1224|28211|356|69277|257462,Complete,Atrayees
bsdb:510/1/1,Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,20,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 3b, text",29 July 2021,Tislam,"Tislam,Fatima",OTUs with different relative abundance based on LEfSe among subjects with periodontitis,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter actinomycetemcomitans,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.",2|1224|1236|135625|712|416916|714;2|1239|186801|3082720|3030910|86331|35519;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|52228|310514;2|976|200643|171549|171552|2974251|228604;2|1224|1236|72274|135621|286|287;2|1239|909932|909929|1843491|970|671224;2|1224|1236|135625|712|416916|1872413,Complete,Fatima
bsdb:510/1/2,Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,20,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 3b, text",29 July 2021,Tislam,"Tislam,Fatima",OTUs with different relative abundance based on LEfSe among subjects with periodontitis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella marshii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.",2|976|200643|171549|171552|2974257|189722;2|201174|1760|2037|2049|2529408|52773;2|1239|91061|186826|1300|1301|1328;2|203691|203692|136|2845253|157|166,Complete,Fatima
bsdb:510/2/1,Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 2,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,27,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 3a, text",29 July 2021,Tislam,"Tislam,Fatima",Differential abundance based on LEfSe among subjects without periodontitis,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium neglectum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral clone DO042,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. oral taxon 808",2|976|200643|171549|171552|1283313|671218;2|1239|909932|1843489|31977|156454|156456;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1689;2|976|117743|200644|49546|1016|1018;2|201174|1760|85007|1653|1716|43768;2|201174|84998|84999|1643824|2767353|1383;2|32066|203490|203491|1129771|32067|157688;2|32066|203490|203491|1129771|32067|157691;2|32066|203490|203491|1129771|32067|157687;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|3030910|86331|114528;2|1239|186801|3082720|3030910|86331|35519;2|976|200643|171549|171552|2974251|28126;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|2974251|439703;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|52228|310514;2|976|200643|171549|171552|838|28133;2|976|200643|171549|171552|2974251|28136;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|2974251|228604;2|976|200643|171549|171552|2974257|228603;2|1224|1236|72274|135621|286|287;2|201174|1760|85004|31953|196081|230143;2|1239|909932|909929|1843491|970|135080;2|1239|909932|909929|1843491|970|135083;2|1239|909932|909929|1843491|970|163583;2|1239|909932|909929|1843491|970|69823;2|976|200643|171549|2005525|195950|712711,Complete,NA
bsdb:510/2/2,Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 2,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,27,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 3, text",29 July 2021,Tislam,Tislam,subjects without periodontitis,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles puraquae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral clone BR014,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral clone ASCB04",2|1224|28216|80840|80864|80865|180282;2|1239|91061|186826|186828|117563|137732;2|1224|28216|206351|481|32257|505;2|1224|28216|80840|2975441|93681|431059;2|976|200643|171549|171552|2974257|407975;2|976|200643|171549|171552|838|163559;2|508458|649775|649776|3029088|638847|638849;2|201174|1760|85006|1268|32207|172042;2|201174|1760|2037|2049|2529408|52773;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|325787,Complete,NA
bsdb:511/1/1,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,44,140,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2D,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor",2|1224|1236|135625|712|724|729;2|1239|909932|1843489|31977|29465;2|29547|3031852|213849|72294|194;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|482|28449;2|1224|28216|206351|481|32257;2|1239|186801|3082720|3118655|44259,Complete,Fatima
bsdb:511/1/2,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,44,140,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2D,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum",2|1224|28216|206351|481|482;2|201174|1760|85007|1653|1716;2|1224|1236|135625|712|713;2|1239|186801|3085636|186803|437755;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|838|28131;2|203691|203692|136|2845253|157;2|1224|1236|72274|135621|286;2|203691|203692|136|2845253|157|59892,Complete,Fatima
bsdb:511/2/1,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 2,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,COVID-19 patients (mild/moderate),COVID-19 patients (severe/critical),Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests deemed to have severe/critical disease,30,22,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Supplementary Table 3,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between mild/moderate and severe/critical COVID-19 patients,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus",2|203691|203692|136|2845253|157;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|739;2|976|200643|171549|171552|838|28131;2|1239|91061|186826|1300|1301|1328;2|1239|909932|909929|1843491|970;2|1239|186801|3082720|3118655|44259;2|203691|203692|136|2845253|157|59892;2|1239|186801|186802|186807|2740,Complete,Fatima
bsdb:511/3/1,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,44,17,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1224|28216|206351|481|482|28449;2|1239|91061|186826|186828|117563;2|1239|909932|1843489|31977|29465;2|29547|3031852|213849|72294|194;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465|39778;2|1239|1737404|1737405|1570339|162289,Complete,Fatima
bsdb:511/3/2,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,44,17,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 3,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",2|1239|186801|3085636|186803|437755;2|203691|203692|136|2845253|157;2|976|200643|171549|171552|838|28131,Complete,Fatima
bsdb:511/4/1,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,32,81,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Supplementary Table 4,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|46255;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803|2719313|358743;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85006|1268|32207|43675;2|201174|1760|85006|1268|32207;2|1239|91061|186826|33958|1578;2|201174|1760|2037|2049|1654;2|1239|91061|186826|186828|117563,Complete,Fatima
bsdb:511/4/2,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,32,81,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Supplementary Table 4,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|976|200643|171549|815|816|47678;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|1506577|36835;2|201174|84998|84999|84107|102106;2|976|200643|171549|815|909656|387090,Complete,Fatima
bsdb:511/5/1,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,32,13,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2719313|358743;2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|1300|1301|1328;2|1239|1737404|1737405|1570339|162289;2|29547|3031852|213849|72294|194;2|201174|84998|84999|1643824|1380,Complete,Fatima
bsdb:511/5/2,Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,32,13,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|909656|387090;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|572511|33035;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|1506577|36835;2|1224|28216|206351|481|482,Complete,Fatima
bsdb:512/1/1,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls and healthcare workers,COVID-19 positive patients,Patients positive for SARS-CoV-2,66,68,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2a,6 August 2021,Claregrieve1,"Claregrieve1,Iram jamshed",Differential microbial abundance between COVID-19 patients and non-COVID patients (COVID negative patients and healthcare workers),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1224|1236|2887326|468|469;2|201174|1760|85006|1268|1269;2|1224|1236|2887326|468|475;2|1224|1236|72274|135621|286;2|201174|1760|85006|1268|32207,Complete,Folakunmi
bsdb:512/2/1,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients positive for SARS-CoV-2,21,68,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figures 2b-h,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive and COVID-19 negative patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|91061|1385|186817|150247;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:512/3/1,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative healthcare workers (controls),COVID-19 positive patients,Patients positive for SARS-CoV-2,45,68,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figures 2b-h,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|91061|1385|186817|150247;2|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:512/3/2,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative healthcare workers (controls),COVID-19 positive patients,Patients positive for SARS-CoV-2,45,68,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figures 2b-h,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cepacia,2|1224|28216|80840|119060|32008|292,Complete,Folakunmi
bsdb:512/4/1,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 4,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,high Ct CoV+ patients,low Ct CoV+ patients,SARS-CoV-2 positive patients with low cycle threshold value (>23.5),23,22,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3,26 December 2023,Folakunmi,Folakunmi,Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Low Ct,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|482;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:512/5/1,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,high Ct CoV+ patients,mid Ct CoV+ patients,SARS-CoV-2 positive patients with mid cycle threshold value (32.9-25.0),23,23,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3,26 December 2023,Folakunmi,Folakunmi,Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|482,Complete,Folakunmi
bsdb:512/5/2,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,high Ct CoV+ patients,mid Ct CoV+ patients,SARS-CoV-2 positive patients with mid cycle threshold value (32.9-25.0),23,23,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3,26 December 2023,Folakunmi,Folakunmi,Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:512/6/1,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 6,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,mid Ct CoV+ patients,low Ct CoV+ patients,SARS-CoV-2 positive patients with low cycle threshold value (>23.5),23,22,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3,26 December 2023,Folakunmi,Folakunmi,Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into Mid and Low Ct,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,2|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:512/7/1,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 7,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,low and mid Ct CoV+ patients,high Ct CoV+ patients,SARS-CoV-2 positive patients with high cycle threshold value (>34.6),45,23,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3A,26 December 2023,Folakunmi,Folakunmi,"Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Low and Mid Ct",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:512/7/2,Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 7,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,low and mid Ct CoV+ patients,high Ct CoV+ patients,SARS-CoV-2 positive patients with high cycle threshold value (>34.6),45,23,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3A,26 December 2023,Folakunmi,Folakunmi,"Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Mid and Low Ct",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216;2|1224|28216|206351|481|482;2|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:513/1/1,Study 513,"cross-sectional observational, not case-control",NA,https://doi.org/10.3390/applmicrobiol1020014,https://www.mdpi.com/2673-8007/1/2/14,"Feehan, A.K., Rose, R., Nolan, D.J., Spitz, A.M., Graubics, K., Colwell, R.R., Garcia-Diaz, J. and Lamers, S.L.",Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment,Applied Microbiology,2021,"SARS-CoV-2, Serratia, hospital, metagenomic sequencing",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who were confirmed PCR positive for SARS-CoV-2,20,79,NA,WMS,NA,Illumina,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S5,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and non-COVID-19 patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|91347|1903411|613;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:513/2/1,Study 513,"cross-sectional observational, not case-control",NA,https://doi.org/10.3390/applmicrobiol1020014,https://www.mdpi.com/2673-8007/1/2/14,"Feehan, A.K., Rose, R., Nolan, D.J., Spitz, A.M., Graubics, K., Colwell, R.R., Garcia-Diaz, J. and Lamers, S.L.",Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment,Applied Microbiology,2021,"SARS-CoV-2, Serratia, hospital, metagenomic sequencing",Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 positive patients without breathing assistance,COVID-19 positive patients with breathing assistance,"Patients who were confirmed PCR positive for SARS-CoV-2 and had treatment with oxygen mask, non-rebreather mask, nasal cannula, BiPAP, CPAP, or ventilator",67,12,NA,WMS,NA,Illumina,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S5,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who had breathing assistance and those who did not,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",2|1224|1236|91347|543|547;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1224|1236|91347|1903411|613,Complete,Atrayees
bsdb:513/3/1,Study 513,"cross-sectional observational, not case-control",NA,https://doi.org/10.3390/applmicrobiol1020014,https://www.mdpi.com/2673-8007/1/2/14,"Feehan, A.K., Rose, R., Nolan, D.J., Spitz, A.M., Graubics, K., Colwell, R.R., Garcia-Diaz, J. and Lamers, S.L.",Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment,Applied Microbiology,2021,"SARS-CoV-2, Serratia, hospital, metagenomic sequencing",Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 positive patients without antibiotic use,COVID-19 positive patients with antibiotic use,COVID-19 positive patients with antibiotic use,81,27,NA,WMS,NA,Illumina,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S5,27 July 2023,Atrayees,Atrayees,Differential microbial abundance between COVID-19 patients who used antibiotics and who didn't,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",2|1239|1737404|1737405|1570339|150022;2|1224|1236|91347|1903411|613,Complete,Atrayees
bsdb:514/1/1,Study 514,"cross-sectional observational, not case-control",31087436,10.1111/aji.13147,NA,"Akiyama K, Nishioka K, Khan KN, Tanaka Y, Mori T, Nakaya T , Kitawaki J",Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2019,"cervical mucus, endometriosis, metagenomic analysis, microbiota",Experiment 1,Japan,Homo sapiens,Uterine cervix,UBERON:0000002,Endometriosis,EFO:0001065,Women scheduled for laparoscopic surgery for benign uterine/ ovarian conditions,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,39,30,No antibiotics were taken 6 months prior to sample collection,16S,56,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 4,8 August 2021,Samara.Khan,Samara.Khan,Enterobactericeae and streptococcus were significantly higher in the cervical mucus of the endometriosis group than the control group.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|91347|543;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:515/1/NA,Study 515,"cross-sectional observational, not case-control",29771400,10.26355/eurrev_201805_14899,NA,"Wang XM, Ma ZY , Song N","Inflammatory cytokines IL-6, IL-10, IL-13, TNF-α and peritoneal fluid flora were associated with infertility in patients with endometriosis",European review for medical and pharmacological sciences,2018,NA,Experiment 1,China,Homo sapiens,Uterovesical pouch,UBERON:0011049,Endometriosis,EFO:0001065,Non-endometriosis patients with infertility,Endometriosis patients with infertility,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,30,55,None,16S,45,Ion Torrent,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:516/1/1,Study 516,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M, Li D, Zhang Z, Sun H, An M , Wang G",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,N/A,16S,4,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,8 August 2021,Samara.Khan,"Samara.Khan,Fatima","Researchers used t-tests to calculate the differences in microbiota at the taxon level between the control and experimental groups.

The following bacterial taxa were more abundant in mice with simulated endometriosis than in mice without endometriosis.",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",2|201174;2|1224|28216|80840|506;2|1224|28216;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1224|28216|80840;2|1239;2|1224|28216|80840|995019|577310,Complete,Fatima
bsdb:516/1/2,Study 516,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M, Li D, Zhang Z, Sun H, An M , Wang G",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,N/A,16S,4,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,8 August 2021,Samara.Khan,Samara.Khan,"Researchers used the LEfse method to determine the predominant microbiota in each sample. They then used t-tests to calculate the differences in microbiota at the taxon level between the control and experimental groups.

The following bacterial taxa were less abundant in mice with simulated endometriosis than in mice without endometriosis.",decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643;2|976|200643|171549,Complete,Fatima
bsdb:516/2/1,Study 516,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M, Li D, Zhang Z, Sun H, An M , Wang G",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,N/A,16S,4,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,14 March 2022,Fatima,"WikiWorks,Fatima",LDA coupled with effect size measurements identified the most differentially abundant taxa between the two groups,increased,k__Bacteria|p__Bacillota,2|1239,Complete,Chloe
bsdb:516/2/2,Study 516,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M, Li D, Zhang Z, Sun H, An M , Wang G",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,N/A,16S,4,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,14 March 2022,Fatima,"WikiWorks,Fatima",LDA coupled with effect size measurements identified the most differentially abundant taxa between the two groups,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota",2|976|200643|171549|171552|1283313;2|976|200643;2|976|200643|171549;2|976,Complete,Chloe
bsdb:517/1/1,Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 1,Japan,Homo sapiens,Endometrium,UBERON:0001295,Endometriosis,EFO:0001065,Untreated control women,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the control patients and 16 of the endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,32,32,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,8 August 2021,Samara.Khan,Samara.Khan,"Regardless of GnRHa treatment, patients with endometriosis had higher levels of streptococcaceae and moraxellaceae than those without endometriosis.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",2|1239|91061|186826|1300;2|1224|1236|2887326|468,Complete,Atrayees
bsdb:517/2/1,Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 2,Japan,Homo sapiens,Endometrium,UBERON:0001295,Endometriosis,EFO:0001065,Endometriosis patients not treated with GnRHa,Endometriosis patients treated with GnRHa,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the 32 endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,16,16,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,8 August 2021,Samara.Khan,Samara.Khan,"Streptococcaceae, Staphylococaceae, Enterobacteriaceae were significantly increased (p<0.05 for each) in GnRHa-treated women with endometriosis than in GnRHa-untreated women.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1224|1236|91347|543;2|1239|91061|186826|1300;2|1239|91061|1385|90964,Complete,Atrayees
bsdb:517/2/2,Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 2,Japan,Homo sapiens,Endometrium,UBERON:0001295,Endometriosis,EFO:0001065,Endometriosis patients not treated with GnRHa,Endometriosis patients treated with GnRHa,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the 32 endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,16,16,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,8 August 2021,Samara.Khan,Samara.Khan,Lactobacillaceae was significantly decreased (p<0.01) in GnRHa-treated women with endometriosis compared to GnRHa-untreated women with endometriosis,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,Atrayees
bsdb:517/3/1,Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 3,Japan,Homo sapiens,Ovary,UBERON:0000992,Endometriosis,EFO:0001065,Patients with non-endometrioma cysts,Patients with ovarian endometrioma cysts,Patients with ovarian endometrioma had endometrial cysts in their ovaries. Researchers took samples of the fluid inside these cysts. Ovarian endometrioma is one of the many ways endometriosis manifests in the female reproductive system.,8,8,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 August 2021,Samara.Khan,Samara.Khan,There was a significantly higher percentage of Streptococcaceae (p<0.01) and Staphylococaceae (p<0.05) in the cystic fluid derived from women with ovarian endometrioma comparing to that in cystic fluid collected from non-endometrioma cysts.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1239|91061|186826|1300;2|1239|91061|1385|90964,Complete,Atrayees
bsdb:517/3/2,Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 3,Japan,Homo sapiens,Ovary,UBERON:0000992,Endometriosis,EFO:0001065,Patients with non-endometrioma cysts,Patients with ovarian endometrioma cysts,Patients with ovarian endometrioma had endometrial cysts in their ovaries. Researchers took samples of the fluid inside these cysts. Ovarian endometrioma is one of the many ways endometriosis manifests in the female reproductive system.,8,8,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,7 August 2023,Atrayees,Atrayees,There was a significantly higher percentage of Streptococcaceae (p<0.01) and Staphylococaceae (p<0.05) in the cystic fluid derived from women with ovarian endometrioma comparing to that in cystic fluid collected from non-endometrioma cysts.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,Atrayees
bsdb:518/1/1,Study 518,case-control,33839907,10.1007/s00404-021-06057-z,NA,"Shan J, Ni Z, Cheng W, Zhou L, Zhai D, Sun S , Yu C",Gut microbiota imbalance and its correlations with hormone and inflammatory factors in patients with stage 3/4 endometriosis,Archives of gynecology and obstetrics,2021,"Dysbiosis, Endometriosis, Estradiol, Gut microbiota, Inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,12,12,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Folakunmi,Welile,Idiaru angela",Patients with endometriosis demonstrated a significantly higher abundance of the following taxa compared to control patients. There were 36 taxa unique to endometriosis patients that were completely absent in control patients. Some taxa were excluded because they had an unidentified genus/ species,increased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales|f__Blastocatellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhodobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|57723;2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|2569097|39488;2|976|200643|171549;2|1239|186801|3085636|186803|572511;2|95818;2|32066|203490|203491|203492|180162;2|201174|1760|85007|1653|1716;2|1117;2|1239|186801|3085636|186803|189330;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186828|117563;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|186801|3085636|186803|2316020|33038;2|201174|1760|85007|1762|1763;2|201174|1760|85006|1268|1742993;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|1300|1301;2|1239|186801|186802|543314|35517;2|57723|1562566|1748771|1748772;2|976|200643|171549|171552;2|1224|28211|356|119043;2|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:518/1/2,Study 518,case-control,33839907,10.1007/s00404-021-06057-z,NA,"Shan J, Ni Z, Cheng W, Zhou L, Zhai D, Sun S , Yu C",Gut microbiota imbalance and its correlations with hormone and inflammatory factors in patients with stage 3/4 endometriosis,Archives of gynecology and obstetrics,2021,"Dysbiosis, Endometriosis, Estradiol, Gut microbiota, Inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,12,12,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Folakunmi",The following taxa were decreased in endometriosis patients and increased in the control group. There were 11 genera unique to the control group. Some taxa were excluded because they had an unidentified genus/ species,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|s__bacterium ND3007,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|877420;2|976|200643|171549|1853231|283168;2|1224|28216|80840|995019|577310;2|1239|186801|186802|216572|1263|41978;2|1452070;2|1239|186801|3085636|1185407;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|707003;2|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:519/1/1,Study 519,laboratory experiment,31037294,10.1093/humrep/dez041,NA,"Chadchan SB, Cheng M, Parnell LA, Yin Y, Schriefer A, Mysorekar IU , Kommagani R",Antibiotic therapy with metronidazole reduces endometriosis disease progression in mice: a potential role for gut microbiota,"Human reproduction (Oxford, England)",2019,"endometriosis, gut bacteria, inflammation, metronidazole, microbiome",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Non-endo mice,Endo mice,Uterine tissue was transplanted onto the peritoneal wall in order to induce endometriosis in these mice.,5,5,Mice had never been given antibiotics prior to the start of the experiment,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",Differential microbial abundance between non-endo and endo mice: fecal samples from mice with simulated endometriosis had higher levels of Bacteroidetes and Firmicutes than non-endo mice. The bacteroides genera was absent in non-endo mice but present in endo mice.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:520/2/1,Study 520,"cross-sectional observational, not case-control",32046455,10.1007/s43032-019-00113-5,NA,"Perrotta AR, Borrelli GM, Martins CO, Kallas EG, Sanabani SS, Griffith LG, Alm EJ , Abrao MS",The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study,"Reproductive sciences (Thousand Oaks, Calif.)",2020,"Diagnosis, Endometriosis, Microbiome, Pathogenesis, Vaginal microbiome",Experiment 2,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,patients with rASRM stages 1 - 2,patients with rASRM stages 3 - 4,Patients with vaginal and rectal microbiome profiles and their association to severity of endometriosis (rASRM) stages 3 - 4,12,8,Participants were excluded if they had taken antibiotics within the past 3 months,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3B,13 July 2023,Atrayees,"Atrayees,ChiomaBlessing","Correlations of OTU abundance with stage of disease, showing abundance in stages 3 - 4 compared to stages 1 - 2",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:520/2/2,Study 520,"cross-sectional observational, not case-control",32046455,10.1007/s43032-019-00113-5,NA,"Perrotta AR, Borrelli GM, Martins CO, Kallas EG, Sanabani SS, Griffith LG, Alm EJ , Abrao MS",The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study,"Reproductive sciences (Thousand Oaks, Calif.)",2020,"Diagnosis, Endometriosis, Microbiome, Pathogenesis, Vaginal microbiome",Experiment 2,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,patients with rASRM stages 1 - 2,patients with rASRM stages 3 - 4,Patients with vaginal and rectal microbiome profiles and their association to severity of endometriosis (rASRM) stages 3 - 4,12,8,Participants were excluded if they had taken antibiotics within the past 3 months,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3B,13 July 2023,Atrayees,"Atrayees,ChiomaBlessing","Correlations of OTU abundance with stage of disease, showing abundance in stages 3 - 4 compared to stages 1 - 2",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",2|1224|28216|80840|80864|12916;2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|1940338;2|1239|186801|186802|404402;2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|162289;2|1224|28211|356|69277|28100;2|976|200643|171549|171552|838;2|201174|1760|85009|31957|1743;2|1224|28211|204457|41297|13687;2|1239|91061|186826|1300|1301;2|1239|1737404;2|201174|1760|2037|2049|184869,Complete,ChiomaBlessing
bsdb:521/1/1,Study 521,case-control,33925708,10.3390/ijms22094608,NA,"Lee SR, Lee JC, Kim SH, Oh YS, Chae HD, Seo H, Kang CS , Shin TS",Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid,International journal of molecular sciences,2021,"16S rDNA, endometriosis, extracellular vesicles, microbiome",Experiment 1,South Korea,Homo sapiens,Uterovesical pouch,UBERON:0011049,Endometriosis,EFO:0001065,Surgical controls,Stage 3/4 endometriosis patients,Stage 3/4 endometriosis patients that were diagnosed with endometriosis via laparoscopic surgery; stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,45,45,Patients were excluded if they had taken antibiotics 12 weeks prior to sample collection,16S,34,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 1 and Results section,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",Differential microbial abundance between peritoneal fluid samples among women with endometriosis when compared to surgical controls.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:521/1/2,Study 521,case-control,33925708,10.3390/ijms22094608,NA,"Lee SR, Lee JC, Kim SH, Oh YS, Chae HD, Seo H, Kang CS , Shin TS",Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid,International journal of molecular sciences,2021,"16S rDNA, endometriosis, extracellular vesicles, microbiome",Experiment 1,South Korea,Homo sapiens,Uterovesical pouch,UBERON:0011049,Endometriosis,EFO:0001065,Surgical controls,Stage 3/4 endometriosis patients,Stage 3/4 endometriosis patients that were diagnosed with endometriosis via laparoscopic surgery; stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,45,45,Patients were excluded if they had taken antibiotics 12 weeks prior to sample collection,16S,34,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 1 and Results section,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",Differential microbial abundance between peritoneal fluid samples among women with endometriosis when compared to surgical controls.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|2887326|468|469;2|1224|28211|356|212791;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:522/1/1,Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,"16S rRNA gene amplicon sequencing, Endometriosis, Microbial community composition, Microbial distribution",Experiment 1,China,Homo sapiens,"Lower part of vagina,Upper part of vagina,Cervical mucus","UBERON:0015243,UBERON:0003974,UBERON:0000316",Endometriosis,EFO:0001065,Controls Subject undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Women with endometriosis,14,36,6 Months,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2,8 February 2024,Peace Sandy,Peace Sandy,"The signature OTUs identified in the different sites of female reproductive tract were shown, including a vagina (CL), b posterior vaginal fornix (CU), c cervical mucus (CV), d endometrium (ET) and e peritoneal fluid (PF). Blue bar and purple bar note higher abundancy were occurred in EMS patients and healthy women, representatively. The signature OTUs were defined by Wilcoxon-rank sum test with p value < 0.05",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium",2|1239|91061|186826|33958|1578|147802;2|1239|91061|186826|81852|2737;2|201174|1760|85006|1268|1663;2|1224|1236|72274|135621|286|33069;2|1224|28211|204457|41297|165695;2|1224|28216|80840|80864;2|1224|28216|80840|80864|80865;2|976|200643|171549|2005520|156973;2|1224|1236|72274|135621;2|1239|526524|526525|128827;2|1224|28211|204458|76892;2|1224|28211|204455|31989|265;2|1224|1236|135622|267890|22;2|1224|1236|72274|135621|286|306;2|201174|1760|85006|1268;2|1224|1236|2887326|468|469;2|1239|91061|186826|81852|1350;2|201174|1760|85006|85023|55968;2|1239|91061|1385|186822|44249;2|1224|1236|72274|135621|286;2|1239|1737404|1737405|1737406;2|1224|28211|356|45401|81,Complete,Peace Sandy
bsdb:522/1/2,Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,"16S rRNA gene amplicon sequencing, Endometriosis, Microbial community composition, Microbial distribution",Experiment 1,China,Homo sapiens,"Lower part of vagina,Upper part of vagina,Cervical mucus","UBERON:0015243,UBERON:0003974,UBERON:0000316",Endometriosis,EFO:0001065,Controls Subject undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Women with endometriosis,14,36,6 Months,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2,8 February 2024,Peace Sandy,Peace Sandy,"The signature OTUs identified in the different sites of female reproductive tract were shown, including a vagina (CL), b posterior vaginal fornix (CU), c cervical mucus (CV), d endometrium (ET) and e peritoneal fluid (PF). Blue bar and purple bar note higher abundancy were occurred in EMS patients and healthy women, representatively. The signature OTUs were defined by Wilcoxon-rank sum test with p value < 0.05",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcoides|s__Macrococcoides caseolyticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium multivorum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agromyces,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|91061|186826|186827|1375;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|1239|91061|186826|33958|1578|1591;2|32066|203490|203491|1129771;2|201174|1760|2037|2049|2050;2|201174|84998|84999|84107;2|1224|1236|135614|1775411;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|2316020|33038;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838|28128;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802;2|1239|91061|186826|81852|1350|37734;2|1224|28211|356;2|1239|186801|186802|216572|119852;2|1239|91061|1385|90964|3076173|69966;2|1224|1236|72274|135621;2|976|117747|200666|84566|28453|28454;2|201174|1760|85006|1268|1663;2|1224|1236|91347|543;2|1224|1236|2887326|468|469;2|1224|28211|766|942|953;2|201174|1760|85006|85023|33877;2|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:523/1/1,Study 523,laboratory experiment,32681566,10.1111/aji.13307,NA,"Ni Z, Sun S, Bi Y, Ding J, Cheng W, Yu J, Zhou L, Li M , Yu C",Correlation of fecal metabolomics and gut microbiota in mice with endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2020,"endometriosis, intestines, metabolomics, microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Non-endo mice,Endo mice,Endometriosis was induced in female mice via transplantation of endometrial fragments.,6,6,N/A,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3 and Results section,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",Differential microbial abundance of mice with simulated endometriosis compared to controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|1432051;2|1239|526524|526525|128827|1573534;2|1239;2|201174|84998|1643822|1643826|644652;2|1239|186801|3085636|186803|877420;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1506577,Complete,Claregrieve1
bsdb:523/1/2,Study 523,laboratory experiment,32681566,10.1111/aji.13307,NA,"Ni Z, Sun S, Bi Y, Ding J, Cheng W, Yu J, Zhou L, Li M , Yu C",Correlation of fecal metabolomics and gut microbiota in mice with endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2020,"endometriosis, intestines, metabolomics, microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Non-endo mice,Endo mice,Endometriosis was induced in female mice via transplantation of endometrial fragments.,6,6,N/A,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",Differential microbial abundance of mice with simulated endometriosis compared to controls.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|1239|526524|526525|128827|174708;2|1224|1236|91347|543|544;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1224;2|976|200643|171549|171550|28138;2|74201,Complete,Claregrieve1
bsdb:524/1/1,Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis),"Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis); The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation",76,40,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,11 August 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae",2|201174|1760|2037|2049|1654;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|1898203;2|1224|28211|204441|41295,Complete,Atrayees
bsdb:524/1/2,Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis),"Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis); The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation",76,40,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,11 August 2021,Madhubani Dey,"Madhubani Dey,Merit",Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|200940|3031449|213115|194924|872;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|2485925;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1224|28216|80840|995019|577310;2|1239|186801|3082720|3120161|1481960;2|976|200643|171549|171551;2|1239|186801|3082720|186804|1505652;2|976|200643|171549|1853231,Complete,Atrayees
bsdb:524/2/1,Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,"Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis; The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation; Fibrosis was scored following the CRN grading system54 by a single pathologist.",76,25,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,11 August 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|201174|1760|2037|2049|1654;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506553,Complete,Atrayees
bsdb:524/2/2,Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,"Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis; The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation; Fibrosis was scored following the CRN grading system54 by a single pathologist.",76,25,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,11 August 2021,Madhubani Dey,"Madhubani Dey,Merit",Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|1239|186801|3082720|3120161|1481960;2|1239|186801|186802|216572|1508657|2053608;2|1239|186801|3082720|186804|1505652;2|976|200643|171549|171551;2|976|200643|171549|1853231,Complete,Atrayees
bsdb:525/1/1,Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,"16S rRNA, Chronic pelvic pain (CPP), endometriosis/adenomyosis (EM/AM), function prediction, vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Atrayees",The following taxa were found to be decreased in women with endometriosis associated CPPS.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:525/2/1,Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,"16S rRNA, Chronic pelvic pain (CPP), endometriosis/adenomyosis (EM/AM), function prediction, vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Atrayees",The following taxa were increased in women with endometriosis associated CPPS pain,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85004|31953|419014;2|1224|1236|135614|32033|40323;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:525/2/2,Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,"16S rRNA, Chronic pelvic pain (CPP), endometriosis/adenomyosis (EM/AM), function prediction, vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Atrayees",The following taxa were decreased in women with endometriosis associated CPPS pain,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|177971;2|32066|203490|203491|1129771|168808,Complete,Atrayees
bsdb:525/3/1,Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,"16S rRNA, Chronic pelvic pain (CPP), endometriosis/adenomyosis (EM/AM), function prediction, vaginal microbiome",Experiment 3,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,Metastats,NA,TRUE,NA,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,17 July 2023,Atrayees,Atrayees,The following taxa were increased in women with endometriosis associated CPPS pain,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,2|201174|1760|85004|31953|419014,Complete,Atrayees
bsdb:526/1/1,Study 526,case-control,33313185,10.21037/atm-20-1309,NA,"Chen S, Gu Z, Zhang W, Jia S, Wu Y, Zheng P, Dai Y , Leng J",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,"16s-rRNA sequencing, Endometriosis, bioinformatic analysis, microbiome",Experiment 1,China,Homo sapiens,Cervical cavity,UBERON:0013761,"Adenomyosis,Endometriosis","EFO:0001065,EFO:1001757",Endometriosis patients (EM) and Patients without endometriosis(Control-CT),Endometriosis/ adenomyosis patients (AMEM),All participants were diagnosed with adenomyosis accompanied with endometriosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,92,14,No antibiotic use within 30 days,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"within results text(under ""Microbiota composition of different diseases"" ,paragraph 5, lines 4-7), figure 6",11 August 2021,Samara.Khan,"Samara.Khan,Folakunmi","The following taxa were increased in patients with endometriosis and adenomyosis compared to those with just endometriosis, as well as those without endometriosis (control).",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|201174|84998|84999|1643824|1380;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|201174|84998|84999|84107;2|1224|1236|91347|543|1940338;2|1239|1737404|1582879;2|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:526/2/1,Study 526,case-control,33313185,10.21037/atm-20-1309,NA,"Chen S, Gu Z, Zhang W, Jia S, Wu Y, Zheng P, Dai Y , Leng J",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,"16s-rRNA sequencing, Endometriosis, bioinformatic analysis, microbiome",Experiment 2,China,Homo sapiens,Cervical cavity,UBERON:0013761,"Adenomyosis,Endometriosis","EFO:0001065,EFO:1001757","Patients without endometriosis (CT), patients with only endometriosis(EM)) and patients with only adenomysis(AM)",Endometriosis/ adenomyosis patients (AMEM),All participants were diagnosed with adenomyosis accompanied with endometriosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,120,14,No antibiotic use within 30 days,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"within results text(under ""Microbiota composition of different diseases"" ,paragraph 5, lines 4-7), figure 6",11 August 2021,Samara.Khan,"Samara.Khan,Folakunmi","The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those without endometriosis, patients with only endometriosis and patients with only adenomysis.",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|29547|3031852|213849|72294;2|201174|84998|84999|84107,Complete,Folakunmi
bsdb:526/3/1,Study 526,case-control,33313185,10.21037/atm-20-1309,NA,"Chen S, Gu Z, Zhang W, Jia S, Wu Y, Zheng P, Dai Y , Leng J",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,"16s-rRNA sequencing, Endometriosis, bioinformatic analysis, microbiome",Experiment 3,China,Homo sapiens,Cervical cavity,UBERON:0013761,"Adenomyosis,Endometriosis","EFO:0001065,EFO:1001757",Adenomysis patients,Endometriosis/ adenomyosis patients (AMEM),All participants were diagnosed with endometriosis and/or adenomyosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,28,14,No antibiotic use within 30 days,16S,34,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"within results text (under ""Microbiota composition of different diseases"" ,paragraph 5, lines 4-7), figure 6",15 November 2023,Folakunmi,Folakunmi,The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those with only adenomyosis.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|201174|84998|84999|1643824|1380;2|29547|3031852|213849|72294|194;2|1239|1737404|1582879;2|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:527/1/1,Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,Folakunmi",The following taxa were decreased among those with endometriosis compared to healthy controls.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|84998|1643822|1643826|447020;2|976|200643|171549;2|976|200643|171549|2005519;2|201174|84998|84999|84107;2|1239|186801|53433|972;2|1239|186801|3085636|186803|28050;2|976|200643|171549|171552|577309;2|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:527/1/2,Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",The following taxa were increased among those with endometriosis compared to healthy controls after a false-discovery rate adjustment,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572|119852;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|1224|1236|91347|543;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:527/2/1,Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,6 months,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",Differential microbial abundance between endometriosis patients and healthy controls after a sensitivity analysis and adjustment for false-discovery rate.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,2|976|200643|171549,Complete,Claregrieve1
bsdb:527/2/2,Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,6 months,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1",Differential microbial abundance between endometriosis patients and healthy controls after a sensitivity analysis and adjustment for false-discovery rate.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:528/1/NA,Study 528,laboratory experiment,31887116,10.1371/journal.pone.0226835,NA,"Hantschel J, Weis S, Schäfer KH, Menger MD, Kohl M, Egert M , Laschke MW",Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation,PloS one,2019,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Sham(Healthy controls),Endometriosis mice,Mice for whom endometrial tissue was transplanted into the peritoneal cavity to simulate endometriosis. The sample was taken 3 days before the transplantation of uterine tissue fragments,6,8,None were given prior to the start of the experiment,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:528/2/NA,Study 528,laboratory experiment,31887116,10.1371/journal.pone.0226835,NA,"Hantschel J, Weis S, Schäfer KH, Menger MD, Kohl M, Egert M , Laschke MW",Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation,PloS one,2019,NA,Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Sham(Healthy controls),Endometriosis mice,Mice for whom endometrial tissue was transplanted into the peritoneal cavity to simulate endometriosis. The sample was taken 7 days after the induction of endometriosis (after EI).,8,8,None were given prior to the start of the experiment,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:528/3/NA,Study 528,laboratory experiment,31887116,10.1371/journal.pone.0226835,NA,"Hantschel J, Weis S, Schäfer KH, Menger MD, Kohl M, Egert M , Laschke MW",Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation,PloS one,2019,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Sham(Healthy controls),Endometriosis mice,Mice for whom endometrial tissue was transplanted into the peritoneal cavity to simulate endometriosis. The sample was taken 21 days after the induction of endometriosis (after EI).,7,5,None were given prior to the start of the experiment,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:529/1/1,Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,"Rheumatoid arthritis,Osteoarthritis","EFO:0000685,MONDO:0005178",healthy controls,arthritis patient,arthritis,155,177,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 2, text",16 August 2021,Tislam,Tislam,"(c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|32066|203490|203491|203492|848;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|186828|117563;2|201174|1760|2037|2049|1654;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|28132;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,Chloe
bsdb:529/1/2,Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,"Rheumatoid arthritis,Osteoarthritis","EFO:0000685,MONDO:0005178",healthy controls,arthritis patient,arthritis,155,177,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 2, text",16 August 2021,Tislam,Tislam,"(c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana",2|1224|1236|2887326|468|469;2|976|117743|200644|2762318|59732;2|1224|1236|72274|135621|286;2|1224|28211|356|212791;2|1224|1236|135614|32033|40323;2|1224|28211|204457|41297|13687;2|976|117743|200644|2762318|343873;2|1224|28211|204458|76892|41275|293;2|976|200643|171549|815|816;2|1224|28216|80840|80864|283;2|1224|28211|204457|41297|13687|172044;2|1224|28211|356|82115|13159,Complete,Chloe
bsdb:529/2/1,Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,"Rheumatoid arthritis,Osteoarthritis","EFO:0000685,MONDO:0005178",Osteoarthritis,rheumatoid arthritis,patient with rheumatoid arthritis,67,110,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",17 August 2021,Tislam,Tislam,"c) Histogram of the LDA scores, where
the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1224|1236|135625|712|724|735;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313|76122;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465|39778;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482|28449;2|1224|28216|206351|481|482,Complete,Chloe
bsdb:529/2/2,Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,"Rheumatoid arthritis,Osteoarthritis","EFO:0000685,MONDO:0005178",Osteoarthritis,rheumatoid arthritis,patient with rheumatoid arthritis,67,110,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,17 August 2021,Tislam,Tislam,"(c) Histogram of the LDA scores, where the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654;2|1224|28216|80840|119060|47670;2|201174|1760|85006|1268|32207;2|1239|91061|186826|186828|117563;2|201174|1760|85006|1268|32207|2047;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|2316020|33038;2|1239|91061|186826|186827|46123,Complete,Chloe
bsdb:530/1/1,Study 530,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y, Zheng W, Cai QY, Shrubsole MJ, Pei Z, Brucker R, Steinwandel MD, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,592,Participants who took antibiotics within a year before sample collection.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2,3,and 4",14 March 2023,Nnadichioma,"Nnadichioma,Atrayees,Aiyshaaaa,Merit",Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|216816;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|201174|84998|84999|1643824|2767353|1382;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|1632;2|1239|91061|186826|33958|2742598|47493;2|1239|91061|186826|33958|2742598|1598;2|201174;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|55565;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|2529408|1660;2|201174|84998|84999|84107;2|201174|1760|85006|1268|32207|43675;2|201174|84998|84999|1643824|1380;2|976|200643|171549|171552|838|652722;2|1239|91061|186826|1300|1301|712621;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906|187326;2|201174|1760|2037|2049|1654|114702;2|1239|91061|186826|33958;2|203691|203692|136|2845253|157|158,Complete,Atrayees
bsdb:530/1/2,Study 530,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y, Zheng W, Cai QY, Shrubsole MJ, Pei Z, Brucker R, Steinwandel MD, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,592,Participants who took antibiotics within a year before sample collection.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and 4,14 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Atrayees",Individual taxa showing a differential relative abundance between current-smokers and never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",2|1224|28216|80840|119060;2|1224|1236|135615|868|2717;2|1239|91061|186826|81852|1350;2|1224|28216|206351|481|32257;2|1224|28216|206351|481|32257|502;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|1107316;2|1224|28216|206351|481;2|976|200643|171549|171552|2974257|425941;2|976|117743|200644|49546|1016|1019;2|1239|186801|3085636|186803;2|1239|186801|186802|543314|56774;2|1239|186801|3085636|186803|1164882|617123;2|1224;2|1224|28216|206351|481|482|29434;2|1224|28216|206351|481|482|28449;2|1224|1236|135625|712;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|735;2|1224|1236|135625|712|724|736;2|976|117743|200644|49546;2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1301|45634,Complete,Atrayees
bsdb:530/2/1,Study 530,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y, Zheng W, Cai QY, Shrubsole MJ, Pei Z, Brucker R, Steinwandel MD, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Former-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,477,Participants who took antibiotics within a year before sample collection.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2,3,and 4",28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Merit,Atrayees",Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|216816;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|1632;2|1239|91061|186826|33958|2742598|47493;2|1239|91061|186826|33958|2742598|1598;2|1239|91061|186826|1300|1301|712621;2|201174|1760|2037|2049;2|201174;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1224|1236|135625|712|724|735;2|1239|91061|186826|1300|1301|45634;2|201174|1760|2037|2049|1654|114702;2|201174|1760|85004|31953,Complete,Atrayees
bsdb:530/2/2,Study 530,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y, Zheng W, Cai QY, Shrubsole MJ, Pei Z, Brucker R, Steinwandel MD, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Former-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,477,Participants who took antibiotics within a year before sample collection.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, 3 and 4",28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Atrayees",Individual taxa showing a differential relative abundance between current-smokers and never-smokers,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 070,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",2|976|117743|200644|49546|1016|1019;2|1224|1236|135615|868|2717;2|1239|91061|186826|81852|1350;2|1224|28216|206351|481|32257|502;2|1239|186801|3085636|186803|1164882|617123;2|1239|186801|3085636|186803;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482|1107316;2|1239|91061|186826|1300|1301|671226;2|203691|203692|136|2845253|157|158;2|1239|186801|186802|543314|56774;2|1224|28216|80840|119060;2|1224|28216|206351|481|32257;2|976|200643|171549|171552|838;2|1239|91061|186826|81850;2|201174|1760|2037|2049|1654|55565;2|201174|84998|84999|84107;2|201174|84998|84999|1643824|1380;2|201174|84998|84999|1643824|2767353|1382;2|1224|1236|135625|712|724;2|1224|1236|135625|712|416916;2|1224;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351|481|482|29434;2|1224|28216|206351|481|482|28449;2|1224|1236|135625|712;2|1224|1236|135625|712|724|736;2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1301|45634,Complete,Atrayees
bsdb:530/3/1,Study 530,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y, Zheng W, Cai QY, Shrubsole MJ, Pei Z, Brucker R, Steinwandel MD, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Former-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",477,592,Participants who took antibiotics within a year before sample collection.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, 3, and 4",28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Atrayees",Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 070,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|55565;2|201174|1760|2037|2049|1654|114702;2|201174;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678|216816;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|201174|84998|84999|1643824|2767353|1382;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|1632;2|1239|91061|186826|33958|2742598|47493;2|1239|91061|186826|33958|2742598|1598;2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171552|838|652722;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|712621;2|1239|91061|186826|1300|1301|671226;2|203691|203692|136|2845253|157|158;2|1239|91061|186826|33958;2|201174|1760|85004|31953|1678;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:530/3/2,Study 530,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y, Zheng W, Cai QY, Shrubsole MJ, Pei Z, Brucker R, Steinwandel MD, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Former-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",477,592,Participants who took antibiotics within a year before sample collection.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and 4,28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Merit,Atrayees",Individual taxa showing a differential relative abundance between current-smokers and never-smokers,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis|s__Neisseria pharyngis subsp. flava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|1224|1236|135625|712|416916;2|976|117743|200644|49546|1016|1019;2|1239|91061|186826|81852|1350;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724|735;2|1224|1236|135625|712|724|736;2|1224|28216|206351|481|32257|502;2|1239|186801|3085636|186803|1164882|617123;2|1239|186801|3085636|186803;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|495;2|1224|28216|206351|481|482|1107316;2|1224|28216|206351|481|482|29434;2|1224|28216|206351|481|482|29434|47658;2|976|200643|171549|171552|2974257|425941;2|1224;2|1239|91061|186826|1300|1301|45634;2|1239|186801|186802|543314|56774;2|1224|28216|206351|481;2|1224|1236|135625|712|724;2|1224|1236|135625|712;2|976|117743|200644|49546;2|1224|28216|80840|119060;2|1224|28216|206351|481|32257;2|1224|1236|135615|868|2717,Complete,Atrayees
bsdb:531/1/1,Study 531,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y, Zheng L, Qing P, Zhao H, Li Y, Su L, Zhang Q, Zhao Y, Luo Y , Liu Y",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA,
anti-citrullinated protein antibodies;",23,29,Individuals having a history of antibiotics treatment or surgery in the last 3 months were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3B, text",16 August 2021,Tislam,"Tislam,Atrayees,Peace Sandy","FIGURE 3  LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1239|91061|1385;2|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:531/1/2,Study 531,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y, Zheng L, Qing P, Zhao H, Li Y, Su L, Zhang Q, Zhao Y, Luo Y , Liu Y",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA,
anti-citrullinated protein antibodies;",23,29,Individuals having a history of antibiotics treatment or surgery in the last 3 months were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",17 August 2021,Tislam,"Tislam,Peace Sandy","FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia",2|1239|186801|3082720|3118655|44259;2|1224|1236;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1224|1236|72274;2|1224;2|203691|203692|136|137|146;2|203691|203692|136|137;2|203691|203692|136;2|203691|203692,Complete,Peace Sandy
bsdb:531/2/1,Study 531,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y, Zheng L, Qing P, Zhao H, Li Y, Su L, Zhang Q, Zhao Y, Luo Y , Liu Y",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid Arthritis,Patients with Rheumatoid Arthritis,23,27,Individuals having a history of antibiotics treatment or surgery in the last 3 months were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,increased,NA,NA,NA,decreased,Signature 1,"Figure 3, text",21 January 2024,Peace Sandy,Peace Sandy,"FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",2|1239;2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489|31977;2|201174;2|201174|1760|2037;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|95818|2093818|2093825;2|203691|203692|136|2845253|157;2|1239|909932|909929|1843491|970;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|906;2|201174|84998|84999;2|201174|84998|84999|1643824;2|201174|84998|84999|1643824|1380,Complete,Peace Sandy
bsdb:531/2/2,Study 531,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y, Zheng L, Qing P, Zhao H, Li Y, Su L, Zhang Q, Zhao Y, Luo Y , Liu Y",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid Arthritis,Patients with Rheumatoid Arthritis,23,27,Individuals having a history of antibiotics treatment or surgery in the last 3 months were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,increased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",21 January 2024,Peace Sandy,Peace Sandy,"FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta",2|1239|186801|3082720|3118655|44259;2|1224|1236;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1224|1236|72274;2|1224;2|203691|203692|136|137;2|203691|203692|136;2|203691|203692;2|203691|203692|136|137|146,Complete,Peace Sandy
bsdb:531/3/1,Study 531,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y, Zheng L, Qing P, Zhao H, Li Y, Su L, Zhang Q, Zhao Y, Luo Y , Liu Y",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA, anti-citrullinated protein antibodies;",27,29,Individuals having a history of antibiotics treatment or surgery in the last 3 months were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3, text",21 January 2024,Peace Sandy,Peace Sandy,"FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1239|91061|1385;2|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:531/3/2,Study 531,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y, Zheng L, Qing P, Zhao H, Li Y, Su L, Zhang Q, Zhao Y, Luo Y , Liu Y",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA, anti-citrullinated protein antibodies;",27,29,Individuals having a history of antibiotics treatment or surgery in the last 3 months were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",21 January 2024,Peace Sandy,Peace Sandy,"FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|201174|84998|84999|1643824;2|1239;2|95818|2093818|2093825;2|201174|84998|84999;2|1239|909932|1843489|31977|906;2|1239|909932;2;2|976|200643|171549|171552|838;2|1239|909932|909929;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977;2|201174|84998|84999|1643824|1380,Complete,Peace Sandy
bsdb:532/1/1,Study 532,case-control,27102666,10.1186/s13073-016-0299-7,NA,"Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV, Murray J, Nelson H, Matteson EL , Taneja V",An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis,Genome medicine,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients,32,40,"Any patient or control on antibiotics, consuming probiotics, or having a known history of inflammatory bowel disease or other autoimmune diseases like diabetes and multiple sclerosis were excluded.",16S,345,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3, text",16 August 2021,Tislam,"Tislam,Rimsha,Claregrieve1,Merit",Differential microbial abundance between healthy controls and RA patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Actinomycetota",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|1239|91061;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|1903409|551;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|201174,Complete,Claregrieve1
bsdb:532/1/2,Study 532,case-control,27102666,10.1186/s13073-016-0299-7,NA,"Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV, Murray J, Nelson H, Matteson EL , Taneja V",An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis,Genome medicine,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients,32,40,"Any patient or control on antibiotics, consuming probiotics, or having a known history of inflammatory bowel disease or other autoimmune diseases like diabetes and multiple sclerosis were excluded.",16S,345,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",16 August 2021,Tislam,"Tislam,Rimsha,Claregrieve1,Merit",Differential microbial abundance between healthy controls and RA patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",2|976|200643|171549|2005519;2|203691|203692|136|1643685;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|1971605,Complete,Claregrieve1
bsdb:533/1/1,Study 533,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S, Palmas V, Melis M, Pisanu S, Cusano R, Uva P, Perra D, Madau V, Sarchioto M, Oppo V, Simola N, Morelli M, Santoru ML, Atzori L, Melis M, Cossu G , Manzin A",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 2a,2 April 2023,Atrayees,Atrayees,significantly differential taxa between patients with Parkinson's disease and Healthy controls.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfonauticaceae|g__Desulfonauticus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|o__Caldicellulosiruptorales|f__Caldicellulosiruptoraceae|g__Caldicellulosiruptor,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae",2|74201|203494;2|74201|203494|48461|203557;2|74201|203494|48461|1647988|239934;2|1224;2|1224|1236|91347|543|561;2|201174;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|31979|1485;2|1224|1236|91347|1903411|613;2|200940|3031449|213115|2956789|206664;2|200940|3031449|213115|213117;2|201174|1760|85006|85023;2|201174|84998|84999|84107;2|1224|1236|91347|543|547;2|201174|84998|1643822|1643826|84108;2|74201|203494|48461|203557|48463;2|1239|186801|186802|186806;2|1239|186801|186802|186806|33951;2|1239|186801|3085636|186803|207244;2|200940|3031449|213115|194924|872;2|1239|3071001|3071002|44000;2759|4751|5204|155619|139380|1124673,Complete,Claregrieve1
bsdb:533/1/2,Study 533,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S, Palmas V, Melis M, Pisanu S, Cusano R, Uva P, Perra D, Madau V, Sarchioto M, Oppo V, Simola N, Morelli M, Santoru ML, Atzori L, Melis M, Cossu G , Manzin A",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 2b,2 April 2023,Atrayees,Atrayees,significantly differential taxa between patients with Parkinson's disease and Healthy controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Aphanizomenonaceae|g__Dolichospermum,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Candidatus Blochmanniella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|1224|28216|80840|80864;2|201174|1760|85006|85019;2|1239|186801|3085636|186803|830;2|201174|1760|85006|85019|1696;2|976|200643|171549|1853231|283168;2|1239|186801|3085636|186803|46205;2|1117;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|33042;2|1117|3028117|1161|1892259|748770;2|976|117747|200666|84566;2|1224|28216|80840|995019|40544;2|1224|28216|80840|506;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|841;2|1224|1236|91347|543|570;2|1224|1236|91347|543|203804;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803;2|976|200643|171549|815|816;2|976|200643|171549|815;2|976|200643,Complete,Claregrieve1
bsdb:533/2/1,Study 533,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S, Palmas V, Melis M, Pisanu S, Cusano R, Uva P, Perra D, Madau V, Sarchioto M, Oppo V, Simola N, Morelli M, Santoru ML, Atzori L, Melis M, Cossu G , Manzin A",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,30 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between HCs and PD patients,increased,"k__Bacteria|p__Bacillota|o__Caldicellulosiruptorales|f__Caldicellulosiruptoraceae|g__Caldicellulosiruptor,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|1239|3071001|3071002|44000;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|31979|1485|1506;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186806;2|1239|186801|186802|186806|33951;2|1239|186801|3085636|186803|207244,Complete,Claregrieve1
bsdb:533/2/2,Study 533,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S, Palmas V, Melis M, Pisanu S, Cusano R, Uva P, Perra D, Madau V, Sarchioto M, Oppo V, Simola N, Morelli M, Santoru ML, Atzori L, Melis M, Cossu G , Manzin A",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2,30 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between HCs and PD patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|830;2|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:534/1/1,Study 534,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, Holscher HD , Woods JA",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI > 30 (classified as obese),18,14,3 months,16S,4,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2d,29 December 2022,Claregrieve1,Claregrieve1,Differential abundance between obese and lean participants after the 6 week exercise program,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|976|200643|171549|815|816;2|201174|84998|84999|84107|102106,Complete,Claregrieve1
bsdb:534/1/2,Study 534,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, Holscher HD , Woods JA",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI > 30 (classified as obese),18,14,3 months,16S,4,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2d,29 December 2022,Claregrieve1,Claregrieve1,Differential abundance between obese and lean participants after the 6 week exercise program,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:534/2/1,Study 534,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, Holscher HD , Woods JA",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI >30 (classified as obese),18,14,3 months,16S,NA,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2d,29 December 2022,Claregrieve1,"Claregrieve1,Lwaldron",Differential abundance between obese and lean participants after the 6 week sedentary washout post-exercise program,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|1239|186801|3085636|186803|189330;2|201174|84998|84999|84107|102106,Complete,Claregrieve1
bsdb:534/2/2,Study 534,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, Holscher HD , Woods JA",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI >30 (classified as obese),18,14,3 months,16S,NA,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2e,16 March 2023,Lwaldron,Lwaldron,Differential abundance between obese and lean participants after the 6 week sedentary washout post-exercise program,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050,Complete,NA
bsdb:535/1/1,Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects receiving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure S2, Table S4",10 September 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between antibiotic-treated and -untreated elderly subjects,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|201174|1760|85004|31953|1678|41200;2|1239|909932|1843488|909930|904;2|1239|186801|3085636|186803|830;2|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:535/1/2,Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects receiving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table S4,16 September 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between antibiotic-treated and -untreated elderly subjects,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|31979|420345;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2759|4751|4890|147545|5042|1131492|5073;2|1224|1236|91347|1903414|583,Complete,Claregrieve1
bsdb:535/2/1,Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated subjects in day hospital,Antibiotic treated subjects in day hospital,subjects who were antibiotic-treated in a day hospital,33,7,NA,16S,4,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Chi-Square",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1",comparison of microbiota between antibiotic-treated and untreated groups in day hospital facility,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1239|91061|186826|33958|1578;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|437755;2|1239|1737404|1737405|1570339|162289;2|256845|1313211|278082|255528|172900;2|1239|91061|186826|33958|46255,Complete,Claregrieve1
bsdb:535/2/2,Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated subjects in day hospital,Antibiotic treated subjects in day hospital,subjects who were antibiotic-treated in a day hospital,33,7,NA,16S,4,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Chi-Square",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1",comparison of microbiota between antibiotic-treated and untreated groups in day hospital facility,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:535/3/1,Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated community dwelling subjects,Antibiotic treated community dwelling subjects,community-dwelling subjects treated with antibiotics within 1 month of study,64,9,NA,16S,4,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Chi-Square",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1",comparison of microbiota between antibiotic-treated and untreated community-dwelling subjects,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|1239;2|1224,Complete,Claregrieve1
bsdb:535/3/2,Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated community dwelling subjects,Antibiotic treated community dwelling subjects,community-dwelling subjects treated with antibiotics within 1 month of study,64,9,NA,16S,4,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Chi-Square",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1",comparison of microbiota between antibiotic-treated and untreated community-dwelling subjects,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|1239;2|1224,Complete,Claregrieve1
bsdb:535/4/1,Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 4,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated subjects in long stay facility,Antibiotic treated subjects in long stay facility,subjects in long stay facility who have had antibiotic treatment in the past month,32,16,NA,16S,4,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Chi-Square",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1",comparison of microbiota between antibiotic-treated and untreated subjects in long stay facility,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:536/1/1,Study 536,randomized controlled trial,30478001,10.1016/j.ebiom.2018.11.035,NA,"Wei S, Mortensen MS, Stokholm J, Brejnrod AD, Thorsen J, Rasmussen MA, Trivedi U, Bisgaard H , Sørensen SJ","Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial",EBioMedicine,2018,"Antibiotics, Asthma, Azithromycin, Children, Gut microbiota, RCT",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Azithromycin,CHEBI:2955,The group given a placebo,The group given an azithromycin oral solution,"1-3-year-olds diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Exclusion criteria included macrolide allergy, heart, liver, neurological, kidney disease, and or one or more clinical signs of pneumonia. Participants were prescribed a 3-day course of oral azithromycin solution of 10mg/kg per day.",33,39,none mentioned,16S,4,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary table 2,24 September 2021,Gina,Gina,Short term effects: the relative abundance of significant taxa between groups at different phylogenetic levels.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.",2|201174;2|201174|1760|85004;2|1239;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|165187,Complete,NA
bsdb:536/1/2,Study 536,randomized controlled trial,30478001,10.1016/j.ebiom.2018.11.035,NA,"Wei S, Mortensen MS, Stokholm J, Brejnrod AD, Thorsen J, Rasmussen MA, Trivedi U, Bisgaard H , Sørensen SJ","Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial",EBioMedicine,2018,"Antibiotics, Asthma, Azithromycin, Children, Gut microbiota, RCT",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Azithromycin,CHEBI:2955,The group given a placebo,The group given an azithromycin oral solution,"1-3-year-olds diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Exclusion criteria included macrolide allergy, heart, liver, neurological, kidney disease, and or one or more clinical signs of pneumonia. Participants were prescribed a 3-day course of oral azithromycin solution of 10mg/kg per day.",33,39,none mentioned,16S,4,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary table 2,24 September 2021,Gina,Gina,Short term effect: the relative abundance of significant taxa between groups at different phylogenetic levels.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",2|1239|186801|3085636|186803;2|1239|186801|186802|216572|946234,Complete,NA
bsdb:537/1/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with idiopathic parkinson's disease,Patients with idiopathic parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,1 month,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,"Supplementary table 3, Signature 1 is for increased abundance in those with Parkinson's",19 September 2021,Fcuevas3,"Fcuevas3,Fatima,Atrayees",Analysis of relative taxa abundance in controls and different disease groups.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pyronemataceae|g__Paurocotylis|s__Paurocotylis pila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3082768|424536;2|1224|1236|91347|543;2|1224;2|74201|203494|48461|203557;2|1239;2759|4751|4890|147549|5185|110846|47200|47201;2|976|200643|171549|171551;2|1224|1236|91347|543|561,Complete,Atrayees
bsdb:537/1/2,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with idiopathic parkinson's disease,Patients with idiopathic parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,1 month,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,"Supplementary table 3,",28 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in controls and different disease groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572;2|1239;2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:537/2/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,the trend over Parkinson's disease progression,Patients with idiopathic Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,breast feeding,constipation,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance in different groups of Parkinson's disease patients.",20 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|74201;2|74201|203494|48461|203557,Complete,Atrayees
bsdb:537/2/2,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,the trend over Parkinson's disease progression,Patients with idiopathic Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,breast feeding,constipation,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance in different groups of Parkinson's disease patients.",28 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:537/3/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with MSA(multiple system atrophy) disease,Patients diagnosed with synucleinopathy multiple system atrophy (MSA),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,Supplementary table 3,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in controls and different disease groups.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Eukaryota|k__Metazoa|p__Chordata|c__Actinopteri|o__Cichliformes|f__Cichlidae|s__Astronotinae|g__Chaetobranchopsis,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|74201|203494|48461|1647988|239934;2|1239|91061|186826|33958;2|74201;2|74201|203494|48461|203557;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|186801|3082768|990719;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2759|33208|7711|186623|1489911|8113|318552|74107;2|201174;2|201174|84998|84999|84107,Complete,Atrayees
bsdb:537/3/2,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with MSA(multiple system atrophy) disease,Patients diagnosed with synucleinopathy multiple system atrophy (MSA),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,Supplementary table 3,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in controls and different disease groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572|216851;2|976|200643|171549|171552;2|1239;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:537/4/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with PSP(progressive supranuclear palsy) disease,Patients diagnosed with tauopathy progressive supranuclear palsy (PSP),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,"Supplementary table 3, Signature 1 is for increased abundance in those with PSP",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in controls and different disease groups,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|74201|203494|48461|1647988|239934;2|1239|186801|3082768|424536;2|1239|186801|186802|216572|119852;2|74201;2|74201|203494|48461|203557;2|1224;2|1224|1236|91347|543,Complete,Atrayees
bsdb:537/4/2,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with PSP(progressive supranuclear palsy) disease,Patients diagnosed with tauopathy progressive supranuclear palsy (PSP),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,Supplementary table 3,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in controls and different disease groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:537/5/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 5,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with De-novo Parkinson's disease,Patients with de novo Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,39,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary table 4,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:537/6/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 6,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's disease,patients with early Parkinson's disease,Patients with early Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,57,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance among patients with early Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|74201|203494|48461|1647988|239934;2|1239|186801|3082768|424536;2|1224|1236|91347|543;2|74201;2|74201|203494|48461|203557;2|1224;2|1239|186801|186802|216572|119852,Complete,Atrayees
bsdb:537/6/2,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 6,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's disease,patients with early Parkinson's disease,Patients with early Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,57,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance among participants with early Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3085636|186803;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:537/7/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 7,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with mid stage Parkinson's,Patients with mid stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,53,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary table 4,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|74201|203494|48461|1647988|239934;2|1239|186801|3082768|424536;2|1224|1236|91347|543;2|1224;2|74201;2|74201|203494|48461|203557;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|976|200643|171549|171551;2|976|200643|171549|2005525|375288,Complete,Atrayees
bsdb:537/7/2,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 7,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with mid stage Parkinson's,Patients with mid stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,53,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary table 4,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803;2|1239;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572;2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:537/8/1,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 8,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with advanced stage Parkinson's,Patients with advanced stage Parkinson&#039;s disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,44,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance among those with advanced Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543;2|1224;2|74201;2|74201|203494|48461|203557;2|1224|1236|91347|543|561;2|1239|91061|186826|1300;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|186801|3082768|990719;2|976|200643|171549|2005525|375288;2|201174;2|201174|1760|85004|31953|1678;2|976|200643|171549|171551;2|201174|1760|85004|31953;2|201174|84998|84999|84107,Complete,Atrayees
bsdb:537/8/2,Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 8,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with advanced stage Parkinson's,Patients with advanced stage Parkinson&#039;s disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,44,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance among those with advanced Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:538/1/1,Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,baseline of the ciprofloxacin treated,ciprofloxacin treated,UTI patients treated with ciprofloxacin 500mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between baseline (timepoint 1) and timepoint 2 in ciprofloxacin treated patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|201174|1760|85004|31953;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:538/1/2,Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,baseline of the ciprofloxacin treated,ciprofloxacin treated,UTI patients treated with ciprofloxacin 500mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between baseline (timepoint 1) and timepoint 2 in ciprofloxacin treated patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:538/2/1,Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Baseline of the Nitrofurantoin treated,Nitrofurantoin treated,UTI patients treated with nitrofurantoin macrocrystals 100mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between baseline and post-treatment timepoints in nitrofurantoin treated group,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:538/2/2,Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Baseline of the Nitrofurantoin treated,Nitrofurantoin treated,UTI patients treated with nitrofurantoin macrocrystals 100mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between baseline and post-treatment timepoints in nitrofurantoin treated group,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:538/6/1,Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 6,Switzerland,Homo sapiens,Feces,UBERON:0001988,"Antimicrobial agent,Urinary tract infection","EFO:0003103,CHEBI:33281",control group (timepoint 2),Ciprofloxacin treated group (timepoint 2),ciprofloxacin group at end of antibiotic treatment,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S2,15 October 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between the control group and ciprofloxacin-treated group at timepoint 2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:538/7/1,Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 7,Switzerland,Homo sapiens,Feces,UBERON:0001988,"Antimicrobial agent,Urinary tract infection","CHEBI:33281,EFO:0003103",controls (timepoint 2),nitrofurantoin treated group (timepoint 2),nitrofurantoin-treated group at end of treatment,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S2,15 October 2021,Mmarin,"Mmarin,Claregrieve1",Differential microbial abundance between the control group and nitrofurantoin-treated group at timepoint 2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|171550|239759;2|976|200643|171549;2|976|200643;2|976;2|1239|186801|186802|216572|216851;2|976|200643|171549|171550,Complete,Claregrieve1
bsdb:539/1/1,Study 539,case-control,32381601,10.1681/ASN.2019101131,https://jasn.asnjournals.org/content/31/6/1358.abstract,"Denburg MR, Koepsell K, Lee JJ, Gerber J, Bittinger K , Tasian GE",Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease,Journal of the American Society of Nephrology : JASN,2020,"intestine, kidney stones, metabolism, pediatric nephrology",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Nephrolithiasis,EFO:0004253,Healthy Controls,Patients with kidney stones,The patients suffering from Kidney Stones (nephrolithiasis) are individuals with incident and recurrent kidney stones consisting of 100% calcium (of which at least 50% was calcium oxalate) that spontaneously passed or were removed surgically within the prior 3 years.,44,44,3 months,WMS,NA,Illumina,T-Test,0.05,TRUE,NA,"age,race,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,figure 1,26 March 2023,Blessing Kaz,"Blessing Kaz,Aiyshaaaa,Atrayees",The relative abundance of bacterial taxa among participants with kidney stone disease.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Nitratidesulfovibrio|s__Nitratidesulfovibrio vulgaris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pyogenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia heliotrinireducens,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis",2|1239|186801|3085636|186803|841|301301;2|1239|526524|526525|128827|1573534|39483;2|1239|186801|3082720|186804|1870884|1496;2|1239;2|1239|186801|186802;2|1239|186801|186802|216572|459786|351091;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|1263|1161942;2|1239|91061|186826|81852|1350|1352;2|1239|186801|186802|216572|253238|253239;2|1239|186801|186802|186806|1730|1736;2|1239|186801|186802|216572|1263|1264;2|1239|186801|3085636|186803|830|43305;2|1239|91061|186826|1300|1301|1307;2|203691|203692|136|2845253|157|167;2|1239|186801|186802|216572|1637257|884684;2|200940|3031449|213115|194924|2802295|881;2|1239|91061|186826|1300|1301|1314;2|1239|186801|186802|31979|1485|1491;2|200940|3031449|213115|194924|872|876;2|201174|84998|1643822|1643826|84108|84110;2|29547|3031852|213849|72294|194|197;2|1239|91061|186826|81852|1350|1351;2|29547|3031852|213849|72294|194|195;2|1239|186801|186802|31979|1485|1502;2|201174|1760|85004|31953|1678|28025,Complete,Atrayees
bsdb:540/1/1,Study 540,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W, Hajjo R, Abu-Siniyeh A , Hajjaj S",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 1,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoking subjects who smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table 3, 4",3 April 2023,Khadeeejah,"Khadeeejah,Atrayees,Claregrieve1",Differential microbial abundance between non-smokers versus smokers (regardless of gender).,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239;2|32066|203490;2|976|200643|171549|171552|838;2|1224;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:540/1/2,Study 540,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W, Hajjo R, Abu-Siniyeh A , Hajjaj S",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 1,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoking subjects who smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Table 3, 4",3 April 2023,Khadeeejah,"Khadeeejah,Atrayees,Claregrieve1",Differential microbial abundance between non-smokers versus smokers (regardless of gender).,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,2|1224|28216|206351|481|482,Complete,Claregrieve1
bsdb:540/2/1,Study 540,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W, Hajjo R, Abu-Siniyeh A , Hajjaj S",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 2,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoker subjects smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 7, Table 5",30 May 2023,Atrayees,"Atrayees,Claregrieve1",Differential microbial abundance between non-smokers versus smokers by LefSe,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes)",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|91061|1385|186817|1386|1409,Complete,Claregrieve1
bsdb:540/2/2,Study 540,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W, Hajjo R, Abu-Siniyeh A , Hajjaj S",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 2,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoker subjects smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 7, Table 5",30 May 2023,Atrayees,"Atrayees,Claregrieve1",Differential microbial abundance between non-smokers versus smokers by LefSe,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Pseudomonadota",2|976|117743|200644|2762318|59735;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|976|200643|171549|2005525|195950;2|32066|203490;2|1224,Complete,Claregrieve1
bsdb:541/1/1,Study 541,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,30 days,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Data 5A,22 September 2021,Titas,"Titas,Atrayees,Chloe",Significantly decreased gut mOTU between schizophrenia patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|1239|91061|186826|33958|1578|1579;2|1239|186801|186802|31979|1485|1502;2|976|200643|171549|815|909656|310297,Complete,Chloe
bsdb:541/1/2,Study 541,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,30 days,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,increased,NA,NA,NA,increased,Signature 2,Supplementary Data 5A,23 September 2021,Titas,"Titas,Chloe",Significantly increased gut mOTU between schizophrenia patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|1239|909932|1843488|909930|904|187327;2|74201|203494|48461|1647988|239934|239935;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958|2742598|1613;2|1239|186801|186802|216572|1017280|106588;2|1239|91061|186826|1300|1301|1343;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:541/2/1,Study 541,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls at baseline,Schizophrenic patients (38 participant subsample) at baseline,"38 participants with schizophrenia selected for followup. Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,38,30 days,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 10,3 January 2024,Chloe,Chloe,Taxa decreased in schizophrenic subsample compared to healthy controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,2|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:541/3/1,Study 541,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Baseline Healthy controls,3 Month Follow-up Schizophrenic patients (38 participant subsample),"38 participants with schizophrenia selected for followup at 3 months. Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,38,30 days,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 10,3 January 2024,Chloe,Chloe,Baseline healthy controls compared to 3 month Follow up schizophrenia (38 samples),increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter segnis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter vibrioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|1224|28211|204458|76892|75|88688;2|1224|28211|204458|76892|75|155892;2|1239|186801|3082720|186804|1257|341694;2|1224|1236|91347|543|570|548;2|1239|186801|186802|384638;2|1239|186801|186802|216572|39492;2|1224|1236|91347|543|570|244366;2|74201|203494|48461|1647988|239934|239935;2|1224|1236|91347|543|547|158836;2|1224|1236|91347|543|547|550;2|976|200643|171549|171550|239759|328814;2|1224|1236|91347|543|547|69218;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|815|909656|310297,Complete,Chloe
bsdb:541/3/2,Study 541,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Baseline Healthy controls,3 Month Follow-up Schizophrenic patients (38 participant subsample),"38 participants with schizophrenia selected for followup at 3 months. Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,38,30 days,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data 10,3 January 2024,Chloe,Chloe,Decreased in participants with schizophrenia at 3 months compared to baseline controls,decreased,"k__Bacteria|s__butyrate-producing bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SS3/4",2|2811711;2|1239|186801|186802|216572|1263|457412;2|1239|186801|186802|245014,Complete,Chloe
bsdb:541/4/1,Study 541,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Antipsychotic drug,CHEBI:35476,Baseline Schizophrenic patients (38 participant subsample),3 Month Follow-up Schizophrenic patients (38 participant subsample),Alterations in abundance of mOTUs in the gut of SCZ patients after 3-month antipsychotics treatment,38,38,30 days,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 11,3 January 2024,Chloe,Chloe,Increased in 3 month follow-up schizophrenia patients treated with antipsychotics compared to baseline,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes",2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|570|548,Complete,ChiomaBlessing
bsdb:542/1/1,Study 542,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring HC, Thorsen J, Saunte DM, Lilje B, Bay L, Riis PT, Larsen N, Andersen LO, Nielsen HV, Miller IM, Bjarnsholt T, Fuursted K , Jemec GB",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 1,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Healthy controls,Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,24,30,1 month,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig4A and B,18 January 2024,Andre,"Andre,Peace Sandy","A, Differential abundance at genus level between hidradenitis suppurativa (HS) lesional skin and healthy controls. Note significantly higher relative abundance of Propionibacterium in healthy controls and significantly higher relative abundance of Porphyromonas and Peptoniphilus. B, Differential abundance at species level between HS lesional skin and healthy controls. Note higher relative abundance of Propionibacterium acnes in healthy controls than in lesional samples.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus murdochii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus koenoeneniae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|165779|411577;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1737405|1570339|165779|33037;2|201174|1760|85007|1653|1716|43770;2|1239|909932|1843489|31977|39948;2|1239|1737404|1582879;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|150022|1260;2|201174|1760|85007;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|2981628|755172;2|1239|1737404|1737405|1570339|162289|507751;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171551|836;2|976|200643|171549|171552;2|1224|28211|204457|41297|13687;2|976|200643|171549|171551|836;2|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:542/1/2,Study 542,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring HC, Thorsen J, Saunte DM, Lilje B, Bay L, Riis PT, Larsen N, Andersen LO, Nielsen HV, Miller IM, Bjarnsholt T, Fuursted K , Jemec GB",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 1,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Healthy controls,Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,24,30,1 month,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig4A and B,18 January 2024,Andre,"Andre,Peace Sandy","A, Differential abundance at genus level between hidradenitis suppurativa (HS) lesional skin and healthy controls. Note significantly higher relative abundance of Propionibacterium in healthy controls and significantly higher relative abundance of Porphyromonas and Peptoniphilus. B, Differential abundance at species level between HS lesional skin and healthy controls. Note higher relative abundance of Propionibacterium acnes in healthy controls than in lesional samples.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1224|1236|2887326|468|469|40214;2|1224|28216|80840|80864|283;2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85009|31957|1743;2|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:542/2/1,Study 542,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring HC, Thorsen J, Saunte DM, Lilje B, Bay L, Riis PT, Larsen N, Andersen LO, Nielsen HV, Miller IM, Bjarnsholt T, Fuursted K , Jemec GB",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 2,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Non lesional skin of Hidradenitis suppurativa patients,Lesional skin of Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,29,30,1 month,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Fig4C and D,18 January 2024,Andre,"Andre,Peace Sandy","C, Differential abundance at genus level between HS lesional skin and HS nonlesional skin. Note significantly higher relative abundance of Porphyromonas and Peptoniphilus in lesional skin than in nonlesional skin, Propionibacterium is more abundant in nonlesional skin. D, Differential abundance at species level between HS lesional skin and HS nonlesional skin. Note significantly reduced relative abundance of Propionibacterium acnes in HS lesional skin; higher relative abundances of Porphyromonas and Peptoniphilus are found in lesional skin. P values listed are adjusted for anatomical location. Black dots indicate the medians of each distribution.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii",2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1737405|1570339|165779|33037;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294|194|827;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|501496;2|976|200643|171549|171551|836|322095;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|1224|1236|2887326|468|469|470,Complete,NA
bsdb:542/2/2,Study 542,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring HC, Thorsen J, Saunte DM, Lilje B, Bay L, Riis PT, Larsen N, Andersen LO, Nielsen HV, Miller IM, Bjarnsholt T, Fuursted K , Jemec GB",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 2,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Non lesional skin of Hidradenitis suppurativa patients,Lesional skin of Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,29,30,1 month,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Fig4C and D,18 January 2024,Andre,"Andre,Peace Sandy","C, Differential abundance at genus level between HS lesional skin and HS nonlesional skin. Note significantly higher relative abundance of Porphyromonas and Peptoniphilus in lesional skin than in nonlesional skin, Propionibacterium is more abundant in nonlesional skin. D, Differential abundance at species level between HS lesional skin and HS nonlesional skin.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Alicycliphilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter|s__Diaphorobacter nitroreducens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rhodoluna,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|470;2|1224|1236|2887326|468|469|40215;2|1224|1236|2887326|468|469|487316;2|1224|28216|80840|80864|201096;2|1224|28216|80840|92793;2|201174|1760|85009|31957|1912216|1747;2|1224|28216|80840|80864|238749;2|1224|28216|80840|80864|238749|164759;2|201174|1760|85006|1268|1269;2|201174|1760|85006|1268|1269|1270;2|1224|1236|2887326|468|475;2|1224|28211|204455|31989|265;2|201174|1760|85009|31957|1743;2|1224|1236|72274|135621|286;2|201174|1760|85006|85023|529883;2|1224|1236|2887326|468|475,Complete,Peace Sandy
bsdb:543/1/1,Study 543,case-control,32415070,10.1038/s41467-020-16222-8,NA,"Vujkovic-Cvijin I, Sortino O, Verheij E, Sklar J, Wit FW, Kootstra NA, Sellers B, Brenchley JM, Ananworanich J, Loeff MSV, Belkaid Y, Reiss P , Sereti I",HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases,Nature communications,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-seronegative controls,Persons with HIV (PWH),chronically HIV-infected people with suppressed viremia on antiretroviral therapy (ART),80,80,NA,16S,4,Illumina,NA,0.05,TRUE,NA,"age,birth country,body mass index,sex,sexual preference",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 4,1 January 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between seronegative controls and persons with HIV,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|1239|186801|186802|541019|342658;2|201174|84998|1643822|1643826|84108|572010;2|1239|186801|186802|216572|459786;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|44748,Complete,Claregrieve1
bsdb:543/1/2,Study 543,case-control,32415070,10.1038/s41467-020-16222-8,NA,"Vujkovic-Cvijin I, Sortino O, Verheij E, Sklar J, Wit FW, Kootstra NA, Sellers B, Brenchley JM, Ananworanich J, Loeff MSV, Belkaid Y, Reiss P , Sereti I",HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases,Nature communications,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-seronegative controls,Persons with HIV (PWH),chronically HIV-infected people with suppressed viremia on antiretroviral therapy (ART),80,80,NA,16S,4,Illumina,NA,0.05,TRUE,NA,"age,birth country,body mass index,sex,sexual preference",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 4,6 January 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between seronegative controls and persons with HIV,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia",2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|31979|1485;2|200940|3031449|213115|194924|35832|35833,Complete,Claregrieve1
bsdb:544/1/1,Study 544,case-control,30157754,10.1186/s12866-018-1232-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114884/,"Zhang Y, Yu X, Yu E, Wang N, Cai Q, Shuai Q, Yan F, Jiang L, Wang H, Liu J, Chen Y, Li Z , Jiang Q",Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study,BMC microbiology,2018,"Colorectal cancer (CRC), Correlation analysis, Gut microbiota, Plasma inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients diagnosed with colorectal cancer,130,130,6 months,16S,34,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,"age,sex","age,alcohol drinking,body mass index,sex,smoking status",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table S1,20 January 2022,Itslanapark,"Itslanapark,Claregrieve1,Atrayees",CRC-associated microbiota in CRC patients compared with controls,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Eukaryota|k__Metazoa|p__Chordata|c__Actinopteri|o__Cyprinodontiformes|f__Nothobranchiidae|g__Scriptaphyosemion|s__Scriptaphyosemion liberiense,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|29547|3031852|213849|72294|194|203;2|1239|909932|1843489|31977|39948|39950;2|201174|84998|1643822|1643826|84111|84112;2|32066|203490|203491|203492|848|851;2|1239|91061|1385|539738|1378|29391;2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|28123;2759|33208|7711|186623|28738|405002|129983|60404;2|1239|526524|526525|128827|123375|102148;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|2316020|33039,Complete,Claregrieve1
bsdb:544/1/2,Study 544,case-control,30157754,10.1186/s12866-018-1232-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114884/,"Zhang Y, Yu X, Yu E, Wang N, Cai Q, Shuai Q, Yan F, Jiang L, Wang H, Liu J, Chen Y, Li Z , Jiang Q",Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study,BMC microbiology,2018,"Colorectal cancer (CRC), Correlation analysis, Gut microbiota, Plasma inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients diagnosed with colorectal cancer,130,130,6 months,16S,34,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,"age,sex","age,alcohol drinking,body mass index,sex,smoking status",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table S1,20 January 2022,Itslanapark,"Itslanapark,Claregrieve1,Aiyshaaaa",CRC-associated microbiota in CRC patients compared with controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|1239|186801|186802|3085642|2048137|39484;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|3085636|186803|572511|871665;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|841|301302;2|1239|91061|186826|1300|1301|1304;2|1239|186801|3085636|186803|2316020|46228,Complete,Claregrieve1
bsdb:545/1/1,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 10 days after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5,27 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young mice after 10 days of antibiotic treatment,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|91061|186826|81852;2|1239|91061|186826;2|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:545/1/2,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 10 days after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5,28 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 10 days of Abx treatment,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239|526524|526525|128827|1470349;2|1239|186801|186802|543314|2137877;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524|526525|128827|1729679;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:545/2/1,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 6 months after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella",2|1239|186801|3082720|186804|1501226;2|1239|186801|3082720|186804;2|1239|526524|526525|128827|1937008,Complete,Claregrieve1
bsdb:545/2/2,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 6 months after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery (lower panels),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus",2|1239|186801|186802|543314|2137877;2|1239|526524|526525|128827|1470349,Complete,Claregrieve1
bsdb:545/3/1,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 10 days after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,2|976|200643|171549,Complete,Claregrieve1
bsdb:545/3/2,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 10 days after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",2|1239|186801|3082720|186804|1501226;2|1239|186801|3082720|186804;2|1239|526524|526525|128827|1729679;2|1239|526524|526525|128827;2|1239|526524|526525,Complete,Claregrieve1
bsdb:545/4/1,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 6 months after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 6 months of recovery (lower panels).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|976|200643|171549;2|1239|526524|526525|128827|1729679;2|976|200643|171549|2005473;2|976|200643|171549|2005473|1918540;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:545/4/2,Study 545,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 6 months after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice after 6 months of recovery,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",2|1239|526524|526525|128827|1937008;2|1239|526524|526525|128827;2|1239|526524|526525,Complete,Claregrieve1
bsdb:546/1/1,Study 546,"cross-sectional observational, not case-control",34425246,10.1016/j.micinf.2021.104880,NA,"Gupta A, Karyakarte R, Joshi S, Das R, Jani K, Shouche Y , Sharma A",Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types,Microbes and infection,2021,"SARS-CoV-2, asymptomatic, host types, nasopharyngeal microbiome, symptomatic",Experiment 1,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-infected controls,COVID-19 cases,COVID-19 infected individuals,26,63,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Supplementary Info - Figure 1,27 September 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between infected and non-infected individuals,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Peace Sandy
bsdb:546/1/2,Study 546,"cross-sectional observational, not case-control",34425246,10.1016/j.micinf.2021.104880,NA,"Gupta A, Karyakarte R, Joshi S, Das R, Jani K, Shouche Y , Sharma A",Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types,Microbes and infection,2021,"SARS-CoV-2, asymptomatic, host types, nasopharyngeal microbiome, symptomatic",Experiment 1,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-infected controls,COVID-19 cases,COVID-19 infected individuals,26,63,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Supplementary Info - Figure 1, Figure 2a-b",27 September 2021,Claregrieve1,"Claregrieve1,Peace Sandy",Differential abundance of microbial taxa between infected and non-infected individuals,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1239;2|976;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|976|200643|171549|171552;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838;2|976|200643|171549|171551,Complete,Peace Sandy
bsdb:547/1/1,Study 547,case-control,34382150,10.1007/s12275-021-1206-5,NA,"Zhou Y, Zhang J, Zhang D, Ma WL , Wang X",Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge,"Journal of microbiology (Seoul, Korea)",2021,"COVID-19, gut microbiota, recovered healthcare workers, symptoms after discharge",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Health-care workers who recovered from COVID-19 and were discharged from the hospital between May and July 2020,14,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4,27 September 2021,Claregrieve1,"Claregrieve1,Peace Sandy","Taxonomic differences of gut microbiota between recovered HCWs and HCs. Comparison of relative abundance at the bacterial phylum (A), family
(B), genus (C), and species (D) between the two groups. p-value < 0.05 is considered to be statistically significant, *p < 0.05, **p < 0.01.",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum",2|201174;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|3085636|186803|2719313|208479;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|946234;2|1239|186801|3082720|186804|1505657;2|1239|186801|3082720|186804|1505657|261299;2|1239|526524|526525|2810280|3025755|1547;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|946234|292800;2|201174|1760|85004|31953|1678|1686;2|1239|186801|186802|3085642|580596|501571,Complete,Peace Sandy
bsdb:547/1/2,Study 547,case-control,34382150,10.1007/s12275-021-1206-5,NA,"Zhou Y, Zhang J, Zhang D, Ma WL , Wang X",Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge,"Journal of microbiology (Seoul, Korea)",2021,"COVID-19, gut microbiota, recovered healthcare workers, symptoms after discharge",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Health-care workers who recovered from COVID-19 and were discharged from the hospital between May and July 2020,14,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4,27 September 2021,Claregrieve1,"Claregrieve1,Peace Sandy","Taxonomic differences of gut microbiota between recovered HCWs and HCs. Comparison of relative abundance at the bacterial phylum (A), family
(B), genus (C), and species (D) between the two groups. p-value < 0.05 is considered to be statistically significant, *p < 0.05, **p < 0.01.",decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia sedimentorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",2|200940|3031449|213115|194924|35832;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|572511|871665;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|3085642|580596;2|200940|3031449|213115|194924;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|1392389;2|1239|186801|186802|1392389|1297617;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804|1501226;2|1239|186801|3082720|186804|1501226|1368474;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40518,Complete,Peace Sandy
bsdb:548/1/1,Study 548,prospective cohort,34423593,10.1002/advs.202102785,NA,"Gao M, Wang H, Luo H, Sun Y, Wang L, Ding S, Ren H, Gang J, Rao B, Liu S, Wang X, Gao X, Li M, Zou Y, Liu C, Yuan C, Sun J, Cui G , Ren Z",Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2021,"COVID-19, SARS-CoV-2, noninvasive biomarkers, oropharyngeal microbiome",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Confirmed COVID-19 cases by RT-PCR,48,94,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Figure 3b, 3d",28 September 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 cases and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria,k__Bacteria|p__Bacillota",2|1224|1236|135619|28256|2745;2|1239|91061|186826|186828|117563;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|1300|1301;2;2|1239,Complete,Claregrieve1
bsdb:548/1/2,Study 548,prospective cohort,34423593,10.1002/advs.202102785,NA,"Gao M, Wang H, Luo H, Sun Y, Wang L, Ding S, Ren H, Gang J, Rao B, Liu S, Wang X, Gao X, Li M, Zou Y, Liu C, Yuan C, Sun J, Cui G , Ren Z",Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2021,"COVID-19, SARS-CoV-2, noninvasive biomarkers, oropharyngeal microbiome",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Confirmed COVID-19 cases by RT-PCR,48,94,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Figure 3b, 3d",28 September 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 cases and healthy controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota,k__Bacteria,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Bacteria|p__Synergistota,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|976;2|1224;2;2|29547;2|203691;2|200940|3024418|213118;2|508458;2|200930|68337;2|74201;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|976|200643|171549|171552|1283313;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:549/1/1,Study 549,case-control,33935458,10.5021/ad.2021.33.2.163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082000/,"Hur MS, Lee JS, Jang M, Shin HJ , Lee YW",Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals,Annals of dermatology,2021,"Atopic keratoconjunctivitis, Atopy, Dysbiosis, Microbiota",Experiment 1,South Korea,Homo sapiens,Ocular surface region,UBERON:0010409,Keratoconjunctivitis,MONDO:0004768,Healthy controls,Atopic keratoconjunctivitis (AKC),"Patients diagnosed with Atopic keratoconjunctivitis (AKC) by an ophthalmologist, and with no systemic immune-associated diseases.",10,20,4 weeks for systemic treatment; 2 weeks for topical treatment,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,22 June 2023,Andre,Andre,Relative abundance of genus composition,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1224|1236|72274|135621|286;2|1239|91061|1385|90964|1279;2|1224|1236|135625|712|724,Complete,Chloe
bsdb:549/1/2,Study 549,case-control,33935458,10.5021/ad.2021.33.2.163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082000/,"Hur MS, Lee JS, Jang M, Shin HJ , Lee YW",Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals,Annals of dermatology,2021,"Atopic keratoconjunctivitis, Atopy, Dysbiosis, Microbiota",Experiment 1,South Korea,Homo sapiens,Ocular surface region,UBERON:0010409,Keratoconjunctivitis,MONDO:0004768,Healthy controls,Atopic keratoconjunctivitis (AKC),"Patients diagnosed with Atopic keratoconjunctivitis (AKC) by an ophthalmologist, and with no systemic immune-associated diseases.",10,20,4 weeks for systemic treatment; 2 weeks for topical treatment,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1+ 2,22 June 2023,Andre,"Andre,Chloe",Relative abundance of phylum and genus composition,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria",2|1224|28216|80840|119060|48736;2|201174|1760|85004|31953|1678;2|1224|1236|91347|1903414|583;2,Complete,Chloe
bsdb:549/1/3,Study 549,case-control,33935458,10.5021/ad.2021.33.2.163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082000/,"Hur MS, Lee JS, Jang M, Shin HJ , Lee YW",Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals,Annals of dermatology,2021,"Atopic keratoconjunctivitis, Atopy, Dysbiosis, Microbiota",Experiment 1,South Korea,Homo sapiens,Ocular surface region,UBERON:0010409,Keratoconjunctivitis,MONDO:0004768,Healthy controls,Atopic keratoconjunctivitis (AKC),"Patients diagnosed with Atopic keratoconjunctivitis (AKC) by an ophthalmologist, and with no systemic immune-associated diseases.",10,20,4 weeks for systemic treatment; 2 weeks for topical treatment,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 3,Table 1,23 June 2023,Andre,Andre,Relative abundance of phylum composition,decreased,k__Bacteria,2,Complete,NA
bsdb:550/1/1,Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 1,Norway,Homo sapiens,Saliva,UBERON:0001836,Juvenile idiopathic arthritis,EFO:0002609,healthy controls,JIA patients,children with juvenile idiopathic arthritis,34,59,Patients on antibiotics prior to sampling were excluded.,16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,28 September 2021,Tislam,"Tislam,Atrayees",Differentially abundant taxa,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 352,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 417,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|976|200643|171549|171552|1283313|1872471;2|1239|186801|3085636|186803|1164882|979627;2|201174|1760|85006|1268|32207|172042;2|1239|526524|526525|128827|123375|102148;2|1239|186801|3085636|186803|1213720|796942;2|976|200643|171549|171552|2974257|425941;2|1239|186801|3082720|3030910|86331|114527;2|1239|909932|1843489|31977|29465|39777;2|976|117743|200644|49546|1016|44737;2|95818|713054;2|32066|203490|203491|1129771|32067|712365;2|95818;2|1239|526524|526525|128827|123375;2|1239|186801|3082720|3030910|86331,Complete,Atrayees
bsdb:550/1/2,Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 1,Norway,Homo sapiens,Saliva,UBERON:0001836,Juvenile idiopathic arthritis,EFO:0002609,healthy controls,JIA patients,children with juvenile idiopathic arthritis,34,59,Patients on antibiotics prior to sampling were excluded.,16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3C,28 September 2021,Tislam,"Tislam,Atrayees",Differentially abundant taxa.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 314,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",2|1224|1236|135625|712|724|729;2|32066|203490|203491|1129771|32067|712363;2|976|200643|171549|171552|838|28129;2|1224|1236|135625|712|724|249188;2|1239|91061|1385|186817|1386|1423;2|201174|84998|84999|1643824|133925|712411;2|1224|1236|135625|712|724|735;2|201174|1760|85006|1268|32207|2047;2|976|200643|171549|171552|838|712464;2|976|117743|200644|2762318|59735|712187;2|1224;2|1224|1236|135625|712|724;2|1239|91061|1385|186817|1386;2|201174|84998|84999|1643824|133925,Complete,Atrayees
bsdb:550/2/1,Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Temporomandibular joint disorder,EFO:0005279,JIA patients without TMJ,JIA patients with TMJ,children with juvenile idiopathic arthritis,15,44,"Patients on antibiotics on the day of sampling were excluded, but previous antibiotic use were not recorded.",16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6C,",28 September 2021,Tislam,"Tislam,Atrayees","species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 070,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|201174|1760|85006|1268|32207|43675;2|201174|84998|84999|1643824|2767353|1382;2|1239|186801|3085636|186803|265975|237576;2|32066|203490|203491|1129771|2755140|157692;2|1239|91061|186826|1300|1301|671226;2|1239|91061|1385|186817|1386|1423;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|265975;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|186817|1386;2|201174;2759|33090|35493|3398|72025|3803|3814|508215,Complete,Atrayees
bsdb:550/2/2,Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Temporomandibular joint disorder,EFO:0005279,JIA patients without TMJ,JIA patients with TMJ,children with juvenile idiopathic arthritis,15,44,"Patients on antibiotics on the day of sampling were excluded, but previous antibiotic use were not recorded.",16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6C, text",28 September 2021,Tislam,"Tislam,Atrayees","species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 874,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp. oral taxon 044,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|838|652722;2|221235|1226342;2|1239|186801|3085636|186803|265975|1501329;2|1224|28216|206351|481|538|539;2|976|200643|171549|171552|2974257|228603;2|221235|1226341;2|976|200643|171549|171552|1283313|1872471;2|29547|3031852|213849|72294|194|712200;2|1224|28216|206351|481|32257|505;2|976|200643|171549|171552|2974257|425941;2|976|200643|171549|171551|836|1583331;2|1224|28216|206351|481|482|495;2|976|200643|171549|171552|838|60133;2|976|117743|200644|2762318|59735|1962306;2|1224|1236|135625|712|724|729;2|1224;2|1224|28216|206351|481|538;2|1224|1236|135625|712|724;2|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:551/1/1,Study 551,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,https://pubmed.ncbi.nlm.nih.gov/29276170/,"Zou J, Chassaing B, Singh V, Pellizzon M, Ricci M, Fythe MD, Kumar MV , Gewirtz AT",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High fat diet (HFD: 50 cell),High fat diet (HFD:200 Inul ),"High fat diet - [HFD] enriched with inulin increased gut epithelial proliferation, prevented colon atrophy",6,6,None,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3D,6 October 2021,Lorakasselman,"Lorakasselman,Aiyshaaaa,Merit,Peace Sandy",Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of inulin with standard HFD (50g cellulose),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107;2|201174|84998|84999;2|976|200643|171549|171550,Complete,Peace Sandy
bsdb:551/1/2,Study 551,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,https://pubmed.ncbi.nlm.nih.gov/29276170/,"Zou J, Chassaing B, Singh V, Pellizzon M, Ricci M, Fythe MD, Kumar MV , Gewirtz AT",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High fat diet (HFD: 50 cell),High fat diet (HFD:200 Inul ),"High fat diet - [HFD] enriched with inulin increased gut epithelial proliferation, prevented colon atrophy",6,6,None,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3D,7 October 2021,Chloe,"Chloe,Lorakasselman,Aiyshaaaa,Peace Sandy",Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of Inulin with standard HFD,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|1385;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186807|51514;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:551/2/1,Study 551,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,https://pubmed.ncbi.nlm.nih.gov/29276170/,"Zou J, Chassaing B, Singh V, Pellizzon M, Ricci M, Fythe MD, Kumar MV , Gewirtz AT",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Chow,High fat diet (HFD:200 Inul ),"High-fat diet - (HFD) enriched with inulin increased guy epithelial proliferation, prevented colon atrophy",6,6,None,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S3 E,30 January 2024,Peace Sandy,Peace Sandy,D-E) Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of Inulin with standard HFD (D) or chow (E).,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300;2|1239|526524|526525|128827|174708,Complete,Peace Sandy
bsdb:551/2/2,Study 551,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,https://pubmed.ncbi.nlm.nih.gov/29276170/,"Zou J, Chassaing B, Singh V, Pellizzon M, Ricci M, Fythe MD, Kumar MV , Gewirtz AT",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Chow,High fat diet (HFD:200 Inul ),"High-fat diet - (HFD) enriched with inulin increased guy epithelial proliferation, prevented colon atrophy",6,6,None,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S3 E,30 January 2024,Peace Sandy,Peace Sandy,D-E) Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of inulin with standard HFD (D) or chow (E).,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2759|4751|5204|155619|139380|1124673;2|976|200643|171549;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|1239|186801|186802|31979|49082;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572;2|1239|186801|186802;2|1239|526524|526525|2810280|135858,Complete,Peace Sandy
bsdb:552/1/1,Study 552,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen MA, Thorsen J, Dominguez-Bello MG, Blaser MJ, Mortensen MS, Brejnrod AD, Shah SA, Hjelmsø MH, Lehtimäki J, Trivedi U, Bisgaard H, Sørensen SJ , Stokholm J",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,Week 24,Week 36,gestational age of 36 weeks,56,57,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,28 October 2021,Joyessa,"Joyessa,Fatima,Claregrieve1",Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1224|1236|2887326|468|475;2|1239|91061|186826|1300|1301;2|1239|91061|1385|90964|1279;2|1239|91061|186826|81852|1350;2|201174|1760|85007|1653|1716;2|1239|91061|1385|539738|1378,Complete,Claregrieve1
bsdb:552/1/2,Study 552,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen MA, Thorsen J, Dominguez-Bello MG, Blaser MJ, Mortensen MS, Brejnrod AD, Shah SA, Hjelmsø MH, Lehtimäki J, Trivedi U, Bisgaard H, Sørensen SJ , Stokholm J",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,Week 24,Week 36,gestational age of 36 weeks,56,57,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,28 October 2021,Joyessa,"Joyessa,Fatima,Claregrieve1",Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:552/2/1,Study 552,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen MA, Thorsen J, Dominguez-Bello MG, Blaser MJ, Mortensen MS, Brejnrod AD, Shah SA, Hjelmsø MH, Lehtimäki J, Trivedi U, Bisgaard H, Sørensen SJ , Stokholm J",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,36,Birth,birth timepoint,57,57,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,15 November 2021,Joyessa,"Joyessa,Claregrieve1",Differentially abundant microbial taxa between the 36 week timepoint and birth timepoint,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85007|1653|1716;2|1239|91061|186826|81852|1350;2|1239|91061|1385|539738|1378;2|1224|1236|2887326|468|475;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:552/2/2,Study 552,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen MA, Thorsen J, Dominguez-Bello MG, Blaser MJ, Mortensen MS, Brejnrod AD, Shah SA, Hjelmsø MH, Lehtimäki J, Trivedi U, Bisgaard H, Sørensen SJ , Stokholm J",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,36,Birth,birth timepoint,57,57,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,30 August 2022,Claregrieve1,Claregrieve1,Differentially abundant microbial taxa between the 36 week timepoint and birth timepoint,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:553/1/1,Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 1,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,Viable control pregnancy,First or second-trimester miscarriage,NA,81,77,NA,16S,12,Illumina,Chi-Square,0.05,NA,NA,"age,body mass index,gestational age",NA,NA,NA,NA,NA,increased,increased,Signature 1,Figure 2A,14 October 2021,Titas,Titas,NA,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Fatima
bsdb:553/2/1,Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 2,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,Viable control pregnancy,First trimester miscarriage,NA,81,64,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,2D,14 October 2021,Titas,Titas,NA,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Fatima
bsdb:553/2/2,Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 2,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,Viable control pregnancy,First trimester miscarriage,NA,81,64,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2D + interpretation,14 October 2021,Titas,Titas,Samples deplete of Lactobacillus spp. display increased richness and diversity and colonization by potential pathogens.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|162289;2|544448|2790996|2790998|2129;2|1239|909932|1843489|31977|39948,Complete,Fatima
bsdb:553/3/1,Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 3,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,missed miscarriage,complete/incomplete miscarriage,"A missed miscarriage is when a baby has died in the womb, but the mother hasn't had any symptoms, such as bleeding or pain.
A complete miscarriage has taken place when all the pregnancy tissue has left your uterus.",61,13,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,14 October 2021,Titas,"Titas,Fatima",Vaginal microbiota composition on the basis of incomplete and/or complete miscarriages,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Fatima
bsdb:554/1/1,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls(HC),patients with parkinson's disease,The patients who have been diagnosed with Parkinson's Disease(PD). Parkinson’s disease (PD) is a common neurodegenerative disorder characterized by motor and non-motor symptoms.,48,51,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,4,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 1,Figure 3,18 October 2021,Fcuevas3,"Fcuevas3,Lwaldron,Aiyshaaaa","Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|171552|838;2|1239|186801|186802|216572,Complete,Fatima
bsdb:554/1/2,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls(HC),patients with parkinson's disease,The patients who have been diagnosed with Parkinson's Disease(PD). Parkinson’s disease (PD) is a common neurodegenerative disorder characterized by motor and non-motor symptoms.,48,51,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,4,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 2,Figure 3,18 October 2021,Fcuevas3,"Fcuevas3,Lwaldron,Aiyshaaaa","Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1239|91061;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005473,Complete,Fatima
bsdb:554/2/1,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 1,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,24 May 2023,Fcuevas3,Fcuevas3,"2A. Phylum, increased abundances.",increased,k__Bacteria|p__Verrucomicrobiota,2|74201,Complete,Fatima
bsdb:554/2/2,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 2,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,24 May 2023,Fcuevas3,Fcuevas3,2B. Class. Increased abundances.,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia",2|1239|186801;2|1239|909932;2|74201|203494,Complete,Fatima
bsdb:554/2/3,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 3,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,Fcuevas3,"2B. Class, decreased abundances.",decreased,k__Bacteria|p__Bacillota|c__Bacilli,2|1239|91061,Complete,Fatima
bsdb:554/2/4,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 4,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,Fcuevas3,"2C. Order, increased abundances.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",2|1239|186801|186802;2|1239|909932|909929;2|74201|203494|48461,Complete,Fatima
bsdb:554/2/5,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 5,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,Fcuevas3,"2C. Order, decreased abundances.",decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,2|1239|91061|186826,Complete,Fatima
bsdb:554/2/6,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 6,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,Fcuevas3,"2D. Family, increased abundances.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|909932|1843488|909930;2|1239|186801|186802|216572;2|976|200643|171549|171551;2|976|200643|171549|171550;2|1239|909932|1843489|31977;2|74201|203494|48461|203557,Complete,Fatima
bsdb:554/2/7,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 7,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,"Fcuevas3,Fatima","2D. Family, decreased abundances.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1239|91061|186826|33958;2|976|200643|171549|2005473,Complete,Fatima
bsdb:554/2/8,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 8,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests,25 May 2023,Fcuevas3,Fcuevas3,"2E. Genus, increased abundances.",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:554/2/9,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 9,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests,25 May 2023,Fcuevas3,Fcuevas3,"2E. Genus, decreased abundances.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803|2569097|39488;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301,Complete,Fatima
bsdb:554/2/10,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 10,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,Fcuevas3,"2F. Species, increased abundances.",increased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2157|28890|183925|2158|2159|2172|2173;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171552|2974251|165179;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40519;2|1239|186801|3085636|186803|2316020|33039,Complete,Fatima
bsdb:554/2/11,Study 554,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 11,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests,25 May 2023,Fcuevas3,Fcuevas3,"2F. Species, decreased abundances.",decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,2|1239|91061|186826|33958|1578|1596,Complete,Fatima
bsdb:555/1/1,Study 555,case-control,33681234,10.3389/fmed.2020.00538,NA,"Liu Z, Wu Y, Luo Y, Wei S, Lu C, Zhou Y, Wang J, Miao T, Lin H, Zhao Y, Liu Q , Liu Y",Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis,Frontiers in medicine,2020,"16S rRNA sequencing, environment/gene interaction, gut microbiota, rheumatoid arthritis, spouses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid arthritis patient,Rheumatoid arthritis patient,20,30,6 Months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3B, text",16 October 2021,Tislam,"Tislam,Peace Sandy","Discriminant analysis of LEfSe multistage species difference.  (B) Indicator bacteria with LDA scores of ≥ 2 in three groups were screened out. Different-colored regions represent different constituents (red, RA; green, HC; blue, SP). Circles indicate phylogenetic levels from domain to genus. Circle diameters are proportional to abundances for each group. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|186801|3085636|186803|572511;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|128827|1573535;2|1239|91061|186826|33958;2|1239|91061|186826;2|201174|1760|85006|1268;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207,Complete,Peace Sandy
bsdb:555/1/2,Study 555,case-control,33681234,10.3389/fmed.2020.00538,NA,"Liu Z, Wu Y, Luo Y, Wei S, Lu C, Zhou Y, Wang J, Miao T, Lin H, Zhao Y, Liu Q , Liu Y",Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis,Frontiers in medicine,2020,"16S rRNA sequencing, environment/gene interaction, gut microbiota, rheumatoid arthritis, spouses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid arthritis patient,Rheumatoid arthritis patient,20,30,6 Months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3, text",19 October 2021,Tislam,"Tislam,Peace Sandy","Discriminant analysis of LEfSe multistage species difference. (B) Indicator bacteria with LDA scores of ≥ 2 in three groups were screened out. Different-colored regions represent different constituents (red, RA; green, HC; blue, SP). Circles indicate phylogenetic levels from domain to genus. Circle diameters are proportional to abundances for each group. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae|g__Candidatus Microthrix,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Kroppenstedtia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|841;2|976|200643|171549;2|201174|84992|84993;2|544448|31969|2085|2092;2|1239|526524|526525|128827;2|201174|84992|84993|1798913|41949;2|544448|31969|2085|2092|2093;2|544448|31969|2085;2|1239|1737404|1737405|1570339|162290;2|1239|91061|1385|186824|1274351;2|1239|909932|1843489|31977,Complete,Peace Sandy
bsdb:556/1/1,Study 556,case-control,32694705,10.1038/s41598-020-68952-w,NA,"Willis KA, Postnikoff CK, Freeman A, Rezonzew G, Nichols K, Gaggar A , Lal CV",The closed eye harbours a unique microbiome in dry eye disease,Scientific reports,2020,NA,Experiment 1,United States of America,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Normal Control (NC),Dry Eye,Participants with moderate or severe dry eye disease,36,36,Within 1 month was exclusionary,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S5 and Fig. S6.,14 February 2024,Peace Sandy,Peace Sandy,"The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe). 

Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Calotrichaceae|g__Calothrix,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium",2|1239|91061|186826|33958;2|1239|91061|186826|1300|1301;2|1117|3028117|1161|2661849|1186;2|201174|1760|2037|2049|184869;2759|33090|35493|3398|72025|3803|3814|508215;2|1224|1236|135625|712|724;2|1297|188787|68933|188786|65551;2|1239|909932|1843489|31977|39948;2|201174|1760|85006|145357|57495;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851;2|1224|28211|356|82115|357,Complete,Peace Sandy
bsdb:556/1/2,Study 556,case-control,32694705,10.1038/s41598-020-68952-w,NA,"Willis KA, Postnikoff CK, Freeman A, Rezonzew G, Nichols K, Gaggar A , Lal CV",The closed eye harbours a unique microbiome in dry eye disease,Scientific reports,2020,NA,Experiment 1,United States of America,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Normal Control (NC),Dry Eye,Participants with moderate or severe dry eye disease,36,36,Within 1 month was exclusionary,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,NA,14 February 2024,Peace Sandy,Peace Sandy,"The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe).

Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Pleomorphomonadaceae|g__Pleomorphomonas,k__Bacteria|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae|g__Peredibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera",2|1224|1236|72274|135621|286;2|1224|28211|356|119045;2|29547|3031852|213849|72293|209;2|1224|28211|204441|433|434;2|1224|28211|356|41294|374;2|1224|1236|135614|32033|40323;2|201174|84998|84999|84107;2|201174|1760|85007|85029|37914;2|1224|28216|206351|1499392|57739;2|1224|28211|204441|2829815|191;2|1224|28211|356|2843308|261933;2|3018035|3031419|2024979|263369|263370;2|1224|28211|356|45404;2|1224|28211|204455|2854170|295418;2|1224|1236|91347|543|561;2|1224|1236|135613|1046|67575,Complete,Peace Sandy
bsdb:557/1/1,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the GIT microbiome,22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fournierella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|1236|135625|712|713;2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|1283313;2|1239|1737404|1737405|1570339|165779;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|1737404|1737405|1570339|150022;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|1940255;2|508458|649775|649776|3029087|1434006;2|201174|1760|85004|31953|2701;2|1239|186801|3085636|186803|1164882;2|1239|91061|186826|33958|1578;2|201174|1760|85007|2805586|1847725;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|201174|1760|2037|2049|2050;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|909932|1843488|909930|33024;2|1224|1236|72274|135621|286;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|186802|216572|1508657;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300|1301;2|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:557/1/2,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the GIT microbiome,22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|909932|1843489|31977|39948;2|1239|91061|186826|81852|1350;2|32066|203490|203491|203492|848;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838|59823;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1239|186801|3085636|186803|1506577;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:557/2/1,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the GIT microbiome",22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|s__uncultured bacterium",2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|29547|3031852|213849|72294|194;2|1239|186801|186802|186806|1730|290054;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|877420;2|201174|1760|85007|2805586|1847725;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1239|186801|186802|216572;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838|59823;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|186802|216572|1508657|2053608;2|1239|909932|909929|1843491|970;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803;2|976|200643|171549|2005473;2|1239|186801|186802|216572|707003;2|77133,Complete,Folakunmi
bsdb:557/2/2,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the GIT microbiome",22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|201174|1760|2037|2049|1654;2|976|200643|171549|815|816;2|201174|84998|84999|84107|102106;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|1407607;2|201174|1760|85004|31953|2701;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|877420;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171550;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|186802|216572|1508657|2053608;2|1239|186801|186802|216572|1263;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|216572;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:557/3/1,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the pharyngeal cavity microbiome.,22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",2|1239|909932|1843488|909930|904;2|1239|91061|186826|186827|1375;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|177971;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|216851|1946507;2|1239|186801|186802|216572|707003;2|976|200643|171549|815|816;2|29547|3031852|213849|72294|194,Complete,Folakunmi
bsdb:557/3/2,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the pharyngeal cavity microbiome.,22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1239|186801|3085636|186803|43996;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|150022;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|1164882;2|1239|91061|186826|33958|1578;2|201174|1760|85007|2805586|1847725;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1508657;2|1239|909932|909929|1843491|970;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:557/4/1,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the pharyngeal cavity microbiome.",22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|909932|1843488|909930|904;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|906;2|1239|1737404|1737405|1570339|162289;2|1239|186801|186802|216572|292632;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:557/4/2,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the pharyngeal cavity microbiome.",22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2,, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Candidatus Absconditabacteria|o__Candidatus Absconditabacterales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|3085636|186803|1766253;2|1239|1737404|1737405|1570339|165779;2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816;2|221235|2900568;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|236752;2|1239|186801|186802|216572|946234;2|976|200643|171549|2005525|375288;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|1239|186801|186802|216572|1508657;2|32066|203490|203491|1129771|168808;2|1239|186801|186802|1470353;2|1224|1236|91347|543;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:557/5/1,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in vaginal microbiome.,22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,increased,"k__Eukaryota|p__Evosea|o__Mastigamoebida|f__Entamoebidae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2759|2605435|2682482|33084;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2759|33090|35493|3398|72025|3803|3814|508215;2|1224|28216|80840|995019|40544;2|1239|186801|3082720|3118655|1913599|39498;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|216851;2|29547|3031852|213849|72294|194;2|1239|186801|186802|186806|1730|290054;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|1578;2|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:557/5/2,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in vaginal microbiome.,22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,s__metagenome",2|1224|1236|135625|712|713;2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171552|1283313;2|201174|1760|85004|31953|419014;2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|156454;2|976|200643|171549|815|816;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1239|186801|3082768|990719;2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|39948;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|1940338;2|508458|649775|649776|3029087|1434006;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|1300|1357;2|32066|203490|203491|1129771|32067;2|1239|1980693;2|1239|186801|3085636|186803|265975;2|976|200643|171549|2005525|375288;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838|59823;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|203691|203692|136|2845253|157;2|1239|186801|3085636|186803|2316020|33039;256318,Complete,Folakunmi
bsdb:557/6/1,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"this represented the condition approximately one month post-treatment, after the cessation of gepotidacin in vaginal microbiome",22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85004|31953|1678;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|186806|1730|39496;2|508458|649775|649776|3029087|1434006;2|1239|186801|3085636|186803|28050;2|1239|909932|909929|1843491|52225;2|1239|186801|186802|216572|459786;2|1239|1737404|1737405|1570339|543311;2|1224|1236|72274|135621|286;2|1239|186801|186802|216572|1508657;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|32066|203490|203491|1129771|32067;2|976|200643|171549|815|816;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:557/6/2,Study 557,randomized controlled trial,NA,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR, Brown JR",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944),BMC microbiology,2021,"Gepotidacin, microbiome, microbiome, antibiotic, clinical trial, urinary tract infection",Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"this represented the condition approximately one month post-treatment, after the cessation of gepotidacin in vaginal microbiome",22,22,NA,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,s__metagenome,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1239|909932|1843488|909930|904;2|201174|1760|2037|2049|1654;2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|976|117743|200644|49546|1016;2|1239|186801|3082768|990719;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1506577;2|1239|186801|3085636|186803|2316020|33039;256318;2|32066|203490|203491|203492|848,Complete,Folakunmi
bsdb:558/1/1,Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Table 2,18 November 2021,Mmarin,Mmarin,Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1694;2|1224|1236|91347|543;2|1239|186801|3085636|186803;2|1224|28216|80840|995019|40544,Complete,Atrayees
bsdb:558/1/2,Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Table 2,18 November 2021,Mmarin,"Mmarin,Atrayees",Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",2|1239|186801|3085636|186803|207244;2|976|200643|171549;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|40520;2|976|200643|171549|1853231|574697;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005519,Complete,Atrayees
bsdb:558/1/3,Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 3,Figure 5,19 November 2021,Mmarin,"Mmarin,Atrayees","Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1689;2|201174|1760|85004|31953|1678|41200;2|1224|1236|91347|543|1849603;2|1224|28216|80840|995019|40544|437898;2|1224|28216|80840|995019|40544|40545;2|976|200643|171549|815|816|818;2|1224|1236|135614|32033|40323,Complete,NA
bsdb:558/2/1,Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,NA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 5,13 January 2022,Mmarin,Mmarin,"Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1689;2|201174|1760|85004|31953|1678|41200;2|1224|1236|91347|543|1849603;2|1224|28216|80840|995019|40544|437898;2|1224|28216|80840|995019|40544|40545,Complete,NA
bsdb:558/2/2,Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,NA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 5,13 January 2022,Mmarin,Mmarin,"Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|976|200643|171549|2005525|375288;2|976|200643|171549|1853231|283168;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|283168|626933;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|572511|1322;2|1239|186801|186802|216572|1263|41978;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511|53443;2|1239|186801|3085636|186803|207244|1872530;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263|1161942;2|1239|186801|3085636|186803|2316020|33038,Complete,NA
bsdb:559/1/1,Study 559,randomized controlled trial,33440171,10.1016/j.chom.2020.12.012,NA,"Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD , Wu GD",Role of dietary fiber in the recovery of the human gut microbiome and its metabolome,Cell host & microbe,2021,"dietary fiber, vegan, omnivore, amino acid, enteral nutrition, metabolome, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,regular fiber omnivore diet,no fiber liquid omnivore diet,omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group),10,10,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2B,11 November 2021,Lorakasselman,"Lorakasselman,Chloe","The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa
that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|33039,Complete,Chloe
bsdb:559/1/2,Study 559,randomized controlled trial,33440171,10.1016/j.chom.2020.12.012,NA,"Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD , Wu GD",Role of dietary fiber in the recovery of the human gut microbiome and its metabolome,Cell host & microbe,2021,"dietary fiber, vegan, omnivore, amino acid, enteral nutrition, metabolome, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,regular fiber omnivore diet,no fiber liquid omnivore diet,omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group),10,10,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2B,11 November 2021,Lorakasselman,"Lorakasselman,Chloe","The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa
that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|976|200643|171549|815|816|28116;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171552|2974251|165179;2|1239|91061|186826|1300|1301|1308;2|1239|186801|3085636|186803|1766253|39491,Complete,Chloe
bsdb:560/1/1,Study 560,case-control,28449715,10.1186/s13073-017-0428-y,NA,"Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P , Wüllner U",Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients,Genome medicine,2017,"Archaea, Bacteria, Enteric nervous system, Gut-brain axis, Microbiome, Parkinson, Viruses",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy men without Parkinsons's Disease.,Men with Parkinson's Disease.,Only early stage PD men who were naïve to L-DOPA therapy as diagnosed according to the UK Brain Bank criteria.,28,31,"The use of antibiotics in the past three months in principle was an exclusion criterion. However, we included three PD patients and three controls despite the intake of antibiotics for one to three days in a period of 28–34 days prior to feces sampling as the omission of those cases from the analyses did not change any result",16S,NA,Illumina,Kruskall-Wallis,0.1,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 1C,14 November 2021,Fcuevas3,"Fcuevas3,Claregrieve1",Differential microbial abundance between PD participants and controls,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Bacillota,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|2719231|84030;2|1239;2;2|1239|186801|186802|186806|1730|142586;2|1239|186801,Complete,Claregrieve1
bsdb:560/1/2,Study 560,case-control,28449715,10.1186/s13073-017-0428-y,NA,"Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P , Wüllner U",Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients,Genome medicine,2017,"Archaea, Bacteria, Enteric nervous system, Gut-brain axis, Microbiome, Parkinson, Viruses",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy men without Parkinsons's Disease.,Men with Parkinson's Disease.,Only early stage PD men who were naïve to L-DOPA therapy as diagnosed according to the UK Brain Bank criteria.,28,31,"The use of antibiotics in the past three months in principle was an exclusion criterion. However, we included three PD patients and three controls despite the intake of antibiotics for one to three days in a period of 28–34 days prior to feces sampling as the omission of those cases from the analyses did not change any result",16S,NA,Illumina,Kruskall-Wallis,0.1,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 1C,14 November 2021,Fcuevas3,"Fcuevas3,Claregrieve1",Differential microbial abundance between PD participants and controls,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|1239|526524|526525|128827|1573535|1735;2|976|200643|171549|171552|2974251|165179,Complete,Claregrieve1
bsdb:561/1/1,Study 561,case-control,31247001,10.1371/journal.pone.0218252,NA,"Mihaila D, Donegan J, Barns S, LaRocca D, Du Q, Zheng D, Vidal M, Neville C, Uhlig R , Middleton FA",The oral microbiome of early stage Parkinson's disease and its relationship with functional measures of motor and non-motor function,PloS one,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy age-sex matched controls without Parkinson's disease.,Participants with early stage Parkinson's Disease.,Subjects included in the Parkinson’s disease (PD) group had been previously diagnosed by a neurologist and met the general diagnostic criteria for early PD.,36,48,None of the participants underwent antibiotic use in the past month prior to sample collection.,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 4,29 November 2021,Fcuevas3,"Fcuevas3,Claregrieve1,Atrayees",Significantly changed microbiota in early stage PD.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga canimorsus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter|s__Clavibacter michiganensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Eukaryota|k__Metazoa|p__Chordata|c__Actinopteri|o__Gerreiformes|f__Gerreidae|g__Gerres|s__Gerres decacanthus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia|s__Parascardovia denticolens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia",2|201174|1760|85004|31953|1678|28025;2|201174|1760|85004|31953|1678|1689;2|201174|1760|85004|31953|1678|216816;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|3239874|2916678|766764|5475|42374;2|976|117743|200644|49546|1016|28188;2|201174|1760|85006|85017|157920;2|201174|1760|85006|85023|1573|28447;2|201174|1760|85004|31953|2701|2702;2759|33208|7711|186623|2024538|274463|274464|581038;2|1239|91061|186826|33958|2767842|1590;2|1239|91061|186826|33958|1578|1579;2|1239|91061|186826|33958|2767887|1623;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|1598;2|1224|28211|356|119045|407;2|201174|1760|85004|31953|196082|78258;2|201174|1760|85007|85025|1827;2|201174|1760|85004|31953|196081|78259;2|1239|91061|186826|1300|1301|1309;2759|4751|4890|4891|4892|4893|4948|4950;2|1224|28211|356|118882|234;2759|4751|4890|3239874|2916678|766764|5475;2|201174|1760|85004|31953|1678;2|201174|1760|85006|85023|1573;2|201174|1760|85004|31953|2701;2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|196082,Complete,Atrayees
bsdb:561/1/2,Study 561,case-control,31247001,10.1371/journal.pone.0218252,NA,"Mihaila D, Donegan J, Barns S, LaRocca D, Du Q, Zheng D, Vidal M, Neville C, Uhlig R , Middleton FA",The oral microbiome of early stage Parkinson's disease and its relationship with functional measures of motor and non-motor function,PloS one,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy age-sex matched controls without Parkinson's disease.,Participants with early stage Parkinson's Disease.,Subjects included in the Parkinson’s disease (PD) group had been previously diagnosed by a neurologist and met the general diagnostic criteria for early PD.,36,48,None of the participants underwent antibiotic use in the past month prior to sample collection.,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 4. Significantly changed microbiota in early stage PD.,29 November 2021,Fcuevas3,"Fcuevas3,Atrayees",Significantly changed microbiota in early stage PD.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides|s__Candidatus Azobacteroides pseudotrichonymphae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. IHB B 17019,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|s__Flavobacteriaceae bacterium 3519-10,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus|s__Halobacillus mangrovi,k__Viruses|s__Streptococcus phage PhiSpn_200,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Wenyingzhuangia|s__Wenyingzhuangia fucanilytica,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Wenyingzhuangia",2|1239|91061|1385|186817|2800373|1404;2|1224|1236|91347|1903409|32199;2|976|200643|171549|511434;2|976|200643|171549|511434|511435;2|976|117743|200644|2762318|59732|1721091;2|976|117743|200644|49546|531844;2|1239|91061|1385|186817|45667|402384;10239|890041;2|976|117743|200644|49546|1518147|1790137;2|29547|3031852|213849|72294|194|827;2|976|117743|200644|49546|1518147,Complete,Atrayees
bsdb:562/1/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 1,"United States of America,Italy,Luxembourg",Homo sapiens,Vagina,UBERON:0000996,Health study participation,EFO:0010130,NA,healthy adult vagina 50% up,NA,NA,96,No,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult vagina genus >=50%,NA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Lwaldron
bsdb:562/1/3,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 1,"United States of America,Italy,Luxembourg",Homo sapiens,Vagina,UBERON:0000996,Health study participation,EFO:0010130,NA,healthy adult vagina 50% up,NA,NA,96,No,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,"Haoyanzh,Lwaldron",healthy adult vagina species >=50%,NA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,Lwaldron
bsdb:562/2/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 2,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 50% up,NA,NA,362,All records NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult skin genus >=50%,NA,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Eukaryota|p__Ciliophora|c__Litostomatea|o__Haptorida|f__Trachelophyllidae|g__Enchelyodon|s__Enchelyodon sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|91061|1385|90964|1279;2|201174|1760|85009|31957|1912216;2759|5878|5988|5989|197900|55195|55196;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|1269;2|1239|1737404|1737405|1570339|150022;2|1224|1236|2887326|468|475;2|201174|1760|85006|1268|32207,Complete,Lwaldron
bsdb:562/2/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 2,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 50% up,NA,NA,362,All records NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult skin species in >=50% samples,NA,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium namnetense,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella osloensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis",2|201174|1760|85007|1653|1716|38303;2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85009|31957|1912216|33011;2|201174|1760|85009|31957|1912216|1574624;2|1239|1737404|1737405|1570339|150022|1260;2759|4751|5204|1538075|162474|742845|55193|76773;2759|4751|5204|1538075|162474|742845|55193|76775;2|201174|1760|85006|1268|1269|1270;2|1224|1236|2887326|468|475|34062;2|1239|91061|1385|90964|1279|29388;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1290;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303,Complete,Lwaldron
bsdb:562/3/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 3,"China,Denmark,Israel,Netherlands,United Kingdom,United States of America,Australia,Canada,Finland,France,Germany,India,Spain,Ireland,Italy,Japan,Luxembourg,South Korea,Switzerland,United Republic of Tanzania",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 50% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult stool genus in >= 50% samples,NA,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|3085642|2048137;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|2569097;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|976|200643|171549|1853231|574697;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|201174|84998|1643822|1643826|644652;2|1239|186801|3082720|186804|1505657;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|2172004;2|1239|186801|3085636|186803|2316020;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1905344;2|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:562/3/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 3,"China,Denmark,Israel,Netherlands,United Kingdom,United States of America,Australia,Canada,Finland,France,Germany,India,Spain,Ireland,Italy,Japan,Luxembourg,South Korea,Switzerland,United Republic of Tanzania",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 50% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult stool species in >=50% samples,NA,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Eukaryota|p__Ciliophora|c__Spirotrichea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Zingiberales|f__Cannaceae|g__Canna|s__Canna indica",2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1407607|1150298;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|186802|3085642|2048137|1628085;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|189330|39486;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|841|360807;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|204475|745368;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|841|301302;2|976|200643|171549|815|816|28116;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|33042|116085;2|1239|1262992;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85004|31953|1678|216816;2|976|200643|171549|815|816|818;2|976|200643|171549|171550|239759|214856;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|216572|459786|1897011;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|216572|1263|40518;2|976|200643|171549|2005525|375288|46503;2|201174|84998|1643822|1643826|447020|446660;2|1239|186801|186802|216572|459786|1262911;2|976|200643|171549|815|816|47678;2|1239|186801|186802|216572|1263|1160721;2|976|200643|171549|2005519|397864|487174;2|201174|84998|1643822|1643826|644652|471189;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|815|816|371601;2759|5878|33829;2|976|200643|171549|815|909656|357276;2|1239|186801|186802|186806|1730|1262889;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|39492;2|1239|91061|186826|1300|1301|1318;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|28050|28052;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|1535;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|186803|841|1262948;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|1853231|574697|544645;2|201174|84998|84999|84107|102106|147207;2|976|200643|171549|171552|2974251|165179;2|1239|1263000;2|1239|186801|3082720|186804|1505657|261299;2759|33090|35493|3398|4618|4626|4627|4628,Complete,Lwaldron
bsdb:562/4/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,nasal cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,92,Unknown,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult nasal cavity genus in >=50% samples,NA,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia",2|201174|1760|85009|31957|1912216;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2759|4751|5204|1538075|162474|742845|55193,Complete,Lwaldron
bsdb:562/4/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,nasal cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,92,Unknown,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult nasal cavity species in >=50% samples,NA,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2|201174|1760|85007|1653|1716|38284;2759|4751|5204|1538075|162474|742845|55193|76775;2|201174|1760|85009|31957|1912216|33011,Complete,Lwaldron
bsdb:562/5/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 5,"Italy,Philippines,United States of America",Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,oral cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,659,No (n=16),WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult oral cavity genus in >=50% samples,NA,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Serinicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|1654;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|976|200643|171549|171551|836;2|29547|3031852|213849|72294|194;2|201174|1760|2037|2049|2529408;2|976|117743|200644|49546|1016;2|32066|203490|203491|1129771|32067;2|201174|1760|85007|1653|1716;2|1224|28216|80840|119060|47670;2|1224|1236|135625|712|416916;2|976|200643|171549|2005525|195950;2|976|200643|171549|171552|1283313;2|1239|91061|186826|186828|117563;2|201174|1760|85006|2805590|265976;2|1239|186801|3085636|186803|1164882;2|1239|1737404|1737405|1570339|543311;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1239|91061|186826|186827|46123;2|1224|28216|206351|481|32257;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|1213720;2|1239|526524|526525|128827|123375;2|1224|1236|135615|868|2717;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|538;2|1239|186801|3082720|186804|1257,Complete,Lwaldron
bsdb:562/5/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 5,"Italy,Philippines,United States of America",Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,oral cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,659,No (n=16),WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult oral cavity species in >=50% samples,NA,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Asparagales|f__Orchidaceae|s__Epidendroideae|g__Lockhartia|s__Lockhartia amoena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 458,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. HMSC24B09,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus quentini,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] sulci,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola",2|1239|91061|186826|1300|1301|1303;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|28037;2|1224|1236|135625|712|724|729;2|201174|1760|85006|1268|32207|2047;2|1239|91061|1385|539738|1378|1379;2|1239|91061|186826|1300|1301|1305;2|201174|1760|85006|1268|32207|43675;2|1239|91061|1385|539738|1378|84135;2|1239|91061|1385|539738|1378|29391;2|32066|203490|203491|203492|848|851;2|201174|1760|2037|2049|1654|544580;2|1239|91061|186826|1300|1301|68892;2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|2529408|1660;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|490;2|29547|3031852|213849|72294|194|199;2|976|200643|171549|171551|836|322095;2|32066|203490|203491|203492|848|860;2|1224|28216|80840|119060|47670|47671;2|1239|91061|186826|1300|1301|1318;2|976|117743|200644|49546|1016|327575;2|32066|203490|203491|1129771|32067|157687;2|201174|1760|85006|1268|32207|172042;2|1239|909932|1843489|31977|29465|39778;2|976|117743|200644|49546|1016|1019;2|976|117743|200644|49546|1016|1017;2|1224|1236|135625|712|724|726;2|201174|1760|85007|1653|1716|43768;2|1239|91061|186826|186828|117563|46124;2|1239|909932|1843489|31977|29465|1911679;2759|33090|35493|3398|73496|4747|158332|125137|154688;2|1239|91061|186826|1300|1301|1302;2|29547|3031852|213849|72294|194|204;2|976|200643|171549|2005525|195950|712710;2|32066|203490|203491|1129771|32067|712359;2|1239|909932|1843489|31977|29465|39777;2|976|200643|171549|171552|838|28133;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|45634;2|1224|1236|135625|712|416916|712148;2|201174|1760|2037|2049|1654|1739406;2|1239|186801|3085636|186803|1164882|467210;2|1224|1236|135625|712|416916|739;2|976|200643|171549|171552|2974251|28135;2|1224|28216|206351|481|482|495;2|1239|1737404|1737405|1570339|543311|33033;2|201174|84998|84999|1643824|2767353|1382;2|201174|1760|2037|2049|1654|936548;2|1224|28216|206351|481|482|28449;2|976|200643|171549|171552|838|60133;2|32066|203490|203491|1129771|32067|712357;2|1239|91061|186826|1300|1301|113107;2|1239|186801|3085636|186803|265975|237576;2|201174|84998|84999|1643824|2767353|1383;2|201174|1760|85007|1653|1716|61592;2|1239|91061|186826|1300|1301|257758;2|976|117743|200644|49546|1016|1018;2|1239|909932|1843489|31977|29465|2027459;2|201174|1760|2037|2049|1654|1655;2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|2974251|228604;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|1283313|76122;2|1239|186801|3085636|186803|1213720|796942;2|1239|91061|186826|1300|1301|1739309;2|1239|526524|526525|128827|123375|102148;2|976|200643|171549|171552|1283313|712469;2|1239|91061|186826|186827|46123|1581061;2|976|200643|171549|171552|838|470565;2|1224|28216|206351|481|482|488;2|976|117743|200644|49546|1016|45242;2|976|200643|171549|171552|2974251|28136;2|1239|186801|186802|543314|35517;2|1239|186801|3082720|3030910|86331|114527;2|1224|1236|135625|712|724|1078480;2|1239|91061|186826|1300|1301|1759399;2|32066|203490|203491|1129771|32067|671213;2|1224|1236|135615|868|2717|2718;2|1239|91061|186826|186827|46123|46125;2|1239|909932|1843489|31977|906|187326;2|1239|91061|186826|1300|1301|1739491;2|976|200643|171549|171552|838|1177574;2|1224|28216|206351|481|538|539;2|976|200643|171549|171552|838|712461;2|1224|1236|135625|712|724|123834;2|32066|203490|203491|1129771|32067|1227267;2|1239|186801|186802|543314|143393;2|1239|186801|3082720|186804|1257|341694;2|32066|203490|203491|1129771|32067|40542;2|976|200643|171549|171552|838|28129,Complete,Lwaldron
bsdb:562/6/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 6,Italy,Homo sapiens,Milk,UBERON:0001913,Health study participation,EFO:0010130,none - 50% prevalence threshold,milk from healthy adult,non-disease adult participants from curatedMetagenomicData,0,8,Unknown,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult milk genus in >=50% samples,NA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:562/7/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 7,"Italy,Luxembourg,United States of America",Homo sapiens,Vagina,UBERON:0000996,Health study participation,EFO:0010130,NA,healthy adult vagina 70% up,NA,NA,96,No,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult vagina genus in >=70% samples,NA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Lwaldron
bsdb:562/8/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 8,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 70% up,NA,NA,362,All records NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,"Haoyanzh,Lwaldron",healthy adult skin genus in >=70% samples,NA,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216;2759|4751|5204|1538075|162474|742845|55193;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:562/8/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 8,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 70% up,NA,NA,362,All records NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult skin species in >=70% samples,NA,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2759|4751|5204|1538075|162474|742845|55193|76775;2|1239|91061|1385|90964|1279|29388;2|201174|1760|85009|31957|1912216|33011,Complete,Lwaldron
bsdb:562/9/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 9,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 70% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult stool genus in >= 70% samples,NA,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|3085642|2048137;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|2569097;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|2316020;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|1905344,Complete,Lwaldron
bsdb:562/9/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 9,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 70% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult stool species in >= 70% samples,NA,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1407607|1150298;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|186802|3085642|2048137|1628085;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|189330|39486;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|841|360807;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|204475|745368;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|841|301302;2|976|200643|171549|815|816|28116;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|33042|116085;2|1239|1262992;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85004|31953|1678|216816;2|976|200643|171549|815|816|818;2|976|200643|171549|171550|239759|214856;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|216572|459786|1897011;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|946234|292800,Complete,Lwaldron
bsdb:562/10/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 10,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 0% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,7 February 2022,Haoyanzh,Haoyanzh,healthy stool genus in any adult sample,NA,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Acidipropionibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Aeriscardovia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Agitococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Aliarcobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae|g__Alkalilimnicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Allosphingosinicella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Amnimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aquamicrobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Arthrospira,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Atlantibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Bavariicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Calidifontibacter,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Blattodea|f__Rhinotermitidae|s__Coptotermitinae|g__Coptotermes|s__Coptotermes heimi,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Corticimicrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Criibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Cryobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Cytobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Dellaglioa,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Denitrobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Ensifer,k__Eukaryota|p__Evosea|o__Mastigamoebida|f__Entamoebidae|g__Entamoeba,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Ewingella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae|g__Fimbriiglobus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Franconibacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Frischella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae|g__Gemmata,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Geodermatophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Bogoriellaceae|g__Georgenia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Gluconacetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Gluconobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Hephaestia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Hornefia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae|g__Hydrocarboniphaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis|g__Hydrogenibacillus,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Collembola|o__Poduromorpha|f__Hypogastruridae|g__Hypogastrura|s__Hypogastrura sp. BOLD:AAI2333,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Immundisolibacterales|f__Immundisolibacteraceae|g__Immundisolibacter,k__Viruses|k__Orthornavirae|p__Negarnaviricota|c__Insthoviricetes|o__Articulavirales|f__Orthomyxoviridae|g__Alphainfluenzavirus|s__Alphainfluenzavirus influenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Jeotgalibacillus,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Kaistella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Kerstersia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Knoellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacteria|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales|f__Roseiflexaceae|g__Kouleothrix,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Kurthia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lapidilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Lawsonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Eukaryota|p__Euglenozoa|c__Kinetoplastea|o__Trypanosomatida|f__Trypanosomatidae|s__Leishmaniinae|g__Leishmania,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Leptospirales|f__Leptospiraceae|g__Leptospira,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Bacillota|c__Limnochordia|o__Limnochordales|f__Limnochordaceae|g__Limnochorda,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Loigolactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Luteipulveratus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Melaminivora,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Phytobacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Methylibium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Methyloceanibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Microcoleus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Micropruina,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Aquaspirillaceae|g__Microvirgula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Mixta,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Moellerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Murimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella,k__Bacteria|p__Myxococcota|o__Nannocystales|f__Nannocystaceae|g__Nannocystis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsaceae|g__Nocardiopsis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Oenococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae|g__Oscillatoria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paeniclostridium,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Paludisphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Patulibacteraceae|g__Patulibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Paucilactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Pelistega,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Peribacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Phytobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Planifilum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Plantibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Prauserella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Prolinoborus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionimicrobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudoglutamicibacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Psychrobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pulveribacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Archaea|p__Euryarchaeota|c__Thermococci|o__Thermococcales|f__Thermococcaceae|g__Pyrococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rhodanobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseicella,k__Bacteria|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales|f__Roseiflexaceae|g__Roseiflexus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Rossellomorea,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Eukaryota|k__Metazoa|p__Nematoda|c__Chromadorea|o__Rhabditida|f__Hoplolaimidae|s__Rotylenchulinae|g__Rotylenchus|s__Rotylenchus urmiaensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rouxiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Salinicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Salinicola,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Salipiger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Sanguibacteraceae|g__Sanguibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Schizophyllaceae|g__Schizophyllum|s__Schizophyllum sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Schleiferilactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Serinicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Siccibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Solibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae|g__Solimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae|g__Spiroplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Starkeya,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Superficieibacter,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Tepidiphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Tersicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Tetragenococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Nostocoides,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Thermoleophilales|f__Thermoleophilaceae|g__Thermoleophilum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiohalorhabdales|f__Thiohalorhabdaceae|g__Thiohalorhabdus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Tolypothrichaceae|g__Tolypothrix,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Williamsia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Zymomonadaceae|g__Zymomonas",2|1239|91061|186826|186827|46123;2|544448|31969|186329|2146|2147;2|1224|28216|80840|506|222;2|1239|909932|1843488|909930|904;2|201174|1760|85009|31957|1912215;2|1224|28216|80840|80864|12916;2|1224|1236|2887326|468|469;2|201174|1760|2037|2049|76833;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1653174;2|201174|84998|1643822|1643826|447020;2|201174|1760|85004|31953|240233;2|1239|91061|186826|186827|1375;2|1224|1236|135624|84642|642;2|1239|186801|186802|3085642|2048137;2|1224|1236|135625|712|416916;2|1224|1236|2887326|468|186829;2|74201|203494|48461|1647988|239934;2|1224|28216|80840|506|507;2|29547|3031852|213849|2808963|2321111;2|976|200643|171549|171550|239759;2|1239|91061|1385|186817|2675234;2|1224|1236|135613|72276|133193;2|1239|186801|3082720|3118656|114627;2|1224|1236|2887326|468|222991;2|1239|909932|1843489|31977|209879;2|976|200643|171549|171552|1283313;2|201174|1760|85004|31953|419014;2|1224|28211|204457|41297|2823232;2|1239|526524|526525|128827|2749846;2|1224|1236|2887326|468|2707015;2|1224|1236|135624|83763|13334;2|1239|186801|3085636|186803|2569097;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|216572|52784;2|1239|186801|186802|186806|264995;2|1239|909932|1843489|31977|156454;2|1239|186801|186802|3082771|1924093;2|1239|186801|3085636|186803|653683;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|3118652|2039240;2|1239|186801|186802|216572|244127;2|1239|91061|1385|186822|55079;2|1224|28211|356|69277|69278;2|201174|1760|85009|31957|2801844;2|201174|1760|2037|2049|28263;2|1117|3028117|1150|1892252|35823;2759|4751|4890|147545|5042|1131492|5052;2|1224|1236|91347|543|1903434;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|186817|1386;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|1239|91061|186826|81852|697279;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1224|28216|80840|506|517;2|1224|28211|356|2831100|85413;2|201174|1760|85006|85020|43668;2|203691|203692|1643686|143786|29521;2|1239|91061|1385|186822|55080;2|201174|1760|85006|85019|1696;2|1224|28211|204458|76892|41275;2|1239|91061|1385|186820|2755;2|1224|28211|356|118882|234;2|1224|28216|80840|119060|32008;2|1239|186801|186802|3085642|580596;2|976|200643|171549|1853231|574697;2|1239|186801|3085636|186803|830;2|1239|91061|1385|186817|1276290;2|201174|1760|85006|145357|1158982;2759|4751|4890|3239874|2916678|766764|1535326;2157|2283796|183967|1235850|2517203|1291539;2|1239|526524|526525|128827|1470349;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|1239|91061|186826|186828|2747;2|1239|526524|526525|2810280|135858;2|1224|28211|204458|76892|75;2|1224|1236|91347|543|158483;2|1239|186801|3085636|3018741|698776;2|201174|1760|85006|85017|157920;2|32066|203490|203491|203492|180162;2|1224|28211|356|2036754|28209;2|204428|204429|51291|809|810;2|1239|186801|3082768|990719|990721;2|976|117743|200644|2762318|59732;2|201174|1760|85006|85023|1573;2|508458|649775|649776|649777|508459;2|976|117743|200644|2762318|501783;2|1239|186801|3082720|186804|1870884;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1224|28216|80840|80864|283;2|1239|91061|186826|33958|2767879;2|1239|526524|526525|2810280|100883;2|976|200643|171549|2005519|1348911;2|1239|186801|3085636|186803|33042;2759|33208|6656|50557|85823|36985|72653|36986|282472;2|1224|28216|80840|506|2678534;2|201174|1760|85007|1653|1716;2|1239|186801|3082720|3118655|1937664;2|1224|1236|91347|543|413496;2|201174|1760|85006|85023|69578;2|1239|91061|1385|186817|2675230;2|1224|28216|80840|80864|80865;2|1239|91061|186826|33958|2767880;2|201174|84998|1643822|1643826|79603;2|201174|1760|85006|85020|36739;2|1239|91061|186826|186828|82800;2|200940|3031451|3024411|213121|893;2|200940|3031449|213115|213116|898;2|200940|3031449|213115|194924|872;2|1224|28211|356|2831106|46913;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827|1472649;2|1239|186801|3085636|186803|189330;2|1224|28216|80840|75682|75654;2|976|200643|171549|2005520|156973;2|1224|1236|91347|1903412|635;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|2810280|1279384;2|1224|28216|206351|481|538;2|1239|186801|3085636|186803|1432051;2|976|117743|200644|2762318|308865;2|74152|641853|641854|641876|423604;2|976|117743|200644|2762318|59734;2|1224|28211|356|212791;2|201174|84998|84999|84107|1472762;2|1224|28211|356|82115|106591;2759|2605435|2682482|33084|5758;2|1224|1236|91347|543|547;2|1239|186801|3085636|186803|2719313;2|1239|91061|186826|81852|1350;2|976|117743|200644|2762318|2782229;2|1239|91061|186826|186827|171412;2|1224|1236|91347|1903409|551;2|1239|526524|526525|128827|1647;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730;2|1224|1236|91347|1903411|41201;2|1239|91061|1385|33986;2|1239|1737404|1582879;2|1239|91061|186826|186827|66831;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|2005359;2|1239|526524|526525|128827|1573536;2|1239|526524|526525|128827|1573534;2|201174|84998|84999|1643824|2767327;2|1239|186801|3082720|3118655|44259;2|203682|203683|2691355|1914233|1914234;2|1239|1737404|1737405|1570339|150022;2|976|117743|200644|49546|237;2|1239|186801|186802|216572|946234;2|1224|1236|91347|543|1649295;2|508458|649775|649776|3029087|1434006;2|1224|1236|1240482|1240483|1335631;2|1239|91061|186826|33958|2767881;2|1239|186801|3085636|186803|1407607;2|32066|203490|203491|203492|848;2|201174|1760|85004|31953|2701;2|1239|91061|1385|539738|1378;2|203682|203683|2691355|1914233|113;2|1239|186801|186802|204475;2|1239|91061|1385|186817|129337;2|201174|1760|1643682|85030|1860;2|201174|1760|85006|145358|154116;2|1224|1236|1240482|1240483|1193503;2|1239|91061|186826|186827|13075;2|1224|28211|204441|433|89583;2|1224|28211|204441|433|441;2|201174|1760|85006|1268|1742989;2|201174|1760|85007|85026|2053;2|201174|84998|1643822|1643826|644652;2|1239|91061|186826|186828|117563;2|1224|28211|204455|31989|366614;2|1224|1236|135625|712|724;2|1224|1236|91347|1903412|568;2|1239|186801|186802|216572|1892380;2|1239|1737404|1737405|1570339|31983;2|29547|3031852|213849|72293|209;2|1224|28211|204457|41297|1445609;2|1224|28216|80840|75682|963;2|1239|526524|526525|128827|1573535;2|1239|526524|526525|128827|61170;2|1239|186801|186802|543314|2815774;2|1239|186801|3085636|186803|1649459;2|1224|1236|1775403|568386|243627;2|1239|91061|1385|539003|1609627;2|1224|2008785|119069|206349|70774;2759|33208|6656|30001|730331|30002|30003|283377;2|1239|91061|186826|186827|89092;2|1239|526524|526525|128827|1937007;2|1224|1236|1934945|1934946|1934947;10239|2732396|2497569|2497577|2499411|11308|197911|2955291;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|1392389;2|1239|91061|1385|186818|157226;2|508458|649775|649776|3029088|428711;2|976|117743|200644|2762318|2782231;2|1224|28216|80840|506|257820;2|1224|28216|206351|481|32257;2|1224|1236|91347|543|570;2|1224|1236|91347|543|579;2|201174|1760|85006|85021|136099;2|1224|1236|91347|543|1330547;2|200795|32061|32064|1508635|186475;2|1239|91061|1385|186818|1649;2|201174|1760|85006|2805426|57499;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|2719231;2|1239|91061|186826|33958|2759736;2|1239|91061|186826|33958|2767842;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|186801|186802|31979|420345;2|201174|84998|84999|1643824|2767353;2|1239|91061|186826|33958|2767884;2|1239|91061|186826|33958|2767885;2|1224|28216|80840|119060|47670;2|201174|1760|85007|2805586|1847725;2|200940|3031449|213115|194924|41707;2|1239|186801|186802|216572|2172004;2|1224|1236|91347|543|83654;2|201174|1760|85006|85023|110932;2759|33682|5653|2704949|5654|1286322|5658;2|1239|91061|186826|33958|2767893;2|203691|203692|1643688|170|171;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771|32067|712363;2|201174|1760|85006|85023|55968;2|1239|91061|186826|33958|1243;2|1239|91061|186826|33958|2767886;2|1239|91061|186826|33958|2767887;2|1239|1676648|1676649|1676650|1676651;2|1239|91061|186826|33958|2742598;2|1239|91061|186826|33958|2767888;2|1239|91061|1385|186820|1637;2|1239|91061|186826|33958|2767889;2|201174|1760|85006|145357|745364;2|1239|91061|1385|186817|400634;2|1224|1236|135614|32033|68;2|1239|91061|1385|90964|69965;2|1239|186801|186802|216572|1637257;2759|4751|5204|1538075|162474|742845|55193;2|1239|91061|1385|90964|2803850;2|1239|91061|1385|186817|2837505;2|201174|1760|85009|85015|86795;2|1239|186801|3085636|186803|248744;2|1224|28216|80840|75682|149698;2|976|200643|171549|815|1926659;2|1239|186801|3085636|186803|2316020;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1297|188787|68933|188786|65551;2|1224|28216|80840|80864|1649468;2|1239|91061|186826|81852|33969;2|1224|28211|356|69277|68287;2|1224|1236|91347|543|2055876;2157|28890|183925|2158|2159|2172;2157|2283796|183967|1235850|1577788|1080709;2157|28890|183925|2158|2159|2316;2|1224|28216|80840|2975441|316612;2|1224|28211|356|45401|1484898;2|1224|28211|356|119045|2282523;2|201174|1760|85006|85023|33882;2|1117|3028117|1150|1892252|44471;2|201174|1760|85009|31957|29404;2|201174|1760|85009|85015|116071;2|1224|28216|206351|2897176|57479;2|1239|909932|909929|1843491|52225;2|1224|1236|91347|1903409|2100764;2|201174|1760|2037|2049|2050;2|201174|1760|1643682|85030|88138;2|1224|1236|91347|1903414|158848;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085656|3085657|2039302;2|1224|1236|2887326|468|475;2|1224|1236|91347|1903414|581;2|1224|28216|206351|481|212742;2|200930|68337|191393|2945020|248038;2|976|200643|171549|2005473|1918540;2|1239|186801|3085636|186803|1774128;2|201174|1760|85007|1762|1763;2|201174|1760|85007|1762|670516;2|201174|1760|85007|1762|1073531;2|201174|1760|85007|1762|1866885;2|544448|31969|2085|2092|2093;2|544448|2790996|2895623|2767358;2|201174|1760|1643684|85031|53460;2|2818505|3031713|224463|53;2|1239|909932|1843489|31977|909928;2|1224|28216|206351|481|482;2|201174|1760|85006|1268|57494;2|201174|1760|85007|85025|1817;2|201174|1760|85009|85015|1839;2|201174|1760|85012|83676|2013;2|1224|28211|204457|41297|165696;2|976|200643|171549|1853231|283168;2|1239|91061|186826|33958|46254;2|1224|28216|80840|506|90243;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|265975;2|201174|1760|85006|2805590|125287;2|1117|3028117|1150|1892254|1158;2|1239|186801|186802|216572|459786;2|1224|28216|80840|80864|219181;2|1239|91061|1385|186822|44249;2|1239|186801|3082720|186804|1849828;2|203682|203683|2691356|1763524|1763521;2|976|200643|171549|2005525|375288;2|1239|186801|3082720|186804|1849822;2|1224|28211|204455|31989|265;2|976|200643|171549|171552|577309;2|201174|1760|85004|31953|196082;2|1224|28216|80840|995019|577310;2|1224|1236|135625|712|745;2|201174|1497346|588673|361606|361607;2|1224|28216|80840|2975441|318147;2|1239|91061|186826|33958|2767890;2|201174|1760|2037|2049|2740557;2|1224|1236|91347|1903410|122277;2|1239|91061|186826|33958|1253;2|976|117747|200666|84566|84567;2|1224|28216|80840|506|106146;2|1239|186801|3082720|186804|2743582;2|1239|186801|3082720|3118655|1913599;2|1239|186801|186802|186807|2740;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|186817|2675229;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656;2|1224|1236|135623|641|657;2|1224|28211|356|69277|28100;2|1224|1236|91347|543|447792;2|1239|91061|1385|186824|332100;2|1239|91061|1385|186818|162291;2|201174|1760|85006|85023|190323;2|1224|1236|91347|543|702;2|1224|1236|91347|543|1330546;2|201174|1760|85010|2070|142577;2|976|200643|171549|171552|838;2|1239|91061|1385|186817|2800373;2|1224|28216|206351|481|206375;2|201174|1760|85009|31957|1743;2|201174|1760|85009|31957|203133;2|1224|1236|91347|1903414|583;2|1224|1236|91347|1903414|586;2|201174|1760|85006|1268|1742993;2|1224|1236|91347|543|2055880;2|1224|1236|135622|267888|53246;2|1224|1236|91347|543|1504576;2|1239|186801|186802|216572|1017280;2|201174|1760|85006|1268|1742991;2|32066|203490|203491|1129771|2755140;2|1224|1236|72274|135621|286;2|201174|1760|85010|2070|1847;2|1239|186801|186802|186806|113286;2|1224|1236|135614|32033|83618;2|1239|91061|1385|186817|1221880;2|1224|1236|2887326|468|497;2|1224|28216|80840|80864|2678886;2|508458|649775|649776|3029088|638847;2157|28890|183968|2258|2259|2260;2|1224|1236|91347|1903411|34037;2|1224|28216|80840|119060|48736;2|1224|1236|91347|543|160674;2|1224|1236|135613|1046|67575;2|1224|28211|356|82115|379;2|1224|1236|135614|1775411|75309;2|201174|1760|85007|85025|1827;2|1224|28211|766|775|780;2|976|200643|171549|171550|28138;2|1239|186801|3085636|186803|588605;2|1224|1236|135625|712|1960084;2|1239|186801|3085636|186803|841;2|1224|28211|204441|433|2730923;2|200795|32061|32064|1508635|120961;2|1224|28211|204441|433|125216;2|1239|91061|1385|186817|2837508;2|201174|1760|85006|1268|32207;2759|33208|6231|119089|6236|211158|211162|288490|1651279;2|1224|1236|91347|1903411|1565532;2|1224|28211|204455|2854170|295418;2|201174|84995|84996|84997|42255;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1905344;2759|4751|4890|4891|4892|4893|4930;2|201174|1760|85010|2070|1835;2|1239|91061|1385|90964|45669;2|1224|1236|135619|28256|404432;2|1224|28211|204455|2854170|263377;2|1224|1236|91347|543|590;2|201174|1760|85006|145360|60919;2|1239|186801|186802|31979|1266;2|201174|1760|85004|31953|196081;2|201174|1760|2037|2049|2529408;2759|4751|5204|155619|5338|5332|5333|5335;2|1239|91061|186826|33958|2767891;2|1239|909932|909929|1843491|970;2|1239|186801|3085636|186803|1769710;2|201174|1760|85006|2805590|265976;2|1224|1236|91347|1903411|613;2|1239|526524|526525|2810280|519427;2|1224|1236|135622|267890|22;2|1239|186801|3085636|186803|177971;2|1224|1236|91347|543|1649298;2|1224|28216|206351|481|71;2|1224|28211|204441|2829815|204447;2|201174|84998|1643822|1643826|84108;2|32066|203490|203491|1129771|168808;2|1224|1236|91347|2812006|84565;2|1239|91061|1385|186818|648800;2|1224|1236|1775403|568386|413435;2|1239|526524|526525|128827|123375;2|976|117747|200666|84566|28453;2|1224|28211|204457|41297|165695;2|1224|28211|204457|41297|13687;2|1224|28211|204457|41297|165697;2|544448|31969|186328|2131|2132;2|1239|91061|1385|186818|1569;2|1239|91061|1385|90964|1279;2|1224|28211|356|335928|152053;2|1224|1236|135614|32033|40323;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|201174|1760|85011|2062|1883;2|1239|186801|186802|216572|292632;2|1224|1236|135624|83763|674963;2|1224|1236|91347|543|2303321;2|1117|3028117|1890424|1890426|1129;2|508458|649775|649776|649777|2753;2|976|200643|171549|2005525|195950;2|1224|1236|91347|1903409|82986;2|1224|28216|80840|114248;2|1224|2008785|119069|206349|203470;2|1239|186801|3082720|186804|1505652;2|201174|1760|85006|1268|1418588;2|1239|91061|186826|81852|51668;2|201174|1760|85006|85021|99479;2|201174|1497346|588674|320796|192992;2|1224|1236|135614|32033|141948;2|1297|188787|68933|188786|270;2|1224|1236|3085111|3085112|492233;2|1239|526524|526525|2810280|1505663;2|1117|3028117|1161|119859|111782;2|201174|84998|84999|1643824|2847313;2|203691|203692|136|2845253|157;2|201174|1760|85006|2805591|2038;2|201174|1760|2037|2049|1069494;2|201174|1760|85007|85028|2060;2|1239|526524|526525|2810281|191303;2|1224|28216|80840|995019|1918598;2|1239|186801|3085636|186803|1506577;2|544448|2790996|2790998|2129;2|1239|91061|186826|81852|2737;2|201174|1760|2037|2049|184869;2|1224|28216|80840|80864|34072;2|1239|909932|1843489|31977|29465;2|1224|1236|135623|641|662;2|256845|1313211|278082|255528|172900;2|976|117743|200644|2762318|1013;2|1239|91061|1385|186817|2817139;2|201174|1760|85007|85025|85043;2|201174|1760|2037|2049|2692118;2|1224|1236|135614|32033|338;2|1224|1236|91347|1903411|629;2|1224|1236|91347|543|158876;2|1224|28211|204457|2844881|541,Complete,Lwaldron
bsdb:562/11/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 11,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 30% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,24 March 2022,Haoyanzh,Haoyanzh,healthy stool genus prevalence >=30%,NA,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|2316020;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|976|200643|171549|815|909656;2|1239|186801|3085636|186803|1407607;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107|102106;2|1239|186801|186802|3085642|2048137;2|1239|186801|3085636|186803|2569097;2|1239|186801|186802|216572|1263;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|1300|1301;2|1239|186801|186802|204475;2|1239|186801|186802|216572|1905344;2|1239|186801|186802|216572|459786;2|1239|186801|186802|31979|1485;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|946234;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171552|838;2|976|200643|171549|2005519|397864;2|201174|84998|1643822|1643826|644652;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|216572|2172004;2|1224|1236|91347|543|561;2|200940|3031449|213115|194924|35832;2|74201|203494|48461|1647988|239934;2|976|200643|171549|1853231|574697;2|1224|28216|80840|995019|577310;2|1239|186801|3082720|186804|1505657;2|1239|91061|186826|33958|1578;2|1239|526524|526525|2810280|1505663;2|201174|84998|1643822|1643826|84108;2|1239|186801|3085636|186803|2719313;2|976|200643|171549|2005519|1348911;2|201174|84998|1643822|1643826|84111;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|29465;2|201174|84998|84999|84107|1472762;2|1239|186801|186802|1392389;2|1224|1236|135625|712|724;2|1239|186801|186802|3082771|1924093;2|1239|526524|526525|128827|1573535;2157|28890|183925|2158|2159|2172;2|1239|526524|526525|128827|61170;2|976|200643|171549|171552|577309;2|201174|84998|84999|1643824|2847313;2|1239|526524|526525|2810281|191303;2|1224|28216|80840|995019|1918598;2|201174|1760|2037|2049|1654,Complete,Lwaldron
bsdb:563/1/1,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 1,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Controls aged < = 0 years,Controls aged > 10 years,Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old.,50,170,not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2,28 June 2023,Andre,"Andre,Folakunmi",Changes in taxa abundance between control individuals aged <= 10 years and > 10 years,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Myceligenerans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|201174|1760|2037;2|201174|1760|85007|1653|1716;2|201174|1760|85006|85017|253183;2|1224|28211|204455|31989|265;2|201174|1760|85006|85017;2|201174|1760|85009|31957|1743,Complete,Peace Sandy
bsdb:563/1/2,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 1,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Controls aged < = 0 years,Controls aged > 10 years,Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old.,50,170,not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2,28 June 2023,Andre,"Andre,Folakunmi",Changes in taxa abundance between control individuals aged <= 10 years and > 10 years,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85006|85020|43668;2|201174|1760|85006|1268|57493;2|201174|1760|85006|1268|1269;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:563/2/1,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 2,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Controls aged > 10 years with samples collected in the dry season,Controls aged > 10 years with samples collected in the wet season,"Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old with samples collected during the dry season. Of note, all samples from participants <= 10 years old were collected during the wet season, therefore, were not included in the analysis of the seasonal effect on the conjunctival microbiome.",126,94,not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Table 2,28 June 2023,Andre,"Andre,Folakunmi,Peace Sandy",Difference in taxa abundance between normal conjunctiva in wet season and normal conjunctiva in dry season,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus",2|1239|91061|1385|186817|1386;2|1239|91061|1385|186823|432330,Complete,Peace Sandy
bsdb:563/3/1,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 3,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C > 0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C = 0) alone, with samples collected in the dry season",Participants aged = 10 years with clinical signs of conjunctival scarring (Cicatricae = 0)  sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,16 February 2024,Peace Sandy,Peace Sandy,Changes in taxa abundance between groups,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,2|1239|91061|186826|186827|13075,Complete,Peace Sandy
bsdb:563/3/2,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 3,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C > 0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C = 0) alone, with samples collected in the dry season",Participants aged = 10 years with clinical signs of conjunctival scarring (Cicatricae = 0)  sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,16 February 2024,Peace Sandy,Peace Sandy,Changes in taxa abundance between groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:563/4/1,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 4,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Cases aged > 10 years with clinical signs of conjunctival scarring sampled during the dry season,Cases aged = 10 years with clinical signs of conjunctival scarring sampled during the dry season,Participants aged 10 years with clinical signs of conjunctival scarring in dry season,63,63,Not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,20 July 2023,Andre,"Andre,Folakunmi,Peace Sandy",Changes in taxa abundance between groups,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,2|1239|91061|186826|186827|13075,Complete,Peace Sandy
bsdb:563/4/2,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 4,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Cases aged > 10 years with clinical signs of conjunctival scarring sampled during the dry season,Cases aged = 10 years with clinical signs of conjunctival scarring sampled during the dry season,Participants aged 10 years with clinical signs of conjunctival scarring in dry season,63,63,Not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,20 July 2023,Andre,"Andre,Folakunmi,Peace Sandy",Changes in taxa abundance between groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:563/6/1,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 6,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C>0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season",Participants aged >10 years with clinical signs of conjunctival scarring (Cicatricae > 0) and with  trachomatous trichiasis (TT)) sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,Not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,20 July 2023,Andre,"Andre,Folakunmi",Changes in taxa abundance between groups,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria",2|201174|1760|85007|1653|1716;2|201174|1760|85006|1268|57493,Complete,Peace Sandy
bsdb:563/6/2,Study 563,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM , Burr SE",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 6,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C>0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season",Participants aged >10 years with clinical signs of conjunctival scarring (Cicatricae > 0) and with  trachomatous trichiasis (TT)) sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,Not mentioned,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,20 July 2023,Andre,"Andre,Folakunmi",Changes in taxa abundance between groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Myceligenerans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae",2|201174|1760|2037;2|201174|1760|85006|85017|253183;2|1224|28211|204455|31989|265;2|201174|1760|85006|85017,Complete,Peace Sandy
bsdb:564/1/1,Study 564,case-control,26237371,10.1097/MPG.0000000000000928,https://journals.lww.com/jpgn/Fulltext/2016/02000/Influence_of_Intrapartum_Antibiotic_Prophylaxis.20.aspx,"Corvaglia L, Tonti G, Martini S, Aceti A, Mazzola G, Aloisio I, Di Gioia D , Faldella G",Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life,Journal of pediatric gastroenterology and nutrition,2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Control group (@7 days),IAP group (@7 days),"infants born to GBS-positive mothers who had received IAP. According to the institutional treatment protocol for GBS prophylaxis (derived from the Centers for Disease Control and Prevention guidelines (13)), intravenous ampicillin was given every 4 hours until delivery (first dose 2 g, following doses 1 g each).",49,35,"The mother had received any antibiotic other than IAP in the 4 weeks before delivery, maternal IAP was performed with antibiotics other than ampicillin, such as erythromycin.",PCR,NA,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,"delivery procedure,feeding practices,gestational age",NA,NA,NA,NA,NA,NA,NA,Signature 1,text,19 November 2021,Mmarin,"Mmarin,Atrayees",Significant change in taxa between the two groups,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,Atrayees
bsdb:565/1/1,Study 565,case-control,32674496,10.3390/vetsci7030092,NA,"Cintio M, Scarsella E, Sgorlon S, Sandri M , Stefanon B",Gut Microbiome of Healthy and Arthritic Dogs,Veterinary sciences,2020,"arthritis, dogs, gut microbiome, hematological parameters",Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Arthritis,EFO:0005856,healthy dogs,dogs with hip or elbow arthritis,"dogs with evidence of hip/elbow arthritis as follows: clinical anamnesis for limping forelimbs and/or associated with posterior limping; rapid fatigue after effort; decrease in motor activity; radiographic evidence of osteoarthritis (AD) in one or two joints (elbow, hips)",13,14,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 3b,31 December 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy dogs and arthritic dogs,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|1224|1236|135624;2|1224|1236|135624|83763|13334;2;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186807;2|1239|186801|186802|186807|2740;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551;2|1224|1236|135624|83763;2|1239|186801|3082720|3030910|86331,Complete,Claregrieve1
bsdb:565/1/2,Study 565,case-control,32674496,10.3390/vetsci7030092,NA,"Cintio M, Scarsella E, Sgorlon S, Sandri M , Stefanon B",Gut Microbiome of Healthy and Arthritic Dogs,Veterinary sciences,2020,"arthritis, dogs, gut microbiome, hematological parameters",Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Arthritis,EFO:0005856,healthy dogs,dogs with hip or elbow arthritis,"dogs with evidence of hip/elbow arthritis as follows: clinical anamnesis for limping forelimbs and/or associated with posterior limping; rapid fatigue after effort; decrease in motor activity; radiographic evidence of osteoarthritis (AD) in one or two joints (elbow, hips)",13,14,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 3b,31 December 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy dogs and arthritic dogs,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,2|1239|909932|909929|1843491|158846,Complete,Claregrieve1
bsdb:566/1/1,Study 566,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,HLAB27-,HLAB27+,enthesitis-related arthritis (JIA-ERA) patients with HLA-B27 allele,10,9,3 months,16S,56,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",30 November 2021,Tislam,"Tislam,Claregrieve1",Comparison of relative abundance of bacterial taxa between HLA-B27+ participants and HLB27- participants,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|1224|1236|135625|712|724;2|1224|1236|135625|712;2|201174|84998|1643822|1643826|84111,Complete,Claregrieve1
bsdb:566/1/2,Study 566,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,HLAB27-,HLAB27+,enthesitis-related arthritis (JIA-ERA) patients with HLA-B27 allele,10,9,3 months,16S,56,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima,Claregrieve1",Comparison of relative abundance of bacterial taxa between HLA-B27+ participants and HLB27- participants,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|200940|3031449|213115|194924|35832;2|1239|186801|186802|31979|1485|1506;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|596767;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|459786;2|1239|1737404|1737405|1570339|543311;2|1239|91061|186826|33958,Complete,Claregrieve1
bsdb:566/2/1,Study 566,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,JIA patients with active disease,JIA patients in remission,JIA patients with enthesitis-related arthritis who are in remission,8,21,3 months,16S,56,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,30 November 2021,Tislam,"Tislam,Claregrieve1",Differences in bacterial abundance between JIA patients with active disease and patients in remission,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,2|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:566/2/2,Study 566,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,JIA patients with active disease,JIA patients in remission,JIA patients with enthesitis-related arthritis who are in remission,8,21,3 months,16S,56,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,30 November 2021,Tislam,"Tislam,Claregrieve1",Differences in bacterial abundance between JIA patients with active disease and patients in remission,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|1239|186801|186802|31979|1485|1506;2|1224|28216|80840|995019|577310;2|976|200643|171549|1853231|283168,Complete,Claregrieve1
bsdb:566/3/1,Study 566,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,Healthy subjects,JIA-ERA patients,enthesitis-related arthritis (JIA-ERA) patients,29,19,3 months,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 1,21 June 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between JIA-ERA patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",2|1239|186801|186802|216572;2|1239|186801|186802|31979|1485|1506,Complete,Claregrieve1
bsdb:566/3/2,Study 566,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,Healthy subjects,JIA-ERA patients,enthesitis-related arthritis (JIA-ERA) patients,29,19,3 months,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 1,21 June 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between JIA-ERA patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|186801|3082720|186804;2|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:566/4/1,Study 566,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,Healthy subjects,JIA-nERA patients,polyarticular arthritis (JIA-ERA) patients,29,10,3 months,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 1,21 June 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between JIA-nERA patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|186802|216572;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:567/1/1,Study 567,case-control,23553152,10.3945/ajcn.112.046607,https://www.sciencedirect.com/science/article/pii/S0002916523055120?via=ihub,"Chen HM, Fang DC, Fang JY, Kong X, Lin YW, Liu F, Liu ZJ, Wang JL, Wu JX, Yang CQ, Yang L, Yu YN, Yuan YZ, Zhong L, Zou W",Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma,The American journal of clinical nutrition,2013,"colorectal adenoma, colorectal cancer, dietary fiber, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy control group (HC),Advanced colorectal adenoma group (A-CRA),Patients with a diagnosis of A-CRA by pathological examination were enrolled in the A-CRA group.,47,47,"6 months

None of the patients had received systemic or oral topical corticosteroids, antibiotics,
aspirin, other nonsteroidal antiinflammatory drugs (16), or health products that regulate intestinal microbiota within 6 mo before enrollment",16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,31 May 2022,Jeshudy,"WikiWorks,Jeshudy",Significant differences in some genera identified between the HC (n = 47) and A-CRA (n = 47) groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|976|200643|171549|815|816;2|1239|91061|186826|1300|1301;2|1239|91061|186826|81852|1350,Complete,Rimsha
bsdb:567/1/2,Study 567,case-control,23553152,10.3945/ajcn.112.046607,https://www.sciencedirect.com/science/article/pii/S0002916523055120?via=ihub,"Chen HM, Fang DC, Fang JY, Kong X, Lin YW, Liu F, Liu ZJ, Wang JL, Wu JX, Yang CQ, Yang L, Yu YN, Yuan YZ, Zhong L, Zou W",Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma,The American journal of clinical nutrition,2013,"colorectal adenoma, colorectal cancer, dietary fiber, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy control group (HC),Advanced colorectal adenoma group (A-CRA),Patients with a diagnosis of A-CRA by pathological examination were enrolled in the A-CRA group.,47,47,"6 months

None of the patients had received systemic or oral topical corticosteroids, antibiotics,
aspirin, other nonsteroidal antiinflammatory drugs (16), or health products that regulate intestinal microbiota within 6 mo before enrollment",16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,24 March 2024,Aleru Divine,Aleru Divine,Significant differences in some genera identified between the HC (n = 47) and A-CRA (n = 47) groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|841;2|1239|186801|186802|31979|1485,Complete,Rimsha
bsdb:568/1/1,Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.,New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,FALSE,NA,"age,life style",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3. Genus level comparison among NPD samples.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,Rimsha
bsdb:568/1/2,Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.,New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,FALSE,NA,"age,life style",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,FIGURE 3,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|577309;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301,Complete,Rimsha
bsdb:568/2/1,Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 5 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 5 days after treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.01,NA,NA,"age,life style",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,Rimsha
bsdb:568/3/1,Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,NA,NA,"age,life style",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,Rimsha
bsdb:568/3/2,Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,NA,NA,"age,life style",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Rimsha
bsdb:569/1/1,Study 569,case-control,32280686,10.1155/2020/2948282,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114766/,"Liu X, Cheng Y, Shao L , Ling Z",Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer patients,diagnosed with primary early-stage CRC (aged 46-75 years old) between January 2011 and March 2012,45,53,1 month,16S,NA,RT-qPCR,T-Test,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure1,16 February 2022,Fatima,Fatima,Quantitative real-time PCR analysis of the fecal abundant bacteria in patients with colorectal cancer,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum",2|1224|1236|91347|543;2|32066|203490|203491|203492|848|851,Complete,Fatima
bsdb:569/1/2,Study 569,case-control,32280686,10.1155/2020/2948282,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114766/,"Liu X, Cheng Y, Shao L , Ling Z",Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer patients,diagnosed with primary early-stage CRC (aged 46-75 years old) between January 2011 and March 2012,45,53,1 month,16S,NA,RT-qPCR,T-Test,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure1,16 February 2022,Fatima,Fatima,Quantitative real-time PCR analysis of the fecal abundant bacteria in patients with colorectal cancer,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",2|1239|91061|186826|33958|1578|1591;2|201174|1760|85004|31953|1678|41200;2|1239|186801|186802|31979|1485|1506,Complete,Fatima
bsdb:570/1/1,Study 570,case-control,31100891,10.3390/jcm8050693,NA,"Jeong Y, Kim JW, You HJ, Park SJ, Lee J, Ju JH, Park MS, Jin H, Cho ML, Kwon B, Park SH , Ji GE",Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis,Journal of clinical medicine,2019,"Collinsella, autoimmune disease, dysbiosis, gut microbiome, microbial diversity, rheumatoid arthritis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,female healthy control,female with early RA,female early rheumatoid arthritis patients,25,29,"People using antibiotics, probiotics, or prebiotics at the time of sample collection were excluded
from subject selection.",16S,NA,Illumina,LEfSe,0.1,TRUE,3,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 3, text",30 November 2021,Tislam,"Tislam,Claregrieve1",Differential microbial abundance between RA patients and controls,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia",2|201174;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958|1243;2|508458|649775|649776|649777;2|1239|526524,Complete,Claregrieve1
bsdb:570/1/2,Study 570,case-control,31100891,10.3390/jcm8050693,NA,"Jeong Y, Kim JW, You HJ, Park SJ, Lee J, Ju JH, Park MS, Jin H, Cho ML, Kwon B, Park SH , Ji GE",Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis,Journal of clinical medicine,2019,"Collinsella, autoimmune disease, dysbiosis, gut microbiome, microbial diversity, rheumatoid arthritis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,female healthy control,female with early RA,female early rheumatoid arthritis patients,25,29,"People using antibiotics, probiotics, or prebiotics at the time of sample collection were excluded
from subject selection.",16S,NA,Illumina,LEfSe,0.1,TRUE,3,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 3, text",30 November 2021,Tislam,"Tislam,Claregrieve1",Differential microbial abundance between RA patients and controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota",2|976|200643|171549;2|976|200643;2|976,Complete,Claregrieve1
bsdb:571/1/1,Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Normal Vitamin D status,Knee osteroarthritis,Knee osteoarthritis,6,4,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima",A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1239|186801|186802|216572|52784;2|976|200643|171549|171551,Complete,Fatima
bsdb:571/1/2,Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Normal Vitamin D status,Knee osteroarthritis,Knee osteoarthritis,6,4,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima",A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|1392389;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186807|2740;2|201174|1760|85009|31957|1743;2|1224|1236|91347|543|1335483;2|201174|84998|84999|84107;2|1239|526524|526525|128827,Complete,Fatima
bsdb:571/2/1,Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Vitamin D deficiency,Knee osteroarthritis with vit D deficiency,Knee osteoarthritis,7,7,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,9 March 2022,Fatima,Fatima,differential abundance between KOA_VDD and VDD patients.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552|1283313;2|976|200643|171549|1853231|283168;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838,Complete,Fatima
bsdb:571/2/2,Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Vitamin D deficiency,Knee osteroarthritis with vit D deficiency,Knee osteoarthritis,7,7,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,9 March 2022,Fatima,Fatima,differential abundance between KOA_VDD and VDD patients.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|976|200643|171549|1853231|574697;2|95818|2093818|2093825|2171986|1331051;2|1224|28216|80840|80864|80865;2|201174|84998|1643822|1643826|644652;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551;2|201174|84998|84999|84107;2|1239|186801|186802|1898207,Complete,Fatima
bsdb:572/1/1,Study 572,case-control,24192039,https://doi.org/10.7554/eLife.01202.003,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816614/,"Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, Huttenhower C , Littman DR",Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis,eLife,2013,"arthritis, autoimmunity, inflammation, metagenomics, microbiome, rheumatoid",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Arthritis,EFO:0005856,Healthy controls,New-onset rheumatoid arthritis - NORA,Patients with new-onset rheumatoid arthritis - NORA,28,44,3 Months,16S,12,Roche454,LEfSe,0.05,TRUE,2,"age,ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,30 November 2021,Tislam,"Tislam,Lwaldron,Aiyshaaaa,Peace Sandy,Chloe,Chikamso,Folakunmi","(A) LEfSe (Segata et al., 2011) was used to compare the abundances of all detected clades among all groups, producing an effect size for each comparison (‘Materials and methods’). All results shown are highly significant (q<0.01) by Kruskal-Wallis test adjusted with the Benjamini-Hochberg procedure for multiple testing, except that indicated with an asterisk, which is significant at q<0.05. Negative values (left) correspond to effect sizes representative of NORA groups, while positive values (right) correspond to effect sizes in HLT subjects. Prevotella was found to be over-represented in NORA patients, while Bacteroides was over-represented in all other groups.",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",2|1239|526524|526525|2810280|135858;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|1926307,Complete,Peace Sandy
bsdb:572/1/2,Study 572,case-control,24192039,https://doi.org/10.7554/eLife.01202.003,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816614/,"Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, Huttenhower C , Littman DR",Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis,eLife,2013,"arthritis, autoimmunity, inflammation, metagenomics, microbiome, rheumatoid",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Arthritis,EFO:0005856,Healthy controls,New-onset rheumatoid arthritis - NORA,Patients with new-onset rheumatoid arthritis - NORA,28,44,3 Months,16S,12,Roche454,LEfSe,0.05,TRUE,2,"age,ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,30 November 2021,Tislam,"Tislam,Peace Sandy","(A) LEfSe (Segata et al., 2011) was used to compare the abundances of all detected clades among all groups, producing an effect size for each comparison (‘Materials and methods’). All results shown are highly significant (q<0.01) by Kruskal-Wallis test adjusted with the Benjamini-Hochberg procedure for multiple testing, except that indicated with an asterisk, which is significant at q<0.05. Negative values (left) correspond to effect sizes representative of NORA groups, while positive values (right) correspond to effect sizes in HLT subjects. Prevotella was found to be over-represented in NORA patients, while Bacteroides was over-represented in all other groups.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801;2|1239|186801|3085636|186803;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:573/1/1,Study 573,"cross-sectional observational, not case-control",32083132,10.1155/2020/7828392,https://pubmed.ncbi.nlm.nih.gov/32083132/,"Liu W, Zhang R, Shu R, Yu J, Li H, Long H, Jin S, Li S, Hu Q, Yao F, Zhou C, Huang Q, Hu X, Chen M, Hu W, Wang Q, Fang S , Wu Q",Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),Colorectal Cancer (CC),Patients who visited the department of gastroenterology of Tianyou hospital of Wuhan from January 2017 to December 2017 and received colonoscopy and histopathological examination were recruited to the study. Patients with colorectal adenocarcinoma were recorded as the colorectal cancer (CC) group.,42,51,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 4,9 December 2021,Itslanapark,Itslanapark,Difference analysis at the phylum level between Colorectal Cancer and Healthy Controls. Wilcoxon tests were used to analyze differences in the abundance between the two groups. Significant differences were evaluated by False Discovery Rate.,increased,"k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Synergistota",2|32066;2|1224;2|203691;2|508458,Complete,Fatima
bsdb:573/1/2,Study 573,"cross-sectional observational, not case-control",32083132,10.1155/2020/7828392,https://pubmed.ncbi.nlm.nih.gov/32083132/,"Liu W, Zhang R, Shu R, Yu J, Li H, Long H, Jin S, Li S, Hu Q, Yao F, Zhou C, Huang Q, Hu X, Chen M, Hu W, Wang Q, Fang S , Wu Q",Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),Colorectal Cancer (CC),Patients who visited the department of gastroenterology of Tianyou hospital of Wuhan from January 2017 to December 2017 and received colonoscopy and histopathological examination were recruited to the study. Patients with colorectal adenocarcinoma were recorded as the colorectal cancer (CC) group.,42,51,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 4,10 December 2021,Itslanapark,Itslanapark,Difference analysis at the phylum level between Colorectal Cancer and Healthy Controls. Wilcoxon tests were used to analyze differences in the abundance between the two groups. Significant differences were evaluated by False Discovery Rate.,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Fatima
bsdb:574/1/1,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,2 December 2021,Mmarin,Mmarin,"AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|91347|543|547;2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:574/1/2,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,2 December 2021,Mmarin,Mmarin,"AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|207244;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:574/2/1,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 18),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,2|1224|1236|91347|543|547,Complete,Folakunmi
bsdb:574/2/2,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 18),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|201174|84998|1643822|1643826|447020;2|1239|186801|3085636|186803|28050,Complete,Folakunmi
bsdb:574/3/1,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 3,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 60),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|1236|91347|543|547;2|976|200643|171549|1853231|283168;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:574/3/2,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 3,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 60),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|84998|1643822|1643826|447020;2|1239|186801|3082720|3118656|114627;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:574/4/1,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 4,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-18),azithromycin-lactulose treated (0-18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,3 December 2021,Mmarin,"Mmarin,Folakunmi","AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively

(day 18)",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,2|1239|186801|3085636|186803|207244,Complete,Folakunmi
bsdb:574/4/2,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 4,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-18),azithromycin-lactulose treated (0-18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,3 December 2021,Mmarin,"Mmarin,Folakunmi","AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively

(day 60)",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:574/5/1,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 5,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-60),azithromycin-lactulose treated (0-60),"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,20 February 2024,Folakunmi,Folakunmi,Significant differences in relative abundance between groups and time points,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,2|976|200643|171549|2005520|156973,Complete,Folakunmi
bsdb:574/5/2,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 5,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-60),azithromycin-lactulose treated (0-60),"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,20 February 2024,Folakunmi,Folakunmi,Significant differences in relative abundance between groups and time points,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3082720|3118656|114627;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:574/6/1,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 6,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated at day 18,azithromycin-lactulose at day 18,"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,20 February 2024,Folakunmi,Folakunmi,Significant differences in relative abundance between groups at day 18 time point,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|128827|1647;2|1239|909932|1843489|31977|906,Complete,Folakunmi
bsdb:574/7/1,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 7,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated at day 60,azithromycin-lactulose at day 60,"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,20 February 2024,Folakunmi,Folakunmi,Significant differences in relative abundance between groups at day 20 time point,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,2|976|200643|171549|2005520|156973,Complete,Folakunmi
bsdb:574/7/2,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 7,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated at day 60,azithromycin-lactulose at day 60,"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,20 February 2024,Folakunmi,Folakunmi,Significant differences in relative abundance between groups at day 20 time point,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3082720|3118656|114627;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:574/8/NA,Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 8,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 60),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:575/1/1,Study 575,prospective cohort,33824448,10.1038/s41390-021-01494-7,NA,"Ainonen S, Tejesvi MV, Mahmud MR, Paalanne N, Pokka T, Li W, Nelson KE, Salo J, Renko M, Vänni P, Pirttilä AM , Tapiainen T",Antibiotics at birth and later antibiotic courses: effects on gut microbiota,Pediatric research,2021,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Control group,perinatal antibiotics,Participants who received any perinatal antibiotics (all three perinatal groups combined),27,73,NA,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,table 2,16 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Composition of the gut microbiome in vaginally delivered infants (N = 100) exposed to perinatal antibiotics as compared with the control group after the first year of life.,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838,Complete,ChiomaBlessing
bsdb:575/1/2,Study 575,prospective cohort,33824448,10.1038/s41390-021-01494-7,NA,"Ainonen S, Tejesvi MV, Mahmud MR, Paalanne N, Pokka T, Li W, Nelson KE, Salo J, Renko M, Vänni P, Pirttilä AM , Tapiainen T",Antibiotics at birth and later antibiotic courses: effects on gut microbiota,Pediatric research,2021,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Control group,perinatal antibiotics,Participants who received any perinatal antibiotics (all three perinatal groups combined),27,73,NA,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,table 2,16 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Composition of the gut microbiome in vaginally delivered infants (N = 100) exposed to perinatal antibiotics as compared with the control group after the first year of life.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549|815|816;2|976|200643,Complete,ChiomaBlessing
bsdb:575/2/NA,Study 575,prospective cohort,33824448,10.1038/s41390-021-01494-7,NA,"Ainonen S, Tejesvi MV, Mahmud MR, Paalanne N, Pokka T, Li W, Nelson KE, Salo J, Renko M, Vänni P, Pirttilä AM , Tapiainen T",Antibiotics at birth and later antibiotic courses: effects on gut microbiota,Pediatric research,2021,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,Antibiotic courses,All perinatal groups that received any antibiotic courses,71,28,NA,16S,NA,Ion Torrent,ANOVA,0.05,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:576/1/1,Study 576,case-control,24316595,10.1093/jnci/djt300,https://pubmed.ncbi.nlm.nih.gov/24316595/,"Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB , Yang L",Human gut microbiome and risk for colorectal cancer,Journal of the National Cancer Institute,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls with no cancer,patients with adenocarcinoma,"patients with newly diagnosed, histologically confirmed adenocarcinoma of the colon or rectum",94,47,1 year,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,sex","age,body mass index,race,sex,smoking behavior",unchanged,decreased,NA,NA,NA,NA,Signature 1,Table 1,10 December 2021,Itslanapark,"Itslanapark,Claregrieve1,ChiomaBlessing",Differential microbial abundance between patients with colorectal cancer and control subjects,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|3085636|186803|33042;2|1239|186801|186802;2|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:577/1/1,Study 577,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M , Wang L",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 1,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female,Male,Male participants,32,15,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Figure 2",12 December 2021,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between men and women,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",2|201174;2|1239;2|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:577/1/2,Study 577,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M , Wang L",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 1,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female,Male,Male participants,32,15,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1,14 December 2021,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between men and women,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Claregrieve1
bsdb:577/2/1,Study 577,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M , Wang L",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 2,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female normal controls,Female participants with asthma,Females participants with asthma,17,15,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2b,31 August 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between female participants with asthma and female normal controls,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,Lwaldron
bsdb:577/2/3,Study 577,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M , Wang L",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 2,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female normal controls,Female participants with asthma,Females participants with asthma,17,15,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 3,Figure 3b,31 August 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between female participants with asthma and female normal controls,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:578/1/1,Study 578,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J, Xavier BB, Stewardson A, Coenen S, Godycki-Cwirko M, Adriaenssens N, Kowalczyk A, Lammens C, Harbarth S, Goossens H , Malhotra-Kumar S",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,"16S rDNA, 16S rRNA, antibiotic resistance, compositional changes, culture independent, faecal flora, gastrointestinal flora, stool, urinary tract infections",Experiment 1,"Belgium,Poland",Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Control group,Antibiotic treated - T2,Receiving nitrofurantoin treatment (100 mg three times daily for 3–15 days),5,8,2 months,16S,345,Roche454,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,11 December 2021,Mmarin,Mmarin,"changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43.
Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.",decreased,k__Bacteria|p__Bacteroidota,2|976,Complete,Peace Sandy
bsdb:578/2/1,Study 578,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J, Xavier BB, Stewardson A, Coenen S, Godycki-Cwirko M, Adriaenssens N, Kowalczyk A, Lammens C, Harbarth S, Goossens H , Malhotra-Kumar S",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,"16S rDNA, 16S rRNA, antibiotic resistance, compositional changes, culture independent, faecal flora, gastrointestinal flora, stool, urinary tract infections",Experiment 2,"Belgium,Poland",Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Antibiotic treated (day 1),Antibiotic treated (day 5-15),Receiving nitrofurantoin treatment (100 mg three times daily for 3–15 days),8,8,2 months,16S,345,Roche454,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,14 January 2022,Mmarin,"Mmarin,Peace Sandy","changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.",increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Peace Sandy
bsdb:578/3/1,Study 578,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J, Xavier BB, Stewardson A, Coenen S, Godycki-Cwirko M, Adriaenssens N, Kowalczyk A, Lammens C, Harbarth S, Goossens H , Malhotra-Kumar S",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,"16S rDNA, 16S rRNA, antibiotic resistance, compositional changes, culture independent, faecal flora, gastrointestinal flora, stool, urinary tract infections",Experiment 3,"Belgium,Poland",Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Control (day 1),Control (day 5-15),Did not receive nitrofurantoin treatment,5,5,2 months,16S,345,Roche454,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,14 January 2022,Mmarin,"Mmarin,Peace Sandy","changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.",increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Peace Sandy
bsdb:579/1/1,Study 579,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen JJ, He S, Fang L, Wang B, Bai SJ, Xie J, Zhou CJ, Wang W , Xie P",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young Healthy Controls(aged 18-29 years),Middle-aged HC (aged 30-59 years),Subjects without major depressive disorder between the ages of 30 to 59 years.,27,44,NOT SPECIFIED,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 9 & Figure 10(A),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1",Differential microbial abundance by LefSe between young HCs and middle-aged HCs,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,2|1239|186801|186802|543314,Complete,Claregrieve1
bsdb:579/1/2,Study 579,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen JJ, He S, Fang L, Wang B, Bai SJ, Xie J, Zhou CJ, Wang W , Xie P",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young Healthy Controls(aged 18-29 years),Middle-aged HC (aged 30-59 years),Subjects without major depressive disorder between the ages of 30 to 59 years.,27,44,NOT SPECIFIED,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 9 & Figure 10(A),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1",Differential microbial abundance by LefSe between young HCs and middle-aged HCs,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|186828;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|1239|91061|186826|186828|117563;2|1239|909932|909929|1843491|158846;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:579/2/1,Study 579,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen JJ, He S, Fang L, Wang B, Bai SJ, Xie J, Zhou CJ, Wang W , Xie P",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young MDD (aged 18-29 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,25,45,Not specified,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 9 & Figure 10(B),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1",Differential microbial abundance by LefSe between young MDDs and middle-aged MDDs,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|3085636|186803|207244;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|644652;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:579/2/2,Study 579,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen JJ, He S, Fang L, Wang B, Bai SJ, Xie J, Zhou CJ, Wang W , Xie P",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young MDD (aged 18-29 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,25,45,Not specified,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 9 & Figure 10(B),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1",Differential microbial abundance by LefSe between young MDDs and middle-aged MDDs,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|1843488|909930;2|1239|909932|909929|1843491|158846;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:579/3/1,Study 579,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen JJ, He S, Fang L, Wang B, Bai SJ, Xie J, Zhou CJ, Wang W , Xie P",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Middle-aged HC (aged 30-59 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,44,45,Not specified,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 7,30 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance by LefSe between middle-aged HCs and MDDs,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1224|28216|80840|995019;2|1239|909932|1843488|909930;2|976|200643|171549|815;2|976|200643|171549|171552;2|1239|186801|3082720|3030910|109326;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|459786;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|33042;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:579/3/2,Study 579,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen JJ, He S, Fang L, Wang B, Bai SJ, Xie J, Zhou CJ, Wang W , Xie P",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Middle-aged HC (aged 30-59 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,44,45,Not specified,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 7,30 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance by LefSe between middle-aged HCs and MDDs,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|186801|3085636|186803;2|201174|84998|84999|84107;2|1239|91061|186826|1300;2|1239|186801|186802|186806;2|201174|1760|2037|2049;2|1239|186801|186802|543314|2137877;2|1239|186801|3085636|186803|207244;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|201174|84998|1643822|1643826|84111;2|1239|186801|3085636|186803|841;2|1239|186801|186802|186806|1730;2|201174|1760|2037|2049|1654,Complete,Claregrieve1
bsdb:579/4/1,Study 579,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen JJ, He S, Fang L, Wang B, Bai SJ, Xie J, Zhou CJ, Wang W , Xie P",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young HC (aged 18-29 years),Young MDD (aged 18-29 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 18-29 years.,27,25,Not specified,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 6,30 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance by LefSe between young HCs and MDDs,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",2|1239|186801|186802|31979;2|1239|186801|3082720|186804;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|31979|1485|1506,Complete,ChiomaBlessing
bsdb:580/1/1,Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HIV-uninfected individuals,HIV+ individuals,People with HIV,93,75,5 days,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1 D,15 December 2021,Joyessa,"Joyessa,Claregrieve1",Differential abundance in saliva of HIV- individuals vs HIV+ individuals,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Candidatus Absconditabacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp.",2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|195950;2|221235;2|1224|28216|206351|481;2|976|200643|171549|171552|838|1486938;2|1239|186801|3085636|186803|830|28121,Complete,Claregrieve1
bsdb:580/1/2,Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HIV-uninfected individuals,HIV+ individuals,People with HIV,93,75,5 days,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1 D,16 December 2021,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance in saliva of HIV- individuals vs HIV+ individuals,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:580/2/1,Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Smoking behavior,Nicotine dependence","EFO:0003768,EFO:0004318",HIV+ non-smokers,HIV+ smokers,People with HIV who currently smoke cigarettes,26,23,5 days,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2E,15 December 2021,Joyessa,"Joyessa,Claregrieve1",Differential bacterial abundance in oral samples from HIV+ individuals by smoking status,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552|1283313;2|976|117743|200644|2762318|59735;2|29547|3031852|213849|72294|194;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|43994;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1224|28216|206351|481;2|1224|1236|135625|712,Complete,Claregrieve1
bsdb:580/2/2,Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Smoking behavior,Nicotine dependence","EFO:0003768,EFO:0004318",HIV+ non-smokers,HIV+ smokers,People with HIV who currently smoke cigarettes,26,23,5 days,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2E,16 December 2021,Joyessa,"Joyessa,Claregrieve1",Differential bacterial abundance in oral samples from HIV+ individuals by smoking status,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:580/3/1,Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Abnormality on pulmonary function testing,HP:0030878,HIV+ patients with normal DLCO,HIV+ patients with reduced DLCO,HIV+ patients with DLCO% predicted <80%,38,37,5 days,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3 I,16 December 2021,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:580/3/2,Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Abnormality on pulmonary function testing,HP:0030878,HIV+ patients with normal DLCO,HIV+ patients with reduced DLCO,HIV+ patients with DLCO% predicted <80%,38,37,5 days,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3I,16 December 2021,Joyessa,"Joyessa,Claregrieve1,Merit",Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",2|976|200643|171549|171552|1283313;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|1164882;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|1213720;2|1224|28216|206351|481;2|976|200643|171549|171552;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|192066;2|1224|28216|206351|481;2|1224|28216|206351;2|1239|1737404|1737405|1570339|543311|1944660;2|32066|203490|203491|203492;2|32066|203490|203491,Complete,Claregrieve1
bsdb:581/1/1,Study 581,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A, Qiu X, Lai W, Li W, Zhang L, Zhu X, He S, Duan J , Chen L",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,"Drug-resistant epilepsy, Epilepsy, Microbiome, Microbiota, Ruminococcus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Drug sensitive epilepsy,Drug resistant epilepsy,Drug resistant epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),49,42,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 2,16 December 2021,Fatima,Fatima,Lefse analysis showing microbiome differences in patients with drug sensitive epilepsy and  drug sensitive epilepsy,decreased,"k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",2;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976;2|976|200643;2|976|200643|171549|2005519|397864,Complete,Lwaldron
bsdb:581/1/2,Study 581,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A, Qiu X, Lai W, Li W, Zhang L, Zhu X, He S, Duan J , Chen L",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,"Drug-resistant epilepsy, Epilepsy, Microbiome, Microbiota, Ruminococcus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Drug sensitive epilepsy,Drug resistant epilepsy,Drug resistant epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),49,42,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 2,16 December 2021,Fatima,Fatima,Lefse analysis showing microbiome differences among drug resistance and drug sensitive epilepsy,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Archaea,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",2|1239|526524;2|1224|1236|2887326|468;2|1239;2|1239|186801|3085636|186803;2|1239|909932;2|1239|909932|909929;2|1239|186801|3085636|186803|841;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930;2157|28890|183925;2157|28890|183925|2158|2159;2157|28890|183925|2158|2159|2172;2157|28890|183925|2158;2|32066;2|32066|203490;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|33042;2|1224|28216|206351;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2157;2157|28890;2|74201|203494|48461;2|74201;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|203557;2|74201|203494;2|1239|186801|186802|204475;2|1239|186801|186802|216572|1263;2|976|200643|171549|171552|577309;2|1239|526524|526525|2810280|100883;2|1224|28216|80840|80864|80865;2|95818;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827|61170;2|1239|526524|526525|128827;2|201174|84998|84999|1643824|1380;2|1239|526524|526525,Complete,Fatima
bsdb:581/2/NA,Study 581,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A, Qiu X, Lai W, Li W, Zhang L, Zhu X, He S, Duan J , Chen L",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,"Drug-resistant epilepsy, Epilepsy, Microbiome, Microbiota, Ruminococcus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Healthy controls,Drug resistant epilepsy,Drug sensitive epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),65,49,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:582/1/1,Study 582,case-control,32370168,10.3390/cancers12051142,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281174/,"Clos-Garcia M, Garcia K, Alonso C, Iruarrizaga-Lejarreta M, D'Amato M, Crespo A, Iglesias A, Cubiella J, Bujanda L , Falcón-Pérez JM",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,77,89,none,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4B,2 January 2022,Itslanapark,Itslanapark,Difference analysis at genus level between Colorectal Cancer patients and Healthy Controls.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|91061|1385|90964|1279,Complete,Rimsha
bsdb:582/1/2,Study 582,case-control,32370168,10.3390/cancers12051142,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281174/,"Clos-Garcia M, Garcia K, Alonso C, Iruarrizaga-Lejarreta M, D'Amato M, Crespo A, Iglesias A, Cubiella J, Bujanda L , Falcón-Pérez JM",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,77,89,none,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4B,2 January 2022,Itslanapark,Itslanapark,Difference analysis at genus level between Colorectal Cancer patients and Healthy Controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|91061|186826|1300|1301,Complete,Rimsha
bsdb:582/2/1,Study 582,case-control,32370168,10.3390/cancers12051142,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281174/,"Clos-Garcia M, Garcia K, Alonso C, Iruarrizaga-Lejarreta M, D'Amato M, Crespo A, Iglesias A, Cubiella J, Bujanda L , Falcón-Pérez JM",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,adenoma patients,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,65,89,none,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4C,15 May 2022,Rimsha,Rimsha,Difference analysis at genus level between Colorectal Cancer patients and adenoma patients.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|1737404|1737405|1570339|543311;2|1239|91061|1385|90964|1279,Complete,Rimsha
bsdb:582/2/2,Study 582,case-control,32370168,10.3390/cancers12051142,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281174/,"Clos-Garcia M, Garcia K, Alonso C, Iruarrizaga-Lejarreta M, D'Amato M, Crespo A, Iglesias A, Cubiella J, Bujanda L , Falcón-Pérez JM",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,adenoma patients,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,65,89,none,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4C,15 May 2022,Rimsha,Rimsha,Difference analysis at genus level between Colorectal Cancer patients and adenoma patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|572511;2|201174|84998|1643822|1643826|447020,Complete,Rimsha
bsdb:583/1/1,Study 583,"cross-sectional observational, not case-control",32024712,10.1128/mSphere.00798-19,https://pubmed.ncbi.nlm.nih.gov/32024712/,"Annavajhala MK, Khan SD, Sullivan SB, Shah J, Pass L, Kister K, Kunen H, Chiang V, Monnot GC, Ricupero CL, Mazur RA, Gordon P, de Jong A, Wadhwa S, Yin MT, Demmer RT , Uhlemann AC",Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy,mSphere,2020,"HIV, antiretroviral agents, antiretroviral therapy, immune dysfunction, immune system activation, mycobiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Oral cavity,Feces","UBERON:0000167,UBERON:0001988",HIV infection,EFO:0000764,PLWH >50 years old with no/mild periodontitis,PLWH >50 years old with severe periodontitis,Patients with severe periodontal disease,4,22,3 Months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,race,sex",NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S5 and Table S6,18 January 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy","Differentially abundant fungal taxa in saliva and subgingival plaque from patients with severe vs. no/mild periodontal disease (DESeq2, p<0.05, padj (FDR)<0.05)",increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|3239874|2916678|766764|5475|5480;2|976|200643|171549|171552|838;2|32066|203490|203491|203492|848;2|201174|1760|85006|1268|32207;2|1224|28216|206351|481|32257;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|437755;2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|724,Complete,Peace Sandy
bsdb:583/1/2,Study 583,"cross-sectional observational, not case-control",32024712,10.1128/mSphere.00798-19,https://pubmed.ncbi.nlm.nih.gov/32024712/,"Annavajhala MK, Khan SD, Sullivan SB, Shah J, Pass L, Kister K, Kunen H, Chiang V, Monnot GC, Ricupero CL, Mazur RA, Gordon P, de Jong A, Wadhwa S, Yin MT, Demmer RT , Uhlemann AC",Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy,mSphere,2020,"HIV, antiretroviral agents, antiretroviral therapy, immune dysfunction, immune system activation, mycobiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Oral cavity,Feces","UBERON:0000167,UBERON:0001988",HIV infection,EFO:0000764,PLWH >50 years old with no/mild periodontitis,PLWH >50 years old with severe periodontitis,Patients with severe periodontal disease,4,22,3 Months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,race,sex",NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S5 and Table S6,24 January 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy","Differentially abundant fungal taxa in saliva and subgingival plaque from patients with severe vs. no/mild periodontal disease (DESeq2, p<0.05, padj (FDR)<0.05)",decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces hansenii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Exserohilum|s__Exserohilum turcicum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia|s__Tausonia pullulans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2759|4751|4890|3239874|2916678|766764|5475|42374;2759|4751|4890|3239874|2916678|766764|4958|4959;2759|4751|4890|147541|92860|28556|91493|93612;2759|4751|5204|155616|90883|1851551|415704|82525;2759|4751|4890|4891|4892|4893|4930|4932;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:584/1/1,Study 584,"cross-sectional observational, not case-control",26288821,10.1016/j.ebiom.2015.04.010,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535156/,"Goedert JJ, Gong Y, Hua X, Zhong H, He Y, Peng P, Yu G, Wang W, Ravel J, Shi J , Zheng Y",Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening: A Population-based Study,EBioMedicine,2015,"Cancer screening, China, Colorectal adenoma, Colorectal cancer, Feces, Microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,normal participants,cra patients,patients with precancerous colorectal adenoma,24,20,none,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table 5,2 January 2022,Itslanapark,Itslanapark,differential relative abundance at the taxa and genera level between CRA patients and controls,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1224;2|1224|1236|72274|135621;2|1224|1236|118969|444;2|1224|1236|135619|28256;2|1224|1236|91347|543;2|1224|1236|91347|1903411|613;2|1224|1236|91347|543|620;2|1224|1236|91347|543|590;2|1224|1236|91347|1903409|53335;2|1224|1236|91347|1903414|581;2|1224|1236|91347|543|158851;2|1224|1236|91347|543|561,Complete,Claregrieve1
bsdb:585/1/1,Study 585,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah MS, DeSantis T, Yamal JM, Weir T, Ryan EP, Cope JL , Hollister EB",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,"Colorectal mucosa,Feces","UBERON:0013067,UBERON:0001988",Colorectal cancer,EFO:0005842,Healthy tumor-adjacent biopsy,CRC tumor biopsy,Colorectal tumor tissues,294,294,Cases with previous chemotherapy and antibiotic use were excluded as well as patients with antibiotic use within 1 - 3 months prior to sample collection.,16S,NA,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Result text",11 March 2024,Scholastica,Scholastica,"Pairwise differences in CRC tumor vs. healthy adjacent tissue. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy samples and adjacent non-affected tissue microbiome(n = 294 pairs, 588 samples)",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota",2|32066|203490|203491|203492|848;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|91061|186826|1300|1301;2|201174,Complete,NA
bsdb:585/1/2,Study 585,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah MS, DeSantis T, Yamal JM, Weir T, Ryan EP, Cope JL , Hollister EB",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,"Colorectal mucosa,Feces","UBERON:0013067,UBERON:0001988",Colorectal cancer,EFO:0005842,Healthy tumor-adjacent biopsy,CRC tumor biopsy,Colorectal tumor tissues,294,294,Cases with previous chemotherapy and antibiotic use were excluded as well as patients with antibiotic use within 1 - 3 months prior to sample collection.,16S,NA,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Result text",11 March 2024,Scholastica,Scholastica,"Description: Pairwise differences in CRC tumor vs. healthy adjacent tissue. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy samples and adjacent non-affected tissue microbiome(n = 294 pairs, 588 samples)",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550;2|1239|186801|186802|216572,Complete,NA
bsdb:585/2/1,Study 585,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah MS, DeSantis T, Yamal JM, Weir T, Ryan EP, Cope JL , Hollister EB",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,"Feces,Colorectal mucosa","UBERON:0001988,UBERON:0013067",Colorectal cancer,EFO:0005842,Tumor biopsy,Fecal samples,Fecal samples from the same colorectal case,42,42,Cases with previous chemotherapy and antibiotic use were excluded as well as patients with antibiotic use within 1 - 3 months prior to sample collection.,16S,NA,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2B, Result text",11 March 2024,Scholastica,Scholastica,"Pairwise differences in tumor biopsy fecal samples. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy and fecal samples (n = 42 pairs, 84 samples)",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511;2|201174|1760|85004|31953|1678,Complete,NA
bsdb:585/2/2,Study 585,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah MS, DeSantis T, Yamal JM, Weir T, Ryan EP, Cope JL , Hollister EB",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,"Feces,Colorectal mucosa","UBERON:0001988,UBERON:0013067",Colorectal cancer,EFO:0005842,Tumor biopsy,Fecal samples,Fecal samples from the same colorectal case,42,42,Cases with previous chemotherapy and antibiotic use were excluded as well as patients with antibiotic use within 1 - 3 months prior to sample collection.,16S,NA,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, Result text",11 March 2024,Scholastica,Scholastica,"Pairwise differences in tumor biopsy fecal samples. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy and fecal samples (n = 42 pairs, 84 samples)",decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|32066|203490|203491|203492|848;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:586/1/1,Study 586,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E, Bacci G, Chiellini C, Fagorzi C, Niccolai E, Taddei A, Ricci F, Ringressi MN, Borrelli R, Melli F, Miloeva M, Bechi P, Mengoni A, Fani R , Amedei A",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,"Fusobacterium nucleatum, colorectal cancer, gut microbiota, oral microbiota, quantitative polymerase chain reaction, taxonomic analysis",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal Cancer Patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections,10,10,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 7A,12 January 2022,Itslanapark,"Itslanapark,Peace Sandy,Atrayees,Folakunmi","Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and
considering the three body sites sampled in this study, namely: biopsy (red), saliva (green), and stool (blue). (A) Different body sites showed a characteristic taxonomic
composition with major clades strongly associated with a particular site. Proteobacteria were mostly associated with biopsy samples whereas Fusobacteria and
Bacteroidetes were mainly associated with saliva and stool samples, respectively.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis",2|976|200643|171549|815;2|976|200643|171549;2|976|200643;2|1239|186801;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802;2|1239|186801|186802|216572;2|976|200643|171549|171551;2|976|200643|171549|171550;2;2|1239|186801|186802|539000,Complete,Folakunmi
bsdb:586/2/1,Study 586,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E, Bacci G, Chiellini C, Fagorzi C, Niccolai E, Taddei A, Ricci F, Ringressi MN, Borrelli R, Melli F, Miloeva M, Bechi P, Mengoni A, Fani R , Amedei A",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,"Fusobacterium nucleatum, colorectal cancer, gut microbiota, oral microbiota, quantitative polymerase chain reaction, taxonomic analysis",Experiment 2,Italy,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal cancer Patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections.,10,10,3 months,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,increased,decreased,NA,NA,NA,Signature 1,Figure 7A,25 January 2022,Itslanapark,"Itslanapark,Adanwa,Peace Sandy,Folakunmi","Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and
considering the three body sites sampled in this study, namely: biopsy (red), saliva (green), and stool (blue). (A) Different body sites showed a characteristic taxonomic
composition with major clades strongly associated with a particular site. Proteobacteria were mostly associated with biopsy samples whereas Fusobacteria and
Bacteroidetes were mainly associated with saliva and stool samples, respectively.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|1239|91061|1385;2|1239|91061;2|1224|28216;2|976|117743|200644|49546;2|976|117743|200644;2|32066|203490;2|32066|203490|203491|1129771;2|201174|1760|85006|1268;2|201174|1760|85006;2|1239|909932;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|1236|135625|712;2|976|200643|171549|171552;2|1239|909932|909929;2|1239|91061|186826|1300;2|1239|909932|1843489|31977;2|95818;2|1239|91061|186826,Complete,Folakunmi
bsdb:586/3/1,Study 586,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E, Bacci G, Chiellini C, Fagorzi C, Niccolai E, Taddei A, Ricci F, Ringressi MN, Borrelli R, Melli F, Miloeva M, Bechi P, Mengoni A, Fani R , Amedei A",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,"Fusobacterium nucleatum, colorectal cancer, gut microbiota, oral microbiota, quantitative polymerase chain reaction, taxonomic analysis",Experiment 3,Italy,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Healthy Controls,Biopsy samples of colorectal cancer patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections.,10,10,3 months,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure 7A,10 January 2024,Folakunmi,Folakunmi,"Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and considering the three body sites sampled in this study, namely: biopsy, saliva, and stool.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|1239|186801|3085636|186803;2|32066|203490|203491|203492;2|1224|28211|356;2|1224|28211;2|28221;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236,Complete,Folakunmi
bsdb:587/1/1,Study 587,"cross-sectional observational, not case-control",31794002,10.1093/ntr/ntz220,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364824/pdf/ntz220.pdf,"Nolan-Kenney R, Wu F, Hu J, Yang L, Kelly D, Li H, Jasmine F, Kibriya MG, Parvez F, Shaheen I, Sarwar G, Ahmed A, Eunus M, Islam T, Pei Z, Ahsan H , Chen Y",The Association Between Smoking and Gut Microbiome in Bangladesh,Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco,2020,NA,Experiment 1,Bangladesh,Homo sapiens,Feces,UBERON:0001988,"Nicotine dependence,Smoking behavior","EFO:0003768,EFO:0004318",Never smokers,Current Smokers,Current smokers of cigarettes and bidis were categorized as current smokers,151,62,1 month.,16S,34,Illumina,"Beta Binomial Regression,Logistic Regression",0.05,TRUE,NA,NA,"age,body mass index,education level,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,4 January 2022,Joyessa,"Joyessa,Aiyshaaaa,Peace Sandy,ChiomaBlessing",Relative Abundances or Presence/ Absence of significant taxa in current smokers compared to never-smokers.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia",2|1239|526524|526525|2810280|135858;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524,Complete,ChiomaBlessing
bsdb:587/2/1,Study 587,"cross-sectional observational, not case-control",31794002,10.1093/ntr/ntz220,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364824/pdf/ntz220.pdf,"Nolan-Kenney R, Wu F, Hu J, Yang L, Kelly D, Li H, Jasmine F, Kibriya MG, Parvez F, Shaheen I, Sarwar G, Ahmed A, Eunus M, Islam T, Pei Z, Ahsan H , Chen Y",The Association Between Smoking and Gut Microbiome in Bangladesh,Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco,2020,NA,Experiment 2,Bangladesh,Homo sapiens,Feces,UBERON:0001988,"Nicotine dependence,Smoking behavior","EFO:0003768,EFO:0004318",Never smokers,Current Smokers,"Current smokers of cigarettes and bidis were categorized as current smokers, further assessed their association with packs of cigarettes smoked",151,62,1 month.,16S,34,Illumina,"Beta Binomial Regression,Logistic Regression",0.05,TRUE,NA,NA,"age,body mass index,education level,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 5,2 February 2024,ChiomaBlessing,ChiomaBlessing,Relative Abundances or Presence/ Absence of Significant Bacterial Taxa Associated With One Increase in Packs Smoked,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",2|1239|526524|526525;2|1239|186801|3082720|186804;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|909932|909929|1843491|52225,Complete,ChiomaBlessing
bsdb:588/1/1,Study 588,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J , Lee KH",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy subjects,colorectal cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,17,21,1 month,16S,34,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,5 January 2022,Itslanapark,"Itslanapark,Chloe",differential abundance of bacteria in patients with colorectal cancer and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula",2|1239|91061|186826|186827|46123;2|1224|1236|2887326|468|469;2|201174|84998|84999|84107|33870;2|1224|1236|118969|118968|776;2|1239|91061|186826|33958|1243;2|1224|28216|80840|119060|131079;2157|28890|183925|2158|2159|2172;2|201174|1760|85006|1268|32207;2|1239|186801|3085636|186803|100132;2|1224|1236|135624|83763|674963;2|74201|203494|48461|203557|574899,Complete,Chloe
bsdb:588/1/2,Study 588,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J , Lee KH",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy subjects,colorectal cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,17,21,1 month,16S,34,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,5 January 2022,Itslanapark,"Itslanapark,Chloe",differential abundance of bacteria in patients with colorectal cancer and healthy controls,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,2|1239|186801|186802|216572|119852,Complete,Chloe
bsdb:588/2/1,Study 588,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J , Lee KH",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,healthy subjects,polyps patients,persons aged 25–95 years old with polyps,17,21,1 month,16S,NA,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,8 March 2023,Chloe,Chloe,"The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",2|1239|186801|186802|216572|244127;2|1239|909932|909929|1843491|52225,Complete,Chloe
bsdb:588/2/2,Study 588,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J , Lee KH",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,healthy subjects,polyps patients,persons aged 25–95 years old with polyps,17,21,1 month,16S,NA,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,8 March 2023,Chloe,Chloe,"The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.",decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Cytophaga",2|29547|3031852|213849|72294|194;2|1239|91061|186826|81852|1350;2|1224|1236|72274|135621|286;2|976|768503|768507|89373|978,Complete,Chloe
bsdb:588/3/1,Study 588,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J , Lee KH",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,polyps patients,cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,21,21,1 month,16S,NA,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,8 March 2023,Chloe,Chloe,"The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|201174|1760|2037|2049|1654;2|29547|3031852|213849|72294|194;2|1239|91061|186826|81852|1350;2|201174|84998|1643822|1643826|84108;2|508458|649775|649776|3029088|638847;2|201174|84998|84999|84107|33870;2157|28890|183925|2158|2159|2172;2|1239|186801|3082720|186804|1257;2|1239|91061|186826|186827|46123;2|1224|1236|118969|118968|776;2|74201|203494|48461|203557|574899;2|1239|91061|186826|33958|1243;2|1239|91061|186826|33958|46255,Complete,Chloe
bsdb:588/3/2,Study 588,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J , Lee KH",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,polyps patients,cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,21,21,1 month,16S,NA,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,8 March 2023,Chloe,Chloe,NA,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",2|1224|1236|135624|84642|642;2|1239|186801|3085636|186803|100132;2|1239|186801|186802|216572|119852;2|1239|909932|909929|1843491|52225;2|32066|203490|203491|1129771|34104,Complete,Chloe
bsdb:589/1/1,Study 589,case-control,23940645,10.1371/journal.pone.0070803,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735522/,"Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL , Ryan EP",Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control,CRC patients,recently diagnosed colon cancer patients prior to surgery for colonic resection,11,10,2 months,16S,4,Roche454,"ANOVA,T-Test",0.01,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Table 3,6 January 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Atrayees",Bacterial species significantly over-represented in CRC stool samples.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter farmeri,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter",2|74201|203494|48461|1647988|239934|239935;2|1239|909932|1843488|909930|33024;2|1224|1236|91347|543|544|67824;2|1239|186801|3082720|3118653|65402,Complete,Atrayees
bsdb:589/1/2,Study 589,case-control,23940645,10.1371/journal.pone.0070803,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735522/,"Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL , Ryan EP",Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control,CRC patients,recently diagnosed colon cancer patients prior to surgery for colonic resection,11,10,2 months,16S,4,Roche454,"ANOVA,T-Test",0.01,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Table 2,6 January 2022,Itslanapark,"Itslanapark,Aiyshaaaa",Bacterial species that were significantly more abundant in the stool of healthy individuals compared to CRC patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio ruminis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus",2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|329854;2|1239|186801|3085636|186803|572511|40520;2|1239|909932|1843489|31977|39948|218538;2|1239|909932|1843489|31977|39948|39950;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|140625|140626;2|1239|186801|3085636|186803|28050|28052;2|1239|909932|909929|1843491|158846|158847;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552|2974251|28135;2|1239|186801|3085636|186803|46205|46206;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|186802|216572|1263|1264,Complete,Atrayees
bsdb:590/1/1,Study 590,time series / longitudinal observational,31078141,10.1186/s40168-019-0687-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf,"Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillén Y, Langhorst J, Parera M, Mandomando I, Carrillo J, Urrea V, Rodríguez C, Casadellà M, Calle ML, Clotet B, Blanco J, Naniche D , Paredes R",Evolution of the gut microbiome following acute HIV-1 infection,Microbiome,2019,"AIDS, HIV-1, HIV-1 pathogenesis, Microbiome, acute HIV-1 infection",Experiment 1,Mozambique,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-1-negative individuals,Recently HIV-1 infected individuals,"Individuals with recent HIV infection (RHI), defined as a negative or indeterminate rapid test serology (first test negative or first test positive and second test negative) and positive HIV-1 viremia",54,49,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,increased,Signature 1,Figure 2,8 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between recently HIV-1 infected and HIV-negative individuals,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,2|1239|186801|3085636|186803|189330,Complete,Claregrieve1
bsdb:590/1/2,Study 590,time series / longitudinal observational,31078141,10.1186/s40168-019-0687-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf,"Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillén Y, Langhorst J, Parera M, Mandomando I, Carrillo J, Urrea V, Rodríguez C, Casadellà M, Calle ML, Clotet B, Blanco J, Naniche D , Paredes R",Evolution of the gut microbiome following acute HIV-1 infection,Microbiome,2019,"AIDS, HIV-1, HIV-1 pathogenesis, Microbiome, acute HIV-1 infection",Experiment 1,Mozambique,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-1-negative individuals,Recently HIV-1 infected individuals,"Individuals with recent HIV infection (RHI), defined as a negative or indeterminate rapid test serology (first test negative or first test positive and second test negative) and positive HIV-1 viremia",54,49,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,increased,Signature 2,Figure 2,8 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between recently HIV-1 infected and HIV-negative individuals,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:591/1/1,Study 591,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H , Huang J",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV– individuals,HIV+ individuals,HIV positive patients,544,744,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,decreased,decreased,unchanged,decreased,decreased,Signature 1,Figure 8,3 April 2023,Atrayees,"Atrayees,ChiomaBlessing",Differential enrichment of genus or species in HIV+ and HIV– individuals.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta",2|1239|186801|3085636|186803|572511;2|1239|526524|526525|128827|118747;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|3085642|580596|2049021;2|1224|1236|91347|543|544;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924|872;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|3030910|86331;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|1239|186801|186802|186806|113286;2|1239|91061|1385|90964|1279;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|2719313|358743;2|1239|186801|3085636|186803|189330|39486;2|201174|84998|1643822|1643826|84111|84112,Complete,ChiomaBlessing
bsdb:591/1/2,Study 591,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H , Huang J",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV– individuals,HIV+ individuals,HIV positive patients,544,744,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,decreased,decreased,unchanged,decreased,decreased,Signature 2,Figure 8,3 April 2023,Atrayees,"Atrayees,ChiomaBlessing",Differential enrichment of genus or species in HIV+ and HIV– individuals.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|84998|1643822|1643826|447020;2|1224|28211|356|82115|357;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|830;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|140625;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|119852;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|32066|203490|203491|1129771|168808;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:591/2/1,Study 591,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H , Huang J",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-MSM,MSM (men who have sex with men),Men who have sex with men,304,328,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,unchanged,decreased,decreased,decreased,decreased,Signature 1,Figure 9,23 January 2024,ChiomaBlessing,ChiomaBlessing,Differential enrichment of genus or species in MSM and non-MSM.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans",2|1224|1236|135625|712|416916;2|544448|31969|186332|186333|2152;2|1239|526524|526525|128827|118747;2|1239|186801|3085636|186803|830;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|200940|3031449|213115|194924|872;2|1239|909932|1843489|31977|39948;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|186807|2740;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|201174|84998|1643822|1643826|84108;2|1224|1236|135624|83763|83770;2|1224|28216|80840|995019|40544;2|256845|1313211|278082|255528|172900;2|1239|186801|3085636|186803|33042|33043;2|1239|186801|3085636|186803|189330|39486,Complete,ChiomaBlessing
bsdb:591/2/2,Study 591,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H , Huang J",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-MSM,MSM (men who have sex with men),Men who have sex with men,304,328,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,unchanged,decreased,decreased,decreased,decreased,Signature 2,Figure 9,23 January 2024,ChiomaBlessing,ChiomaBlessing,Differential enrichment of genus or species in MSM and non-MSM.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|526524|526525|128827|61170;2157|28890|183925|2158|2159|2172;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|976|200643|171549|171551|836;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:592/1/1,Study 592,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T , Yotsuyanagi H",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,"HIV, dysbiosis, human immunodeficiency virus, inflammation, microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV Patients,Patients with HIV infection,61,71,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, Figure 3",9 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between healthy controls and HIV-infected patients with CD4 counts > 500 cells/uL,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes",2|201174;2|1239|186801|3085636|186803|265975;2|1239|526524|526525|128827|123375;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|186801|186802|216572|1926663;2|201174|84998|84999|1643824|133925;2|201174|84998|1643822|1643826|580024;2|1239|186801|3082720|3030910|86331;2|1224|1236|135624;2|201174|84998|84999|1643824|2082587;2|1224|1236|135624|83763;2|1224|1236|135624|83763|83770;2|1239|909932|1843489|31977|906;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|84998|84999|84107|1473205;2|201174|84998|1643822|1643826|84108;2|201174|84998|84999|1643824;2|1239|526524|526525|128827|1573535;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|1239|526524|526525|128827;2|1239|909932|1843488|909930;2|1239|909932|1843488;2|1239|526524|526525|2810280|135858;2|201174|84998|1643822|1643826;2|976|200643|171549|171552|838;2|1239|526524|526525;2|976|200643|171549|171552;2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491;2|1239|909932|1843489|31977|39948;2|1239|91061;2|201174|84998;2|201174|84998|84999;2|1239|909932|1843489|31977;2|1239|909932|1843489;2|1239|909932|909929;2|1239|909932,Complete,Claregrieve1
bsdb:592/1/2,Study 592,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T , Yotsuyanagi H",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,"HIV, dysbiosis, human immunodeficiency virus, inflammation, microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV Patients,Patients with HIV infection,61,71,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,9 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between healthy controls and HIV-infected patients with CD4 counts > 500 cells/uL,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801;2|976|200643|171549|815|816;2|976|200643|171549|815;2|1224|1236|91347|543;2|1239|186801|3085636|186803|207244;2|1239|186801|3085656|3085657|2039302;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|1407607;2|976|200643|171549|171550;2|1224|1236|91347|543|547;2|1239|91061|186826|186828;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712;2|1224|1236|135625|712|724;2|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:593/1/1,Study 593,case-control,33013704,10.3389/fendo.2020.00628,NA,"Zhou L, Ni Z, Yu J, Cheng W, Cai Z , Yu C",Correlation Between Fecal Metabolomics and Gut Microbiota in Obesity and Polycystic Ovary Syndrome,Frontiers in endocrinology,2020,"biomarkers, gut microbiota, obesity, polycystic ovary syndrome, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese women without PCOS,Obese women with PCOS,Obese women with PCOS,15,18,3 months.,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3(G),6 July 2023,Atrayees,"Atrayees,Peace Sandy","LDA chart. The score was obtained by LDA analysis (linear regression analysis). The greater the LDA score, the greater the impact of the representative species abundance on the differences between groups. *p < 0.05; **p < 0.01.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2|1239|186801|3085636|186803|33042;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|1506577,Complete,Peace Sandy
bsdb:593/1/2,Study 593,case-control,33013704,10.3389/fendo.2020.00628,NA,"Zhou L, Ni Z, Yu J, Cheng W, Cai Z , Yu C",Correlation Between Fecal Metabolomics and Gut Microbiota in Obesity and Polycystic Ovary Syndrome,Frontiers in endocrinology,2020,"biomarkers, gut microbiota, obesity, polycystic ovary syndrome, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese women without PCOS,Obese women with PCOS,Obese women with PCOS,15,18,3 months.,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3(G),6 July 2023,Atrayees,"Atrayees,Peace Sandy","LDA chart. The score was obtained by LDA analysis (linear regression analysis). The greater the LDA score, the greater the impact of the representative species abundance on the differences between groups. *p < 0.05; **p < 0.01.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|171550|239759;2|976|200643|171549;2|976|200643|171549|1853231|574697;2|1239|186801|3082768|990719;2|1224|28216|80840|80864|283;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|1185407;2|1239|186801|186802;2|1239|186801|186802|216572|1892380;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803;2|544448|31969;2|544448;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572;2|1239|186801|186802|186807;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|3068309;2|1239|526524|526525|128827|123375;2|1239|186801|186802|216572|292632;2|976|200643|171549;2|976|200643|171549,Complete,Peace Sandy
bsdb:594/1/1,Study 594,"cross-sectional observational, not case-control",28328799,10.1097/MD.0000000000005821,https://pubmed.ncbi.nlm.nih.gov/28328799/,"Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD , Marconi VC",Oral microbiome in HIV-associated periodontitis,Medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Dental plaque,Internal cheek pouch,Saliva","UBERON:0016482,UBERON:0013640,UBERON:0001836",Periodontitis,EFO:0000649,HIV–,HIV+,"Participants who were positive for HIV-1 infection, as verified by ELISA and confirmed by Western blot.",10,40,NA,16S,4,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 1, Figure 3",10 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between HIV+ and HIV- participants,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1224|1236|135625|712|416916;2|1224|28216|206351|481|32257;2|1224|28216|206351|481|482;2|201174|1760|85006|1268|32207;2|1224|28216|206351|481;2|1224|1236|135625|712;2|1239|91061|186826|186827|46123,Complete,Claregrieve1
bsdb:594/1/2,Study 594,"cross-sectional observational, not case-control",28328799,10.1097/MD.0000000000005821,https://pubmed.ncbi.nlm.nih.gov/28328799/,"Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD , Marconi VC",Oral microbiome in HIV-associated periodontitis,Medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Dental plaque,Internal cheek pouch,Saliva","UBERON:0016482,UBERON:0013640,UBERON:0001836",Periodontitis,EFO:0000649,HIV–,HIV+,"Participants who were positive for HIV-1 infection, as verified by ELISA and confirmed by Western blot.",10,40,NA,16S,4,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 1, Figure 3",10 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between HIV+ and HIV- participants,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|909929|1843491|82202;2|976|200643|171549|2005525|195950;2|32066|203490|203491|1129771|32067;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:595/1/1,Study 595,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia-free,CRC patients,patients referred for colonoscopy that had cancerous tumors,61,53,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S2,19 January 2022,Itslanapark,"Itslanapark,Fatima",significant differences in the abundance of specific taxa,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|976|200643|171549|815|816;2|200940|3031449|213115|194924|35832;2|200940|3031449|213115|194924|872;2|32066;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|76859;2|32066|203490|203491|203492|848|851|76856;2|32066|203490|203491|203492|848|76857;2|32066|203490|203491|203492|848|155615;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171552|838|28133;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1224;2|1239|909932|909929|1843491|970;2|1239|186801|186802|216572|707003;2|1239|186801|3082720|186804|1257|341694;2|32066|203490|203491|1129771|32067|157688;2|1239|1737404|1737405|1570339|543311;2|32066|203490|203491|203492|848|860;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|815|816|817;2|200940|3031449|213115|194924|35832|35833;2|1224|28216|206351|481|482;2|29547|3031852|213849|72294|194|203;2|1239|909932|909929|1843491|970|69823;2|32066|203490|203491|1129771|32067|40542;2|1239|186801|3085636|186803|1506553|89153;2|1239|186801|3085636|186803|1506553|1512,Complete,Fatima
bsdb:595/1/2,Study 595,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia-free,CRC patients,patients referred for colonoscopy that had cancerous tumors,61,53,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Figure S2,19 January 2022,Itslanapark,"Itslanapark,Fatima",significant differences in the abundance of specific taxa,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1224|1236|2887326|468|469;2|1239|186801|3085636|186803|2569097|39488;2|1239;2|29547|3031852|213849|72294|194;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40518;2|1239|91061|186826|1300|1301|1304;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:595/2/1,Study 595,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Adenoma patients,CRC patients,patients referred for colonoscopy that had cancerous tumors,42,53,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S2,7 March 2023,Fatima,Fatima,significant differences in the abundance of specific taxa between CRC and Adenoma patients,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|32066|203490;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|76859;2|32066|203490|203491|203492|848|851|76856;2|32066|203490|203491|203492|848|76857;2|32066|203490|203491|203492|848|155615;2|201174|84998|84999|1643824|133925;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|28123;2|1224;2|976|200643|171549|171552|838|28133;2|1239|186801|3082720|186804|1257|341694;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|543311|33033;2|201174|84998|84999|1643824|133925|133926;2|1239|91061|186826|1300|1301|1328,Complete,Fatima
bsdb:595/2/2,Study 595,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Adenoma patients,CRC patients,patients referred for colonoscopy that had cancerous tumors,42,53,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Figure S2,7 March 2023,Fatima,Fatima,significant differences in the abundance of specific taxa between CRC and Adenoma patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|186806|1730,Complete,Fatima
bsdb:595/3/1,Study 595,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia free,Adenoma patients,patients referred for colonoscopy that had cancerous tumors,61,42,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S2,7 March 2023,Fatima,Fatima,significant differences in the abundance of specific taxa between Adenoma patients and neoplasia free,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:595/4/1,Study 595,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia free control,CRC,patients referred for colonoscopy that had cancerous tumors,88,53,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,7 March 2023,Fatima,Fatima,Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas),increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium gonidiaformans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica",2|32066|203490;2|1224;2|200940|3031449|213115|194924|872;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|186801|186802|216572|1017280;2|976|200643|171549|171551|836;2|29547|3031852|213849|72294|194;2|32066|203490|203491|203492|848|76859;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|815|816|817;2|1239|186801|3085636|186803|1506553|1512;2|1239|1737404|1737405|1570339|543311|33033;2|32066|203490|203491|203492|848|155615;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|3085636|186803|1649459|154046;2|1239|1737404|1737405|1570339|543311;2|32066|203490|203491|203492|848|860;2|32066|203490|203491|203492|848|849;2|976|200643|171549|171552|2974251|28135;2|976|200643|171549|171552|838|28133;2|976|200643|171549|171551|836|28123,Complete,Fatima
bsdb:595/4/2,Study 595,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia free control,CRC,patients referred for colonoscopy that had cancerous tumors,88,53,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S3,7 March 2023,Fatima,Fatima,Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas),decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera stadtmanae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",2|1239;2|200940|3031449|213115|194924|35832;2157|28890|183925|2158|2159|2316;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186806|1730;2157|28890|183925|2158|2159|2316|2317;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301|1304;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|186806|1730|39496,Complete,Fatima
bsdb:596/1/1,Study 596,time series / longitudinal observational,25058515,10.1371/journal.ppat.1004262,https://pubmed.ncbi.nlm.nih.gov/25058515/,"Liu CM, Osborne BJ, Hungate BA, Shahabi K, Huibner S, Lester R, Dwan MG, Kovacs C, Contente-Cuomo TL, Benko E, Aziz M, Price LB , Kaul R",The semen microbiome and its relationship with local immunology and viral load in HIV infection,PLoS pathogens,2014,NA,Experiment 1,Canada,Homo sapiens,Semen,UBERON:0001968,HIV infection,EFO:0000764,HIV-uninfected men,HIV-infected men,MSM with HIV infection,22,27,6 months.,16S,3456,Roche454,ANOVA,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Table S2,11 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between HIV- and HIV+ men,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Nostocoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Rhodoferax",2|201174|1760|85004|31953|1678;2|1224|28211|356|212791;2|201174|1760|85010|2070|1847;2|201174|1760|1643682|85030;2|201174|1760|85008|28056;2|1224|28216|80840|75682|149698;2|1224|1236|91347|1903409|551;2|201174|1760|85006|85023|110932;2|1224|28216|80840|80864|12916;2|201174|1760|85009|85015|53387;2|201174|1760|1643684|85031;2|1224|1236|2887326|468|469;2|1239|91061|1385|186817|1386;2|201174|1760|2037;2|976;2|1224|28216|80840;2|1224|28216|80840|80864|34072;2|1224|28211|204455;2|201174|1760|85006|85021|99479;2|1239|186801|186802|541000;2|976|768503|768507|1853232|89966;2|1224|28216|80840|80864|28065,Complete,Claregrieve1
bsdb:596/1/2,Study 596,time series / longitudinal observational,25058515,10.1371/journal.ppat.1004262,https://pubmed.ncbi.nlm.nih.gov/25058515/,"Liu CM, Osborne BJ, Hungate BA, Shahabi K, Huibner S, Lester R, Dwan MG, Kovacs C, Contente-Cuomo TL, Benko E, Aziz M, Price LB , Kaul R",The semen microbiome and its relationship with local immunology and viral load in HIV infection,PLoS pathogens,2014,NA,Experiment 1,Canada,Homo sapiens,Semen,UBERON:0001968,HIV infection,EFO:0000764,HIV-uninfected men,HIV-infected men,MSM with HIV infection,22,27,6 months.,16S,3456,Roche454,ANOVA,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Table S2,11 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between HIV- and HIV+ men,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora",2|1239|909932|1843489|31977|29465;2|201174|1760|85010|2070|402649,Complete,Claregrieve1
bsdb:597/1/1,Study 597,"cross-sectional observational, not case-control",31869338,10.1371/journal.pone.0225622,https://pubmed.ncbi.nlm.nih.gov/31869338/,"Cram JA, Fiore-Gartland AJ, Srinivasan S, Karuna S, Pantaleo G, Tomaras GD, Fredricks DN , Kublin JG",Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination,PloS one,2019,NA,Experiment 1,United States of America,Homo sapiens,Mucosa of rectum,UBERON:0003346,Response to vaccine,EFO:0004645,healthy controls,Vaccinated participants,Participants who were vaccinated,16,20,NA,16S,34,Roche454,Logistic Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4.,15 October 2023,Chinelsy,Chinelsy,The microbiota vary between participants and can be described by weighted UniFrac axis 1 (MDS1). Variations along this axis are evident at the family level within certain classes and orders.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|976|200643|171549|815;2|976|200643|171549|171551;2|976|200643|171549|171552;2|976|200643|171549|171550;2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|1239|186801|186802|186806;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|186801|186802|186807;2|1239|1737404|1737405|1570339;2|1239|186801|3082720|186804,Complete,Chinelsy
bsdb:598/1/1,Study 598,case-control,28743816,10.1128/mBio.00996-17,https://pubmed.ncbi.nlm.nih.gov/28743816/,"Liu CM, Prodger JL, Tobian AAR, Abraham AG, Kigozi G, Hungate BA, Aziz M, Nalugoda F, Sariya S, Serwadda D, Kaul R, Gray RH , Price LB",Penile Anaerobic Dysbiosis as a Risk Factor for HIV Infection,mBio,2017,"anaerobes, cytokines, foreskin inflammation, human immunodeficiency virus, penile microbiome, susceptibility",Experiment 1,Uganda,Homo sapiens,Skin of penis,UBERON:0001331,HIV infection,EFO:0000764,HIV seronegative,HIV seroconverted,HIV-infected trial participants who were randomized to the delayed circumcision arm of the trial and remained uncircumcised who seroconverted during the trial,136,46,24 months.,16S,34,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1,12 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between HIV seroconverters and HIV-negative controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|909932|1843489|31977|39948;2|201174|1760|2037|2049|2050;2|1239|186801|3082720|186804|1257,Complete,Claregrieve1
bsdb:598/1/2,Study 598,case-control,28743816,10.1128/mBio.00996-17,https://pubmed.ncbi.nlm.nih.gov/28743816/,"Liu CM, Prodger JL, Tobian AAR, Abraham AG, Kigozi G, Hungate BA, Aziz M, Nalugoda F, Sariya S, Serwadda D, Kaul R, Gray RH , Price LB",Penile Anaerobic Dysbiosis as a Risk Factor for HIV Infection,mBio,2017,"anaerobes, cytokines, foreskin inflammation, human immunodeficiency virus, penile microbiome, susceptibility",Experiment 1,Uganda,Homo sapiens,Skin of penis,UBERON:0001331,HIV infection,EFO:0000764,HIV seronegative,HIV seroconverted,HIV-infected trial participants who were randomized to the delayed circumcision arm of the trial and remained uncircumcised who seroconverted during the trial,136,46,24 months.,16S,34,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S1,12 January 2022,Joyessa,"Joyessa,Claregrieve1",Differential microbial abundance between HIV seroconverters and HIV-negative controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella",2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|1161127,Complete,Claregrieve1
bsdb:600/1/1,Study 600,case-control,29501802,10.1016/j.bbi.2018.02.016,NA,"Qian Y, Yang X, Xu S, Wu C, Song Y, Qin N, Chen SD , Xiao Q",Alteration of the fecal microbiota in Chinese patients with Parkinson's disease,"Brain, behavior, and immunity",2018,"16S rRNA gene, Gut microbiota, Neurodegenerative disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS were excluded.,45,45,Participants taking antibiotics or probiotic supplements within the three months prior to sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,"age,body mass index,constipation,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 3A.,15 January 2022,Fcuevas3,"Fcuevas3,Claregrieve1",Taxonomic differences of fecal microbiota in PD and healthy groups,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Archaea|p__Nitrososphaerota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Nitrososphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|1224|1236|2887326|468|469;2|976|200643|171549|171550|239759;2|1224|28216|80840|92793;2|1239|186801|186802|3085642|580596;2|976|1853228|1853229|563835;2|1239|186801|186802|31979|1485;2|200940|3031449|213115|194924|872;2|1239|526524|526525|128827;2|1239|526524;2|1239;2|1224|1236|91347|543|570;2|1224|1236|2887326|468;2157|651137|1643678|1033996|1033997;2|976|200643|171549|171552|577309;2|1224|28211|356|82115;2|976|200643|171549|171550;2|976|117747|200666;2|976|117747;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2157|651137;2|1224|1236|135614|32033;2|1224|1236|135614;2|200940|3031449|213115|194924|872;2|1224|28216|80840;2157|651137|1643678|1033996;2157|651137|1643678|1033996|1033997|497726;2|1239|186801|3085636|186803;2|1224|1236|72274,Complete,Claregrieve1
bsdb:600/1/2,Study 600,case-control,29501802,10.1016/j.bbi.2018.02.016,NA,"Qian Y, Yang X, Xu S, Wu C, Song Y, Qin N, Chen SD , Xiao Q",Alteration of the fecal microbiota in Chinese patients with Parkinson's disease,"Brain, behavior, and immunity",2018,"16S rRNA gene, Gut microbiota, Neurodegenerative disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS were excluded.,45,45,Participants taking antibiotics or probiotic supplements within the three months prior to sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,"age,body mass index,constipation,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 3A.,22 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in PD and healthy groups.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium",2|201174|1760|2037;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|976|117743|200644;2|976|117743;2|976|1853228|1853229|563835|504481,Complete,Claregrieve1
bsdb:601/2/1,Study 601,case-control,32844199,10.1093/brain/awaa201,NA,"Qian Y, Yang X, Xu S, Huang P, Li B, Du J, He Y, Su B, Xu LM, Wang L, Huang R, Chen S , Xiao Q",Gut metagenomics-derived genes as potential biomarkers of Parkinson's disease,Brain : a journal of neurology,2020,"Parkinson’s disease, biomarker, gut microbiota, metagenome, shotgun",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without any form of Parkinson's Disease,Participants with idiopathic Parkinson's Disease,All Parkinson’s disease patients eligible for this study were diagnosed with idiopathic Parkinson’s disease according to the UK Brain Bank criteria.,75,78,Antibiotic use within 3 months prior to sample collection.,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,life style,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2A-D.,18 January 2022,Fcuevas3,"Fcuevas3,Atrayees",Differences in phylogenetic abundance between Parkinson’s disease patients and healthy control subjects.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Synergistota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",2|976|200643|171549|171550|239759;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|550;2|1239|186801|3085636|186803|2719313|333367;2|201174|84998|1643822|1643826|644652;2|201174|84998|1643822|1643826|644652|471189;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186828|117563|2049028;2|1239|526524|526525|128827|61170;2|1239|526524|526525|128827|61170|61171;2|1239|186801|3085636|186803|1898203;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2767887|1624;2|976|200643|171549|171552|577309|454154;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1308;2|508458;2|74201;2|1239|91061|186826|186827|46123;2|1239|186801|186802|216572|1535,Complete,Atrayees
bsdb:602/1/1,Study 602,case-control,21737778,https://doi.org/10.1152%2Fajpgi.00154.2011,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220325/,"Carroll IM, Ringel-Kulka T, Keku TO, Chang YH, Packey CD, Sartor RB , Ringel Y",Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome,American journal of physiology. Gastrointestinal and liver physiology,2011,NA,Experiment 1,United States of America,Homo sapiens,"Feces,Colonic mucosa","UBERON:0001988,UBERON:0000317",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Individual who have been diagnosed with diarrhea-predominant Irritable bowel syndrome(IBS-D),21,16,2 Months prior to the study.,PCR,NA,Non-quantitative PCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Table 3.",28 February 2024,Peace Sandy,Peace Sandy,"Percent contribution of predominant T-RFs in fecal and mucosal samples from healthy controls and D-IBS patients. 

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

Table 3.
Hae III- and Msp I-generated T-RFs that contribute to 90% of the fecal microbiota in healthy controls but not D-IBS patients",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae",2|1239|186801|186802|1898207;2|203682|203683|112|126,Complete,Peace Sandy
bsdb:603/1/1,Study 603,"case-control,meta-analysis",33947803,10.1128/mSystems.00112-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269207/,"Jiang P, Wu S, Luo Q, Zhao XM , Chen WH",Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models,mSystems,2021,"gut dysbiosis, human microbiome, intestinal disease, machine learning-based disease classification, noninvasive disease diagnosis",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non disease controls,CRC patients,Patients diagnosed with colorectal cancer,632,354,NA,16S,NA,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1,24 January 2022,Itslanapark,"Itslanapark,Peace Sandy","Disease-specific and shared microbial markers showed distinct prevalence profiles in patients and controls. (A) Microbial markers and their trends (i.e., case- or control-enriched) in common intestinal diseases. Species significantly enriched in cases (or controls) of corresponding disease in meta-analysis are shown (fdr < 0.05 in meta-analysis, Benjamini-Hochberg FDR correction), with their phylum shown on top. Red indicates case-enriched species and blue indicates control-enriched ones.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|658089;2|1239|186801|3085636|186803|841|166486;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|46506;2|976|200643|171549|2030927;2|976|200643|171549|1853231|283168|626933;2|976|200643|171549|2005525|375288|328812;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|1288121;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|818;2|1239|186801|186802|216572|1535;2|1239|186801|186802|384638;2|1239|186801|186802|216572|39492;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|1898203;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|292632;2|1239|909932|909929|1843491|158846|158847;2|1239|909932|909929|1843491|158846,Complete,Peace Sandy
bsdb:603/1/2,Study 603,"case-control,meta-analysis",33947803,10.1128/mSystems.00112-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269207/,"Jiang P, Wu S, Luo Q, Zhao XM , Chen WH",Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models,mSystems,2021,"gut dysbiosis, human microbiome, intestinal disease, machine learning-based disease classification, noninvasive disease diagnosis",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non disease controls,CRC patients,Patients diagnosed with colorectal cancer,632,354,NA,16S,NA,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1,25 January 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Peace Sandy","Disease-specific and shared microbial markers showed distinct prevalence profiles in patients and controls. (A) Microbial markers and their trends (i.e., case- or control-enriched) in common intestinal diseases. Species significantly enriched in cases (or controls) of corresponding disease in meta-analysis are shown (fdr < 0.05 in meta-analysis, Benjamini-Hochberg FDR correction), with their phylum shown on top. Red indicates case-enriched species and blue indicates control-enriched ones.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__Synergistes sp. 3_1_syn1,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes",2|976|200643|171549|171550|239759|1470347;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171552|1283313|76122;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|216572|244127|1872531;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|291644;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|186802|457421;2|200940|3031449|213115|194924|872|876;2|1239|186801|3085636|186803|2719313|333367;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|2719313|358743;2|1239|526524|526525|128827|457422;2|32066|203490|203491|203492|848|851;2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|186828|117563|46124;2|1239|186801|3085636|186803|1649459|154046;2|1239|186801|3085636|186803|658086;2|1239|186801|3085636|186803|658087;2|1239|909932|1843489|31977|906|2023260;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|3082720|186804|1257|1261;2|1239|186801|3082720|186804|1257|1262;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|1239|186801|186802|216572|552398;2|201174|84998|1643822|1643826|84108|2049041;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|1328;2|1239|186801|186802|216572|292632|665956;2|508458|649775|649776|649777|2753|457415;2|1239|526524|526525|128827|1522;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33039;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|1872444;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1303;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|186802|1898207;2|1239|1737404|1737405|1570339|165779|33037;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|2316020|33038;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|906;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|576;2|508458|649775|649776|649777|2753,Complete,Peace Sandy
bsdb:604/1/1,Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls free of neurological disease,Participants with Parkinson's Disease,"Dataset 1. Participants with Parkinson's Disease, diagnosed by a movement disorder specialist using UK Brain Bank criteria.",136,212,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,constipation,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2.,22 January 2022,Fcuevas3,"Fcuevas3,Claregrieve1",Differential abundances of microbial taxa between healthy controls and PD patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|201174|1760|85004|31953|1678;2|201174|1760|85007|1653|1716;2|1239|91061|186826|33958|1578;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:604/1/2,Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls free of neurological disease,Participants with Parkinson's Disease,"Dataset 1. Participants with Parkinson's Disease, diagnosed by a movement disorder specialist using UK Brain Bank criteria.",136,212,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,constipation,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2.,22 January 2022,Fcuevas3,"Fcuevas3,Claregrieve1",Differential abundances of microbial taxa between healthy controls and PD patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:604/2/1,Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control free of neurological disease.,Participants with Parkinson's Disease,Dataset 2. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria,184,323,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,alcohol drinking,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Differential abundances of 15 PD-associated genera replicated in two datasets.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85007|1653|1716;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:604/2/2,Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control free of neurological disease.,Participants with Parkinson's Disease,Dataset 2. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria,184,323,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,alcohol drinking,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Differential abundances of 15 PD-associated genera replicated in two datasets.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|841;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:605/1/1,Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without Parkinson's disease,Participants with Parkinson's Disease,PD was diagnosed according to the United Kingdom PD Society Brain Bank clinical diagnostic criteria.,77,80,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,unchanged,NA,NA,increased,Signature 1,Figure 3A,22 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in PD and control groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|74201;2|74201|203494|48461|203557;2|74201|203494|48461|1647988|239934;2|74201|203494|48461;2|976|200643|171549|1853231;2|976|200643|171549|171550;2|976|200643|171549|1853231|574697;2|200930|68337|191393|191394;2|1224|28211;2|1239|909932|1843489|31977|29465;2|1239|526524;2|1239|526524|526525;2|1239|526524|526525|128827;2|976|200643|171549|1853231|283168;2|544448;2|200930|68337|191393|2945020|248038;2|200930|68337;2|200940|3031449|213115|194924|35832;2|1239|91061|186826|81852;2|1239|91061|186826|81850;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|544448|31969;2|1224|28211|356,Complete,Rimsha
bsdb:605/1/2,Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without Parkinson's disease,Participants with Parkinson's Disease,PD was diagnosed according to the United Kingdom PD Society Brain Bank clinical diagnostic criteria.,77,80,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,unchanged,NA,NA,increased,Signature 2,Figure 3A.,22 January 2022,Fcuevas3,"Fcuevas3,Rimsha",Taxonomic differences of fecal microbiota in PD and control groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Rimsha
bsdb:605/2/1,Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with Parkinson's Disease with non-tremor subtypes,Participants with Parkinson's Disease with tremor subtypes,Participants with Parkinson's Disease with tremor subtypes.,33,47,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4A.,22 January 2022,Fcuevas3,"Fcuevas3,Rimsha",Taxonomic differences of fecal microbiota in non tremor and tremor groups.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",2|74201|203494|48461|1647988|239934;2|1239|186801;2|1239|186801|186802|543314|2137877;2|1239;2|74201;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461,Complete,Rimsha
bsdb:605/2/2,Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with Parkinson's Disease with non-tremor subtypes,Participants with Parkinson's Disease with tremor subtypes,Participants with Parkinson's Disease with tremor subtypes.,33,47,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4A.,22 January 2022,Fcuevas3,"Fcuevas3,Rimsha",Taxonomic differences of fecal microbiota in PD and control groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|28216|80840|506;2|976|200643|171549;2|976;2|976|200643;2|1224|28216|80840|119060|106589;2|200940|3031449|213115|194924|872;2|976|117743|200644|49546|237;2|1239|186801|3082720|3030910|86331;2|201174|1760|85009|31957|1743;2|1224|28216|80840|995019|40544,Complete,Rimsha
bsdb:606/1/1,Study 606,case-control,31440136,10.3389/fnins.2019.00839,NA,"Gorecki AM, Preskey L, Bakeberg MC, Kenna JE, Gildenhuys C, MacDougall G, Dunlop SA, Mastaglia FL, Akkari PA, Koengten F , Anderton RS",Altered Gut Microbiome in Parkinson's Disease and the Influence of Lipopolysaccharide in a Human α-Synuclein Over-Expressing Mouse Model,Frontiers in neuroscience,2019,"Gammaproteobacteria, Parkinson’s disease, Thy1-αSyn, gastrointestinal, lipopolysaccharide, microbiome",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with idiopathic Parkinson's Disease and mild symptoms.,"All patients were confirmed to have idiopathic Parkinson’s disease by a movement disorders neurologist, in accordance with the United Kingdom Brain Bank criteria and mild symptoms.",7,7,No history of antibiotic or non-steroidal anti-inflammatory drug use in the previous 3 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,22 January 2022,Fcuevas3,Fcuevas3,"Mean class abundance in people with Parkinson’s disease and healthy controls, specifically control vs. mild PD.",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,2|1224|1236,Complete,Claregrieve1
bsdb:606/2/1,Study 606,case-control,31440136,10.3389/fnins.2019.00839,NA,"Gorecki AM, Preskey L, Bakeberg MC, Kenna JE, Gildenhuys C, MacDougall G, Dunlop SA, Mastaglia FL, Akkari PA, Koengten F , Anderton RS",Altered Gut Microbiome in Parkinson's Disease and the Influence of Lipopolysaccharide in a Human α-Synuclein Over-Expressing Mouse Model,Frontiers in neuroscience,2019,"Gammaproteobacteria, Parkinson’s disease, Thy1-αSyn, gastrointestinal, lipopolysaccharide, microbiome",Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with mild PD,Participants with severe PD,"All patients were confirmed to have idiopathic Parkinson’s disease by a movement disorders neurologist, in accordance with the United Kingdom Brain Bank criteria and severe symptoms.",7,7,No history of antibiotic or non-steroidal anti-inflammatory drug use in the previous 3 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,22 January 2022,Fcuevas3,Fcuevas3,Mean class abundance in people with mild and severe Parkinson’s disease.,increased,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,2|74201|203494,Complete,Claregrieve1
bsdb:607/1/1,Study 607,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R , Thiele I",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,"Computational modelling, Gut microbiome, Metabolic modelling, Parkinson’s disease, Transsulfuration pathway",Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,6 Months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,constipation,sex",NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2 and Figure 3,22 January 2022,Fcuevas3,"Fcuevas3,Aiyshaaaa,Peace Sandy","Boxplots of seven significantly changed species in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate

Boxplots of eight significantly changed genera in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|244127|169435;2|200940|3031449|213115|194924|35832;2|1239|186801|3082768|990719|990721;2|1239|186801|3082768|990719|990721|626937;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|1263|40518;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33039;2|1239|909932|1843488|909930|904,Complete,Peace Sandy
bsdb:607/1/2,Study 607,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R , Thiele I",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,"Computational modelling, Gut microbiome, Metabolic modelling, Parkinson’s disease, Transsulfuration pathway",Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,6 Months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,constipation,sex",NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2 and Figure 3,22 January 2022,Fcuevas3,"Fcuevas3,Aiyshaaaa,Peace Sandy","Boxplots of seven significantly changed species in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate

Boxplots of eight significantly changed genera in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",2|1239|186801|3085636|186803|841|166486;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281|191303|154288,Complete,Peace Sandy
bsdb:608/1/1,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 1,"Italy,United States of America",Homo sapiens,Oral cavity,UBERON:0000167,Health study participation,EFO:0010130,none,healthy child oral 50% up,NA,NA,81,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child oral genus in >=50% study samples,NA,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838;2|1239|91061|1385|539738|1378;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724,Complete,Lwaldron
bsdb:608/1/2,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 1,"Italy,United States of America",Homo sapiens,Oral cavity,UBERON:0000167,Health study participation,EFO:0010130,none,healthy child oral 50% up,NA,NA,81,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child oral species in >= 50% samples,NA,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|91061|186826|1300|1301|28037;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1303;2|976|200643|171549|171552|838|28132;2|1239|91061|1385|539738|1378|1379;2|1239|91061|186826|1300|1301|68892;2|1239|91061|1385|539738|1378|84135;2|1224|28216|206351|481|482|484;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|39778,Complete,Lwaldron
bsdb:608/2/1,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 2,"Bangladesh,China,Estonia,Finland,Germany,India,Ireland,Italy,Luxembourg,Netherlands,Russian Federation,Spain,Sweden,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none,healthy child stool 50% up,NA,NA,3375,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child stool genus in >= 50% samples,NA,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Lycoperdaceae|g__Calvatia|s__Calvatia complutensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter",2|1239|91061|186826|1300|1301;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|561;2|1239|909932|1843489|31977|29465;2|976|200643|171549|815|816;2759|4751|5204|155619|5338|5426|68761|90956;2|1239|91061|186826|81852|1350;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|2316020,Complete,NA
bsdb:608/2/2,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 2,"Bangladesh,China,Estonia,Finland,Germany,India,Ireland,Italy,Luxembourg,Netherlands,Russian Federation,Spain,Sweden,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none,healthy child stool 50% up,NA,NA,3375,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child stool species in >= 50% samples,NA,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|201174|1760|85004|31953|1678|216816;2|1239|91061|186826|1300|1301|1304;2|1224|1236|91347|543|561|562;2|1239|91061|186826|1300|1301|1318,Complete,NA
bsdb:609/1/1,Study 609,case-control,33362375,10.3748/wjg.v26.i45.7173,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723673/,"Sun XZ, Zhao DY, Zhou YC, Wang QQ, Qin G , Yao SK",Alteration of fecal tryptophan metabolism correlates with shifted microbiota and may be involved in pathogenesis of colorectal cancer,World journal of gastroenterology,2020,"Colorectal adenoma, Colorectal cancer, Indoles, Kynurenine, Microbiota, Tryptophan metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),CRC,Patients with colorectal neoplastic lesions where tumors were removed and pathologically diagnosed with adenomatous polyp or colorectal adenocarcinoma; ages of participants ranged from 18-80.,38,79,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 4C,31 January 2022,Itslanapark,"Itslanapark,Chloe,Aiyshaaaa,Merit",Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",2|74201|203494|48461|1647988|239934;2|1239|186801|3085636|186803|207244;2|1239|91061;2|976|200643|171549;2|976|200643;2|976;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1239|909932|909929|1843491|970;2|1224|28216|80840|995019|40544;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201;2|1224|28211;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547;2|1239|91061|186826|33958|1578|1591,Complete,Chloe
bsdb:609/1/2,Study 609,case-control,33362375,10.3748/wjg.v26.i45.7173,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723673/,"Sun XZ, Zhao DY, Zhou YC, Wang QQ, Qin G , Yao SK",Alteration of fecal tryptophan metabolism correlates with shifted microbiota and may be involved in pathogenesis of colorectal cancer,World journal of gastroenterology,2020,"Colorectal adenoma, Colorectal cancer, Indoles, Kynurenine, Microbiota, Tryptophan metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),CRC,Patients with colorectal neoplastic lesions where tumors were removed and pathologically diagnosed with adenomatous polyp or colorectal adenocarcinoma; ages of participants ranged from 18-80.,38,79,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 4c,10 February 2022,Itslanapark,"Itslanapark,Fatima,Chloe,Merit",Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.",2|1239|186801|186802|216572|52784;2|201174|84998|1643822|1643826|553372;2|1239;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801;2|1239|186801|186802|1898207;2|201174|84998|84999|84107|102106;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|1239|186801|186802|204475;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1506577;2|32066|203490|203491|203492|848|68766;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|2049031,Complete,Chloe
bsdb:610/1/1,Study 610,case-control,22315951,10.1111/j.1365-2036.2012.05007.x,NA,"Chassard C, Dapoigny M, Scott KP, Crouzet L, Del'homme C, Marquet P, Martin JC, Pickering G, Ardid D, Eschalier A, Dubray C, Flint HJ , Bernalier-Donadille A",Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome,Alimentary pharmacology & therapeutics,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,constipated-IBS,"The 14 women IBS patients (age range: 36–59, mean age: 48) included in this study fulfilled the Rome II criteria for IBS. They were classified as IBS with constipation (C-IBS) by a questionnaire following the Rome II subgrouping criteria which have been recognized as valid also in the Rome III criteria.",12,14,"Exclusion criteria included organic intestinal disease, other systemic disease, previous abdominal surgery, lactation, pregnancy, dementia or inadequate cooperative capability and antibiotic therapy during the previous 2 months.",16S,NA,NA,T-Test,0.05,FALSE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1a, 1b",6 April 2022,Rimsha,Rimsha,FISH analysis of main bacterial taxonomic groups in faeces of healthy and IBS patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|201174|1760|85004|31953|1678;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|841,Complete,Rimsha
bsdb:610/1/2,Study 610,case-control,22315951,10.1111/j.1365-2036.2012.05007.x,NA,"Chassard C, Dapoigny M, Scott KP, Crouzet L, Del'homme C, Marquet P, Martin JC, Pickering G, Ardid D, Eschalier A, Dubray C, Flint HJ , Bernalier-Donadille A",Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome,Alimentary pharmacology & therapeutics,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,constipated-IBS,"The 14 women IBS patients (age range: 36–59, mean age: 48) included in this study fulfilled the Rome II criteria for IBS. They were classified as IBS with constipation (C-IBS) by a questionnaire following the Rome II subgrouping criteria which have been recognized as valid also in the Rome III criteria.",12,14,"Exclusion criteria included organic intestinal disease, other systemic disease, previous abdominal surgery, lactation, pregnancy, dementia or inadequate cooperative capability and antibiotic therapy during the previous 2 months.",16S,NA,NA,T-Test,0.05,FALSE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,6 April 2022,Rimsha,Rimsha,Comparison of the population levels of microbial communities involved in carbohydrate metabolism in faecel samples from healthy and C-IBS individials,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Rimsha
bsdb:610/1/3,Study 610,case-control,22315951,10.1111/j.1365-2036.2012.05007.x,NA,"Chassard C, Dapoigny M, Scott KP, Crouzet L, Del'homme C, Marquet P, Martin JC, Pickering G, Ardid D, Eschalier A, Dubray C, Flint HJ , Bernalier-Donadille A",Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome,Alimentary pharmacology & therapeutics,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,constipated-IBS,"The 14 women IBS patients (age range: 36–59, mean age: 48) included in this study fulfilled the Rome II criteria for IBS. They were classified as IBS with constipation (C-IBS) by a questionnaire following the Rome II subgrouping criteria which have been recognized as valid also in the Rome III criteria.",12,14,"Exclusion criteria included organic intestinal disease, other systemic disease, previous abdominal surgery, lactation, pregnancy, dementia or inadequate cooperative capability and antibiotic therapy during the previous 2 months.",16S,NA,NA,T-Test,0.05,FALSE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 3,Table 1,6 April 2022,Rimsha,"Rimsha,Lwaldron",Comparison of the population levels of microbial communities involved in carbohydrate metabolism in faecel samples from healthy and C-IBS individials,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|1678,Complete,Rimsha
bsdb:611/1/1,Study 611,case-control,31281534,10.7150/thno.35186,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592169/,"Yang Y, Misra BB, Liang L, Bi D, Weng W, Wu W, Cai S, Qin H, Goel A, Li X , Ma Y",Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer,Theranostics,2019,"biomarkers, colorectal cancer, gut, metabolomics, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colorectal Cancer patients,patients diagnosed with colorectal cancer,50,50,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 1,Figure 2(b),20 February 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Davvve,Peace Sandy",The differences in abundance between the H group and the CRC groups.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|256845|1313211|278081|566277|256846;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171551|836;2|1224|1236|72274;2|1224;2|1224|1236,Complete,Peace Sandy
bsdb:611/1/2,Study 611,case-control,31281534,10.7150/thno.35186,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592169/,"Yang Y, Misra BB, Liang L, Bi D, Weng W, Wu W, Cai S, Qin H, Goel A, Li X , Ma Y",Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer,Theranostics,2019,"biomarkers, colorectal cancer, gut, metabolomics, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colorectal Cancer patients,patients diagnosed with colorectal cancer,50,50,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 2,Figure 2(b),20 February 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Davvve,Peace Sandy",The differences in abundance between the H group and the CRC groups.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium oxidoreducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Solibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|909932|1843488|909930;2|201174;2|1239;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|1732;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|1239|909932;2|1239|186801|186802|216572;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|46205;2|1239|186801|3082720|186804|1501226;2|1239|909932|909929;2|1239|91061|1385|186818|648800;2|1239|186801|186802|216572|292632,Complete,Peace Sandy
bsdb:612/1/1,Study 612,"case-control,meta-analysis",27171425,10.1371/journal.pone.0155362,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865240/,"Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P , Sinha R",Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing,PloS one,2016,NA,Experiment 1,"United States of America,France",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control subjects,CRC cases,pre treatment colorectal cancer cases,94,47,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,3 February 2022,Itslanapark,"Itslanapark,Claregrieve1",Differential microbial abundance between CRC cases and controls using 16S sequencing,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:613/1/1,Study 613,case-control,30065719,10.3389/fmicb.2018.01607,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057110/,"Deng X, Li Z, Li G, Li B, Jin X , Lyu G",Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy,Frontiers in microbiology,2018,"16S rRNA sequencing, bacterial diversity, chemotherapy, colorectal cancer, surgery",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy individuals,CRC patients,patients diagnosed with colorectal cancer,33,31,NA,16S,45,Illumina,PERMANOVA,0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,11 February 2022,Itslanapark,"Itslanapark,Rimsha",crc patients after chemotherapy,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|s__uncultured Bacteroidetes bacterium",2|1224|1236|135625|712|713;2|1224|28216|80840|506;2|1239|186801|3085636|186803|207244;2|1239|91061;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|820;2|976;2|976|200643;2|1239|186801|3085636|186803|572511|33035;2|1224|1236|91347|543|544;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1117;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|1903409|551;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1239|91061|186826;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1224|1236|135625;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|301302;2|1239|186801|186802|216572|1263|1265;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2759|33090|35493;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977;2|1239|186801|3085636|186803|2316020|33038;2|976|152509,Complete,Rimsha
bsdb:614/1/1,Study 614,case-control,31611994,10.3892/ol.2019.10841,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781660/,"Sheng Q, Du H, Cheng X, Cheng X, Tang Y, Pan L, Wang Q , Lin J",Characteristics of fecal gut microbiota in patients with colorectal cancer at different stages and different sites,Oncology letters,2019,"16S rRNA sequencing, bioinformatics analysis, colorectal cancer, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,CRC,"The CRC patients were selected according to the criteria of no other health complications, no family history of CRC or recurrence of CRC, and no radiotherapy and chemotherapy prior to surgical resection. Patients were then classified according to postoperative clinical data using the tumor-node-metastasis (TNM) staging system for malignant tumors.",30,67,3 months,16S,34,Illumina,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 5,21 February 2022,Itslanapark,Itslanapark,Comparison of relative abundance of genera in fecal samples of patients with CRC and healthy controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum",2|976|200643|171549|171552|838;2|201174|84998|84999|84107|102106;2|976|200643|171549|1853231|283168;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|1164882,Complete,Rimsha
bsdb:614/1/2,Study 614,case-control,31611994,10.3892/ol.2019.10841,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781660/,"Sheng Q, Du H, Cheng X, Cheng X, Tang Y, Pan L, Wang Q , Lin J",Characteristics of fecal gut microbiota in patients with colorectal cancer at different stages and different sites,Oncology letters,2019,"16S rRNA sequencing, bioinformatics analysis, colorectal cancer, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,CRC,"The CRC patients were selected according to the criteria of no other health complications, no family history of CRC or recurrence of CRC, and no radiotherapy and chemotherapy prior to surgical resection. Patients were then classified according to postoperative clinical data using the tumor-node-metastasis (TNM) staging system for malignant tumors.",30,67,3 months,16S,34,Illumina,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 5,21 February 2022,Itslanapark,Itslanapark,Comparison of relative abundance of genera in fecal samples of patients with CRC and healthy controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|1224|1236|91347|543|413496;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|44748,Complete,Rimsha
bsdb:615/1/1,Study 615,"cross-sectional observational, not case-control",31699813,10.1136/annrheumdis-2019-215743,NA,"Kishikawa T, Maeda Y, Nii T, Motooka D, Matsumoto Y, Matsushita M, Matsuoka H, Yoshimura M, Kawada S, Teshigawara S, Oguro E, Okita Y, Kawamoto K, Higa S, Hirano T, Narazaki M, Ogata A, Saeki Y, Nakamura S, Inohara H, Kumanogoh A, Takeda K , Okada Y",Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population,Annals of the rheumatic diseases,2020,"autoimmune diseases, gene polymorphism, rheumatoid arthritis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis,Patients with RA,42,82,12 weeks,WMS,NA,Illumina,PERMANOVA,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,15 March 2023,Nice25,Nice25,Taxonomic differences of fecal microbiota in RA and healthy groups.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella marshii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii",2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171552|838|419005;2|976|200643|171549|171552|838|28128;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28130;2|976|200643|171549|171552|2974257|189722;2|976|200643|171549|815|909656|671267,Complete,Claregrieve1
bsdb:616/1/NA,Study 616,randomized controlled trial,32692788,10.4193/Rhin20.055,NA,"Cherian LM, Bassiouni A, Cooksley CM, Vreugde S, Wormald PJ , Psaltis AJ","The clinical outcomes of medical therapies in chronic rhinosinusitis are independent of microbiomic outcomes: a double-blinded, randomised placebo-controlled trial",Rhinology,2020,NA,Experiment 1,Finland,Homo sapiens,Middle nasal meatus,UBERON:0015219,Chronic rhinosinusitis,EFO:1000024,Healthy controls-without polyps,Patients with chronic rhinosinusitis,"CRS patients diagnosed as per the criteria outlined in the Euro-
pean Position Paper on Rhinosinusitis and Nasal Polyps (EPOS)
2012",50,50,"Patients who were on any oral steroid, topical steroid or oral antibiotic in a 
6-weeks period prior to enrollment, below the age of 18, had a history of  
sinus surgery, documented doxycycline or steroid allergy, 
using CYP450 inhibitors, immunosuppression, uncontrolled 
diabetes, were all excluded.",16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:617/1/1,Study 617,prospective cohort,28112736,10.1038/nm.4272,https://www.nature.com/articles/nm.4272,"Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD , Aagaard KM",Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery,Nature medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Feces,Saliva,Anterior naris,Posterior fornix of vagina,Epithelium of elbow","UBERON:0001988,UBERON:0001836,UBERON:2001427,UBERON:0016486,UBERON:0003229",Microbiome,EFO:0004982,Maternal samples taken at delivery.,Neonatal samples taken at delivery,Neonatal samples taken at delivery,82,82,NA,16S,345,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S3.,6 February 2024,Peace Sandy,Peace Sandy,"Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined  by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1743;2|1224|28211|204457|41297|13687;2|201174|1760|85004|31953|2701;2|976|200643|171549|171552|838;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543,Complete,Peace Sandy
bsdb:617/1/2,Study 617,prospective cohort,28112736,10.1038/nm.4272,https://www.nature.com/articles/nm.4272,"Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD , Aagaard KM",Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery,Nature medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Feces,Saliva,Anterior naris,Posterior fornix of vagina,Epithelium of elbow","UBERON:0001988,UBERON:0001836,UBERON:2001427,UBERON:0016486,UBERON:0003229",Microbiome,EFO:0004982,Maternal samples taken at delivery.,Neonatal samples taken at delivery,Neonatal samples taken at delivery,82,82,NA,16S,345,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S3,6 February 2024,Peace Sandy,Peace Sandy,"Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85007|1653|1716;2|201174|1760|2037|2049|1654;2|976|200643|171549|171551|836;2|976|200643|171549|171552|1283313;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|165779;2|1239|91061|1385|90964|1279;2|201174|1760|85009|31957|1743;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838;2|976|200643|171549|815|816;2|201174|1760|85004|31953|2701;2|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:617/2/1,Study 617,prospective cohort,28112736,10.1038/nm.4272,https://www.nature.com/articles/nm.4272,"Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD , Aagaard KM",Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery,Nature medicine,2017,NA,Experiment 2,United States of America,Homo sapiens,"Feces,Saliva,Anterior naris,Posterior fornix of vagina,Epithelium of elbow","UBERON:0001988,UBERON:0001836,UBERON:2001427,UBERON:0016486,UBERON:0003229",Microbiome,EFO:0004982,Maternal samples taken at 6  weeks postpartum,Infant samples taken at 6 weeks postpartum,Infant samples taken at 6 weeks postpartum,60,60,NA,16S,345,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S3,6 February 2024,Peace Sandy,Peace Sandy,"Fig. S3. Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (C) Maternal samples taken at 6 weeks postpartum (D) Infant samples taken at 6 weeks postpartum",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|150022;2|201174|1760|85009|31957|1743;2|1239|1737404|1737405|1570339|165779;2|1239|91061|1385|90964|1279;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543|570;2|1224|1236|91347|543|561;2|976|200643|171549|815|816,Complete,NA
bsdb:617/2/2,Study 617,prospective cohort,28112736,10.1038/nm.4272,https://www.nature.com/articles/nm.4272,"Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD , Aagaard KM",Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery,Nature medicine,2017,NA,Experiment 2,United States of America,Homo sapiens,"Feces,Saliva,Anterior naris,Posterior fornix of vagina,Epithelium of elbow","UBERON:0001988,UBERON:0001836,UBERON:2001427,UBERON:0016486,UBERON:0003229",Microbiome,EFO:0004982,Maternal samples taken at 6  weeks postpartum,Infant samples taken at 6 weeks postpartum,Infant samples taken at 6 weeks postpartum,60,60,NA,16S,345,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S3,6 February 2024,Peace Sandy,Peace Sandy,"Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined  by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. . (C) Maternal samples taken at 6  weeks postpartum (D) Infant samples taken at 6 weeks postpartum.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85007|1653|1716;2|976|117743|200644|49546|1016;2|201174|1760|2037|2049|1654;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|1283313;2|976|200643|171549|171551|836;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1239|91061|1385|90964|1279;2|201174|1760|85009|31957|1743;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|906;2|201174|1760|85004|31953|2701;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:618/1/1,Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,"Control, mild, and moderate dementia",Severe dementia,MMSE 0-9: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A,28 March 2022,Lwaldron,Lwaldron,4a Features selected by Linear discriminant analysis Effect Size (LEfSe) to discriminate between dementia different stages of cognitive dysfunction and controls. Right-hand bar showing biomarkers of severe dementia.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. Marseille-P3371,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",2|976|200643|171549|815|816|2778071;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|1432051;2|1224|1236|91347|543;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|3085636|186803|1769710;2|1239|186801|3085636|186803|1769710|2021466;2|1239|91061|186826|1300|1301|1304;2|1239|186801|3085636|186803|84036;2|1239|186801|186802|216572|1535;2|1239|186801|186802|543314|35518;2|1239|186801|3085636|186803|2316020|33039;2|1239|91061|186826|1300|1301|1308;2|201174|1760|2037|2049;2|1224|1236|91347;2|201174|1760|2037;2|1239|186801|186802|3082771|1924093|1944639;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572|216851|1946507,Complete,Lwaldron
bsdb:618/2/1,Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,Controls without cognitive impairments,Patients with dementia,"Participants with any level of dementia (mild, moderate, severe).",18,23,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,3a,15 March 2022,Maryemzaki,"Maryemzaki,Lwaldron",Differentially abundant taxa between any level of dementia vs controls,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|3085636|186803|207244|649756;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|3085636|186803|1506553;2|976|200643|171549|815|909656|357276;2|1239|186801|3085636|186803|2316020|33039,Complete,Lwaldron
bsdb:618/2/2,Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,Controls without cognitive impairments,Patients with dementia,"Participants with any level of dementia (mild, moderate, severe).",18,23,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 3a,15 March 2022,Maryemzaki,"Maryemzaki,Lwaldron",Differentially abundant taxa between any level of dementia vs controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MC_35,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|1766253|2021311;2|1239|186801|3085636|186803|1755642;2|1239|186801|3085636|186803|877420;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003,Complete,Lwaldron
bsdb:618/3/1,Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,"control, mild, and severe dementia",moderate dementia,MMSE 10-19: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A (moderate),28 March 2022,Lwaldron,Lwaldron,"Moderate vs control, mild, and severe dementia",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|186826|33958|1578|1604;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|816|29523;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|81850;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061,Complete,Lwaldron
bsdb:618/4/1,Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 4,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,"control, moderate, and severe dementia",mild dementia,MMSE 20-26: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A (mild),28 March 2022,Lwaldron,Lwaldron,"These are ""biomarkers"" of mild dementia that are lower abundance in controls, moderate, and severe dementia.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050|39485,Complete,Lwaldron
bsdb:619/1/NA,Study 619,"cross-sectional observational, not case-control",20566857,10.1073/pnas.1002601107,NA,"Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N , Knight R",Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 1,Venezuela,Homo sapiens,"Mucosa of oral region,Vagina,Skin of forehead,Skin of forearm","UBERON:0003343,UBERON:0000996,UBERON:0016475,UBERON:0003403",Cesarean section,EFO:0009636,vaginal delivery (Va),C-section (Cesarean section),NA,4,5,NA,16S,2,Roche454,ANOSIM,0.001,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:620/1/1,Study 620,prospective cohort,31609493,doi:10.1111/jgh.14868,NA,"Burt AD, Fujishiro M, Hattori S, Hirooka Y, Honda T, Nakamura M, Singh R, Yamamoto K, Yamamura T, Zorron Cheng Tao Pu L",Microbiota profile is different for early and invasive colorectal cancer and is consistent throughout the colon,Journal of Gastroenterology and Hepatology,2020,"colonoscopy, colorectal neoplasms, fusobacterium nucleatum, gastrointestinal microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Early cancer group,Invasive cancer group,Patients undergoing ESD procedure for colorectal cancer,11,14,NA,16S,34,Illumina,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Figure 5, Figure 4",24 May 2022,Jeshudy,"Jeshudy,Fatima",Figure 1: Fusobacterium genera profile for invasive (YES) and early (NO) colorectal cancer.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.",2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|155615;2|32066|203490|203491|203492|848|68766,Complete,Fatima
bsdb:620/1/2,Study 620,prospective cohort,31609493,doi:10.1111/jgh.14868,NA,"Burt AD, Fujishiro M, Hattori S, Hirooka Y, Honda T, Nakamura M, Singh R, Yamamoto K, Yamamura T, Zorron Cheng Tao Pu L",Microbiota profile is different for early and invasive colorectal cancer and is consistent throughout the colon,Journal of Gastroenterology and Hepatology,2020,"colonoscopy, colorectal neoplasms, fusobacterium nucleatum, gastrointestinal microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Early cancer group,Invasive cancer group,Patients undergoing ESD procedure for colorectal cancer,11,14,NA,16S,34,Illumina,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, Figure 3",9 July 2022,Jeshudy,"Jeshudy,Fatima",Oribacterium parvum profile for invasive (YES) and early (NO) colorectal cancer (colon samples).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239|186801|3085636|186803|265975|1501329;2|1239|186801|186802|1898207,Complete,Fatima
bsdb:621/1/1,Study 621,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,27 May 2022,Jeshudy,Jeshudy,Linear discriminant analysis (LDA) effect size (LEfSe) in samples collected after treatment (week 6),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.",2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|28050|2049031,Complete,Fatima
bsdb:621/1/2,Study 621,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3,2 June 2022,Jeshudy,"Jeshudy,Peace Sandy",Linear discriminant analysis (LDA) effect size (LEfSe) in samples collected after treatment (week 6),decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. DL-VIII",2|1239|909932|1843489|31977|29465;2|1239|186801|186802|31979|1485|641107,Complete,Fatima
bsdb:621/2/1,Study 621,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 2,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 4, text",27 May 2022,Jeshudy,"Jeshudy,Fatima","Regression coefficients (β) and P-values for the interaction term comparing the abundance of pre-specified faecal bacterial taxa in aspirin to placebo arm after 3 weeks (upper row) and 6 weeks (lower row) of treatment vs baseline, the ASMIC study",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|74201|203494|48461|1647988|239934;2|1239|186801|3085636|186803|28050|2049031;2|1239|186801|186802|216572;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851,Complete,Fatima
bsdb:621/2/2,Study 621,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 2,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 4, text",27 May 2022,Jeshudy,"Jeshudy,Fatima","Regression coefficients (β) and P-values for the interaction term comparing the abundance of pre-specified faecal bacterial taxa in aspirin to placebo arm after 3 weeks (upper row) and 6 weeks (lower row) of treatment vs baseline, the ASMIC study",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|189330;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:622/1/1,Study 622,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu YN, Yu TC, Zhao HJ, Sun TT, Chen HM, Chen HY, An HF, Weng YR, Yu J, Li M, Qin WX, Ma X, Shen N, Hong J , Fang JY",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Negative control group,CRA and CRC groups,Patients with CRA (colorectal adenoma) or CRC (colorectal carcinoma) confirmed by colonoscopy and pathological examination,52,89,6 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 1,2 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between the control group and the CRA+CRC patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:622/1/2,Study 622,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu YN, Yu TC, Zhao HJ, Sun TT, Chen HM, Chen HY, An HF, Weng YR, Yu J, Li M, Qin WX, Ma X, Shen N, Hong J , Fang JY",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Negative control group,CRA and CRC groups,Patients with CRA (colorectal adenoma) or CRC (colorectal carcinoma) confirmed by colonoscopy and pathological examination,52,89,6 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 1,2 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between the control group and the CRA+CRC patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803|33042;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|32066|203490|203491|203492|848;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:622/2/1,Study 622,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu YN, Yu TC, Zhao HJ, Sun TT, Chen HM, Chen HY, An HF, Weng YR, Yu J, Li M, Qin WX, Ma X, Shen N, Hong J , Fang JY",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 2,China,Mus musculus,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Control (male C57BL/6-APCMin/+ and male wild-type C57BL/6),Fn Mice,Mice administered with F. nucleatum (Fn),10,10,None,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,4 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between control mice and Fn-treated mice,increased,"k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|544448;2|74201;2|32066|203490,Complete,Claregrieve1
bsdb:622/3/1,Study 622,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu YN, Yu TC, Zhao HJ, Sun TT, Chen HM, Chen HY, An HF, Weng YR, Yu J, Li M, Qin WX, Ma X, Shen N, Hong J , Fang JY",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 3,China,Mus musculus,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,DMH Treated Mice,Fn+DMH Treated Mice,Mice treated with Fn and DMH,10,10,None,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,4 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between DMH-treated mice and Fn+DMH treated mice,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Mycoplasmatota",2|32066|203490;2|74201;2|544448,Complete,Claregrieve1
bsdb:622/4/1,Study 622,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu YN, Yu TC, Zhao HJ, Sun TT, Chen HM, Chen HY, An HF, Weng YR, Yu J, Li M, Qin WX, Ma X, Shen N, Hong J , Fang JY",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 4,China,Mus musculus,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Fn+DMH Treated Mice,BBR+Fn+DMH Treated Mice,"Mice treated with BBR, Fn and DMH",10,10,None,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,22 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between Fn+DMH-treated mice and BBR+Fn+DMH treated mice,decreased,"k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Verrucomicrobiota",2|544448;2|74201,Complete,Claregrieve1
bsdb:623/1/1,Study 623,case-control,28753429,10.1016/j.cell.2017.07.008,NA,"Yu T, Guo F, Yu Y, Sun T, Ma D, Han J, Qian Y, Kryczek I, Sun D, Nagarsheth N, Chen Y, Chen H, Hong J, Zou W , Fang JY",Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy,Cell,2017,"Colorectal cancer, F.nucleatum, Toll-like receptor, autophagy, chemoresistance, miRNA, recurrence",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Patients without CRC recurrence,Patients with CRC recurrence,Patient tissues with colorectal cancer recurrence,16,15,6 months,16S,123,Roche454,LEfSe,NA,NA,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,4 June 2022,Jeshudy,Jeshudy,"(B) Linear discriminant analysis (LDA) coupled with the effect size measurements identifies
the significant abundance of data in A. Taxa enriched in recurrent (Red) and non-recurrent
(Blue) patients are indicated with negative (Red) or positive (Blue) LDA scores, respectively.
Only taxa greater than LDA threshold of 3.5 are shown.",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|216572|1486725;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838,Complete,Fatima
bsdb:623/1/2,Study 623,case-control,28753429,10.1016/j.cell.2017.07.008,NA,"Yu T, Guo F, Yu Y, Sun T, Ma D, Han J, Qian Y, Kryczek I, Sun D, Nagarsheth N, Chen Y, Chen H, Hong J, Zou W , Fang JY",Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy,Cell,2017,"Colorectal cancer, F.nucleatum, Toll-like receptor, autophagy, chemoresistance, miRNA, recurrence",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Patients without CRC recurrence,Patients with CRC recurrence,Patient tissues with colorectal cancer recurrence,16,15,6 months,16S,123,Roche454,LEfSe,NA,NA,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1B,4 June 2022,Jeshudy,Jeshudy,"Linear discriminant analysis (LDA) coupled with the effect size measurements identifies
the significant abundance of data in A. Taxa enriched in recurrent (Red) and non-recurrent
(Blue) patients are indicated with negative (Red) or positive (Blue) LDA scores, respectively.
Only taxa greater than LDA threshold of 3.5 are shown.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135614|32033|40323;2|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:624/2/1,Study 624,case-control,34584098,10.1038/s41467-021-25965-x,NA,"Okumura S, Konishi Y, Narukawa M, Sugiura Y, Yoshimoto S, Arai Y, Sato S, Yoshida Y, Tsuji S, Uemura K, Wakita M, Matsudaira T, Matsumoto T, Kawamoto S, Takahashi A, Itatani Y, Miki H, Takamatsu M, Obama K, Takeuchi K, Suematsu M, Ohtani N, Fukunaga Y, Ueno M, Sakai Y, Nagayama S , Hara E",Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion,Nature communications,2021,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Individuals,Patients with early CRC,Patients with early colorectal cancer,129,136,1 Month,16S,12,Illumina,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,5 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between early CRC patients and healthy controls,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis",2|32066|203490|203491|203492|848|851;2|1239|91061|1385|539738|1378|29391;2|1239|186801|3082720|186804|1257|341694,Complete,Claregrieve1
bsdb:624/3/1,Study 624,case-control,34584098,10.1038/s41467-021-25965-x,NA,"Okumura S, Konishi Y, Narukawa M, Sugiura Y, Yoshimoto S, Arai Y, Sato S, Yoshida Y, Tsuji S, Uemura K, Wakita M, Matsudaira T, Matsumoto T, Kawamoto S, Takahashi A, Itatani Y, Miki H, Takamatsu M, Obama K, Takeuchi K, Suematsu M, Ohtani N, Fukunaga Y, Ueno M, Sakai Y, Nagayama S , Hara E",Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion,Nature communications,2021,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Individuals,Patients with advanced CRC,Patients with early colorectal cancer,129,153,1 Month,16S,12,Illumina,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,5 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between advanced CRC patients and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",2|976|200643|171549|171552|1283313|76122;2|1239|909932|1843489|31977|39948|39950;2|32066|203490|203491|203492|848|851;2|1239|91061|1385|539738|1378|29391;2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|3082720|186804|1257|1261;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|28131;2|1239|526524|526525|128827|123375|102148,Complete,Claregrieve1
bsdb:624/4/NA,Study 624,case-control,34584098,10.1038/s41467-021-25965-x,NA,"Okumura S, Konishi Y, Narukawa M, Sugiura Y, Yoshimoto S, Arai Y, Sato S, Yoshida Y, Tsuji S, Uemura K, Wakita M, Matsudaira T, Matsumoto T, Kawamoto S, Takahashi A, Itatani Y, Miki H, Takamatsu M, Obama K, Takeuchi K, Suematsu M, Ohtani N, Fukunaga Y, Ueno M, Sakai Y, Nagayama S , Hara E",Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion,Nature communications,2021,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Surgical resection,EFO:0009744,Before resection,After resection,Patients post surgical resection of Cohort-1 CRC specimens,380,380,1 Month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:625/1/1,Study 625,"cross-sectional observational, not case-control",34442687,10.3390/microorganisms9081608,https://pubmed.ncbi.nlm.nih.gov/34442687/,"Lewis CR, Bonham KS, McCann SH, Volpe AR, D'Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, Deoni SCL , Klepac-Ceraj V",Family SES Is Associated with the Gut Microbiome in Infants and Children,Microorganisms,2021,"childhood, infant, microbiome, socioeconomic status, stress",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower socioeconomic status,Increasing socioeconomic status,588 Metagenomics from infants and children of high and low socioeconomic families as continuous variables.,NA,NA,2 weeks,WMS,NA,Illumina,NA,0.05,NA,NA,NA,"age,delivery procedure,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,FIGURE 2; FIGURE 3,6 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Figure 2. Model Taxonomic Summaries. Stacked bar plots showing the average relative abundance of the genera assessed with socioeconomic status (SES).


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

Figure 3. Parents with higher SES(higher years of education) had children who scored higher in the latent microbiome factor. That is, they were higher on Faecalibacterium, Eubacterium, Anaerostipes, and Lachnospiraceae compared with the scores of infants and children from low SES families.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803,Complete,Chloe
bsdb:625/1/2,Study 625,"cross-sectional observational, not case-control",34442687,10.3390/microorganisms9081608,https://pubmed.ncbi.nlm.nih.gov/34442687/,"Lewis CR, Bonham KS, McCann SH, Volpe AR, D'Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, Deoni SCL , Klepac-Ceraj V",Family SES Is Associated with the Gut Microbiome in Infants and Children,Microorganisms,2021,"childhood, infant, microbiome, socioeconomic status, stress",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower socioeconomic status,Increasing socioeconomic status,588 Metagenomics from infants and children of high and low socioeconomic families as continuous variables.,NA,NA,2 weeks,WMS,NA,Illumina,NA,0.05,NA,NA,NA,"age,delivery procedure,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,FIGURE 3,6 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Parents with higher SES (higher years of education) had children who scored lower 
in Bacteroides relative abundance compared with infants and children from families of low SES.

 Variables are continuous measures. The gut microbiome decreases for a 1 unit increase in SES.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Chloe
bsdb:626/1/1,Study 626,"cross-sectional observational, not case-control",34617511,10.7554/eLife.70349,https://pubmed.ncbi.nlm.nih.gov/34617511,"Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK , Turnbaugh PJ",The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health,eLife,2021,"biogeography, ethnicity, human, human gut microbiome, infectious disease, metabolic syndrome, microbiology, mouse, multi-omics, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,White (W),East Asian (EA),A balanced distribution of both lean and obese adults who identified as East Asians residing within the Bay area of San Fransisco.,24,22,Unspecified,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 1,8 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Aiyshaaaa,Peace Sandy","The gut microbiota is distinct between East Asian (EA) and White (W) subjects living in the Bay Area.
(C) CLR abundances of all bacterial phyla between EA and W subjects. p-values determined using Wilcoxon rank-sum tests.",increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Peace Sandy
bsdb:626/1/2,Study 626,"cross-sectional observational, not case-control",34617511,10.7554/eLife.70349,https://pubmed.ncbi.nlm.nih.gov/34617511,"Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK , Turnbaugh PJ",The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health,eLife,2021,"biogeography, ethnicity, human, human gut microbiome, infectious disease, metabolic syndrome, microbiology, mouse, multi-omics, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,White (W),East Asian (EA),A balanced distribution of both lean and obese adults who identified as East Asians residing within the Bay area of San Fransisco.,24,22,Unspecified,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 1,8 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Aiyshaaaa,Peace Sandy",The gut microbiota is distinct between East Asian (EA) and White (W) subjects living in the Bay Area. (C) CLR abundances of all bacterial phyla between EA and W subjects. p-values determined using Wilcoxon rank-sum tests.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|s__Actinomycetes bacterium,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Synergistota,k__Bacteria|p__Campylobacterota",2|1239;2|201174|1760|1883427;2|74201;2|32066;2|508458;2|29547,Complete,Peace Sandy
bsdb:627/1/1,Study 627,"cross-sectional observational, not case-control",30641975,10.3390/microorganisms7010017,https://pubmed.ncbi.nlm.nih.gov/30641975/,"Bowyer RCE, Jackson MA, Le Roy CI, Ni Lochlainn M, Spector TD, Dowd JB , Steves CJ",Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study,Microorganisms,2019,"SES, microbiome, microbiota, sociobiome, socioeconomic status",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Higher SES (income= > £25,000)","lower SES (income<£25,000)","Lower socioeconomic status(SES) with higher deprivation by income <£25,000",457,342,Unspecified,16S,4,Illumina,edgeR,0.05,TRUE,NA,NA,"age,body mass index,diet",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 2A; Tabel 2,10 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Differential abundance of OTUs with socioeconomic variables and covariates. DeSeq2 calculated the differential abundance of OTUs in: (A). Between the lowest and highest levels of deprivation for education, income, and the IMD, and in models adjusted for age, Body Mass Index (BMI), health deficit (FI), and diet (HEI).
 Table 2. Summary of taxa assigned to OTUs found to be differentially abundant between the most-deprived and least-deprived measures of socioeconomic status in at least two models. Only taxa with multiple OTUs assigned to it, or with multiple SES factors associated with it, and with q-value <, 0.01 are discussed. OTUs relatively enriched in the least deprived compared to the highest for each SES variable are indicated with (+); those enriched in the most deprived compared to the least indicated with (−); where multiple directions of association were observed, this is indicated with (+/−).",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|1224|1236|91347;2|1239|526524|526525;2|1239|91061|186826,Complete,NA
bsdb:627/1/2,Study 627,"cross-sectional observational, not case-control",30641975,10.3390/microorganisms7010017,https://pubmed.ncbi.nlm.nih.gov/30641975/,"Bowyer RCE, Jackson MA, Le Roy CI, Ni Lochlainn M, Spector TD, Dowd JB , Steves CJ",Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study,Microorganisms,2019,"SES, microbiome, microbiota, sociobiome, socioeconomic status",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Higher SES (income= > £25,000)","lower SES (income<£25,000)","Lower socioeconomic status(SES) with higher deprivation by income <£25,000",457,342,Unspecified,16S,4,Illumina,edgeR,0.05,TRUE,NA,NA,"age,body mass index,diet",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 2A; Table 2,10 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Differential abundance of OTUs with socioeconomic variables and covariates. DeSeq2 calculated the differential abundance of OTUs in: (A). Between the lowest and highest levels of deprivation for education, income, and the IMD, and in models adjusted for age, Body Mass Index (BMI), health deficit (FI), and diet (HEI).
Table 2. Summary of taxa assigned to OTUs found to be differentially abundant between the most-deprived and least-deprived measures of socioeconomic status
in at least two models. Only taxa with multiple OTUs assigned to it, or with multiple SES factors associated with it, and with q-value <, 0.01 are discussed. OTUs
relatively enriched in the least deprived compared to the highest for each SES variable are indicated with (+); those enriched in the most deprived compared to the least
indicated with (−); where multiple directions of association were observed, this is indicated with (+/−).",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|186801|186802;2|74201|203494|48461;2|976|200643|171549|171550,Complete,NA
bsdb:628/1/1,Study 628,"cross-sectional observational, not case-control",26859894,10.1371/journal.pone.0148952,https://pubmed.ncbi.nlm.nih.gov/26859894/,"Miller GE, Engen PA, Gillevet PM, Shaikh M, Sikaroodi M, Forsyth CB, Mutlu E , Keshavarzian A",Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults,PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High SES,Low SES,"44 healthy participants from low-income neighborhoods with a median annual income of $20,100 and a 35% unemployment rate and neighborhoods at the high end, with a median income of $129,570 and an unemployment rate under 5%).
(Income level as a continuous variable.)",44,NA,3 months,16S,NA,Roche454,"Linear Regression,Spearman Correlation",0.05,NA,NA,NA,"age,alcohol drinking,body mass index,race,sex,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,FIGURE 3,11 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Scatter-plot of neighborhood SES and bacterial genera. Figs depict associations between neighborhood SES and Prevotella to Bacteroides ratio (upper panel), as well as the relative abundance of Prevotella (middle panel) and Bacteroides (lower panel). Specimens are biopsies excised from sigmoid
mucosa.",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:628/1/2,Study 628,"cross-sectional observational, not case-control",26859894,10.1371/journal.pone.0148952,https://pubmed.ncbi.nlm.nih.gov/26859894/,"Miller GE, Engen PA, Gillevet PM, Shaikh M, Sikaroodi M, Forsyth CB, Mutlu E , Keshavarzian A",Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults,PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High SES,Low SES,"44 healthy participants from low-income neighborhoods with a median annual income of $20,100 and a 35% unemployment rate and neighborhoods at the high end, with a median income of $129,570 and an unemployment rate under 5%).
(Income level as a continuous variable.)",44,NA,3 months,16S,NA,Roche454,"Linear Regression,Spearman Correlation",0.05,NA,NA,NA,"age,alcohol drinking,body mass index,race,sex,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,FIGURE 3,11 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Scatter-plot of neighborhood SES and bacterial genera. Figs depict associations between neighborhood SES and Prevotella to Bacteroides ratio (upper panel), as well as the relative abundance of Prevotella (middle panel) and Bacteroides (lower panel). Specimens are biopsies excised from sigmoid
mucosa.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
bsdb:629/1/1,Study 629,"cross-sectional observational, not case-control",26181352,10.1001/jamaoncol.2015.1377,NA,"Mima K, Sukawa Y, Nishihara R, Qian ZR, Yamauchi M, Inamura K, Kim SA, Masuda A, Nowak JA, Nosho K, Kostic AD, Giannakis M, Watanabe H, Bullman S, Milner DA, Harris CC, Giovannucci E, Garraway LA, Freeman GJ, Dranoff G, Chan AT, Garrett WS, Huttenhower C, Fuchs CS , Ogino S",Fusobacterium nucleatum and T Cells in Colorectal Carcinoma,JAMA oncology,2015,NA,Experiment 1,United States of America,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Tumor Tissue of Colorectal Cancer Cases,Adjacent Non-Tumor Tissue of Colorectal Cancer Cases,Both colon and rectal carcinomas were included on the basis of the colorectal continuum model. Patients were followed up until death or the end of follow-up.,558,558,None,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,family history of cancer,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,12 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential abundance of Fusobacterium nucleatum in 558 pairs of colorectal carcinoma and adjacent non-tumor tissues,increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,2|32066|203490|203491|203492|848|851,Complete,Claregrieve1
bsdb:630/1/1,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage I/II (SI/II),stage I and II CRCs,251,111,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,Jeshudy,"Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",2|201174|84998|84999|84107|102106|74426;2|32066|203490|203491|203492|848|851;2|1239|91061|1385|539738|1378|29391;2|201174|84998|84999|1643824|2767353|1382;2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|3082720|186804|1257|1261;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171551|836|281920;2|201174|1760|2037|2049|2529408|1660;2|1239|526524|526525|128827|123375|102148,Complete,Atrayees
bsdb:630/1/2,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage I/II (SI/II),stage I and II CRCs,251,111,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,Jeshudy,"Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara",2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|28050|28051,Complete,Atrayees
bsdb:630/2/1,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage III/IV (SIII/IV),stage III and IV CRCs,251,74,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,Jeshudy,Phylum distribution of the number of species that are either elevated or depleted in each of the four stages compared to the healthy controls.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus sanfranciscensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio vietnamensis",2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|1643824|2767353|1382;2|201174|1760|2037|2049|2529408|1660;2|1239|526524|526525|128827|123375|102148;2|976|200643|171549|171551|836|281920;2|32066|203490|203491|203492|848|851;2|1239|909932|909929|1843491|970|69823;2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|33958|2767881|1625;2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3082720|186804|1257|1261;2|1239|186801|3082720|186804|1257|341694;2|200940|3031449|213115|194924|35832|35833;2|200940|3031449|213115|194924|2909705|201571,Complete,Atrayees
bsdb:630/2/2,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage III/IV (SIII/IV),stage III and IV CRCs,251,74,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,Jeshudy,"Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara",2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|28050|28051,Complete,Atrayees
bsdb:630/3/1,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),S0,stage 0/pTis CRC (S0),251,73,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,Jeshudy,"Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus sanfranciscensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio longreachensis",2|201174|84998|84999|1643824|2767353|1382;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|171551|836|281920;2|32066|203490|203491|203492|848|851;2|201174|1760|2037|2049|1654|1656;2|201174|1760|2037|2049|2529408|1660;2|1239|526524|526525|128827|123375|102148;2|1239|909932|1843488|909930|33024|626940;2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|33958|2767881|1625;2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|3082720|186804|1257|341694;2|200940|3031449|213115|194924|872|29505,Complete,Atrayees
bsdb:630/3/2,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),S0,stage 0/pTis CRC (S0),251,73,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,Jeshudy,"Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|3085636|186803|28050|28051;2|1239|186801|3085636|186803|28050|39485,Complete,Atrayees
bsdb:630/4/1,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),MP,"multiple polypoid adenomas with low- grade dysplasia (MP, more than three adenomas, mostly more than five adenomas)",251,67,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,Jeshudy,"Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio vietnamensis",2|201174|84998|84999|1643824|2767353|1382;2|32066|203490|203491|203492|848|851;2|201174|1760|2037|2049|2529408|1660;2|1239|909932|1843488|909930|33024|626940;2|1239|909932|909929|1843491|970|69823;2|200940|3031449|213115|194924|2909705|201571,Complete,Atrayees
bsdb:630/4/2,Study 630,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T , Yamada T",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),MP,"multiple polypoid adenomas with low- grade dysplasia (MP, more than three adenomas, mostly more than five adenomas)",251,67,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,Jeshudy,"Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|3085636|186803|28050|28051;2|1239|186801|3085636|186803|28050|39485,Complete,Atrayees
bsdb:631/1/1,Study 631,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C , Wang J",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy Controls,Advanced Colorectal Adenoma,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,42,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4a,14 June 2022,Jeshudy,Jeshudy,Control versus advanced adenoma (n = 55 and 42).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis",2|976|200643|171549|171552|577309|454154;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|204516,Complete,Fatima
bsdb:631/1/2,Study 631,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C , Wang J",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy Controls,Advanced Colorectal Adenoma,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,42,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4a,14 June 2022,Jeshudy,Jeshudy,Control versus advanced adenoma (n = 55 and 42).,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans",2|201174|1760|85004|31953|1678|28025;2|1239|91061|186826|1300|1301|1309,Complete,Fatima
bsdb:631/2/1,Study 631,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C , Wang J",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal Cancer,"colorectal cancer patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,41,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 4c,14 June 2022,Jeshudy,Jeshudy,"Control versus carcinoma (n = 55 and 41). For all MLGs containing >100 genes, the direction of enrichment was determined by Wilcoxon rank-sum test (P < 0.05, Supplementary Data 3). Size of the nodes scales with the number of genes (102~3613) in the MLG.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis",2|201174|1760|2037|2049|1654|1656;2|1239|186801|186802|31979|1485|1506;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|1300|1301|1308;2|201174|1760|85004|31953|1678|28025,Complete,Fatima
bsdb:631/2/2,Study 631,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C , Wang J",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal Cancer,"colorectal cancer patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,41,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 4c,14 June 2022,Jeshudy,Jeshudy,"Control versus carcinoma (n = 55 and 41). For all MLGs containing >100 genes, the direction of enrichment was determined by Wilcoxon rank-sum test (P < 0.05, Supplementary Data 3). Size of the nodes scales with the number of genes (102~3613) in the MLG.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|816|29523;2|976|200643|171549|815|816|28111;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|815|909656|204516;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|816|371601;2|976|200643|171549|815|909656|821;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|1853231|283168|28118;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|1898203;2|1239|186801|3085636|186803|1506553|1512;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|815|816|47678;2|976|200643|171549|171552|577309|454154;2|1224|28216|80840|1891238;2|1224|28216|80840|995019|40544|40545;2|1224|1236|91347|543|561|562;2|1239|909932|1843488|909930|904|187327;2|1239|909932|1843489|31977|29465|39777,Complete,Fatima
bsdb:631/3/1,Study 631,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C , Wang J",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Colorectal Adenoma,Colorectal Cancer,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",42,41,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 4b,14 June 2022,Jeshudy,Jeshudy,"Advanced adenoma vs carcinoma (n = 42, 41).",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus",2|1239|186801|186802|31979|1485|1506;2|1239|91061|186826|1300|1301|1308;2|201174|1760|85004|31953|1678|28025;2|201174|1760|2037|2049|1654|1656,Complete,Fatima
bsdb:631/3/2,Study 631,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C , Wang J",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Colorectal Adenoma,Colorectal Cancer,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",42,41,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 4b,14 June 2022,Jeshudy,Jeshudy,"Advanced adenoma vs carcinoma (n = 42, 41).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",2|976|200643|171549|815|816|371601;2|976|200643|171549|815|909656|204516;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|29523;2|976|200643|171549|1853231|283168|28118;2|200940|3031449|213115|194924|35832|35833;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171550|239759|28117;2|1224|28216|80840|1891238;2|1239|186801|3085636|186803|1898203;2|1239|186801|3085636|186803|1506553|1512;2|1239|909932|1843488|909930|904|187327;2|1224|1236|91347|543|561|562;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|28111;2|1224|28216|80840|995019|40544|40545;2|1239|909932|1843489|31977|29465|39777,Complete,Fatima
bsdb:632/1/1,Study 632,prospective cohort,27558272,10.1038/srep31775,https://pubmed.ncbi.nlm.nih.gov/27558272/,"Levin AM, Sitarik AR, Havstad SL, Fujimura KE, Wegienka G, Cassidy-Bushrow AE, Kim H, Zoratti EM, Lukacs NW, Boushey HA, Ownby DR, Lynch SV , Johnson CC","Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity",Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Neonates (median age = 1.2 months),Infants (median age = 6.6 months),Infants (median age: 6.6 months) children from a Detroit-based birth cohort,130,168,NIL,16S,4,Illumina,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,"age,breast feeding,delivery procedure,education level,household income,marital status,smoking status",increased,NA,NA,NA,NA,increased,Signature 1,"FIGURE 5 , FIGURE 6",13 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each 
factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.

Top genera significantly associated with each factor retained in multi-factor models of infant gut microbiome composition.
For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: BMI, body mass index; ISV, infant study visit at 6-months of age.",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964|1279;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|189330;2|1239|909932|909929|1843491|158846;2|976|200643|171549|171552|577309;2|1239|1737404|1737405|1570339|162289;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803|2383;2|976|200643|171549|815|816;2|976|200643|171549|2005520|156973;2|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:632/1/2,Study 632,prospective cohort,27558272,10.1038/srep31775,https://pubmed.ncbi.nlm.nih.gov/27558272/,"Levin AM, Sitarik AR, Havstad SL, Fujimura KE, Wegienka G, Cassidy-Bushrow AE, Kim H, Zoratti EM, Lukacs NW, Boushey HA, Ownby DR, Lynch SV , Johnson CC","Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity",Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Neonates (median age = 1.2 months),Infants (median age = 6.6 months),Infants (median age: 6.6 months) children from a Detroit-based birth cohort,130,168,NIL,16S,4,Illumina,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,"age,breast feeding,delivery procedure,education level,household income,marital status,smoking status",increased,NA,NA,NA,NA,increased,Signature 2,"FIGURE 5 , FIGURE 6",13 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.

Top genera significantly associated with each factor retained in multi-factor models of infant gut microbiome composition. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: BMI, body mass index; ISV, infant study visit at 6-months of age.",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964|1279;2|1239|909932|1843489|31977|906;2|201174|1760|2037|2049|184869;2|1239|186801|186802|216572|119852;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:633/1/1,Study 633,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z, Guo B, Gao R, Zhu Q , Qin H",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 1,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal Cancer Patients,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",30,31,2 months,16S,3,Roche454,"T-Test,Chi-Square,Fisher's Exact Test,LEfSe",0.05,FALSE,3,"age,body mass index,sex",NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 1,"Figure 2B, Figure 3",25 July 2023,Andre,"Andre,Deacme,ChiomaBlessing",Different structures of gut microbiota between healthy individuals and CRC patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1224|1236|91347|543|1940338;2|32066|203490|203491|203492|848;2|1239|91061|186826|1300|1357;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|32066|203490|203491|203492;2|976|200643;2|976|200643|171549|171552;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539738;2|976|200643|171549|171551;2|1224|1236|135622|267890|22;2|1224|1236|135622|267890;2|1239|1737404|1737405|1570339|543311;2|1239|909932|1843489|31977|39948,Complete,Lwaldron
bsdb:633/1/2,Study 633,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z, Guo B, Gao R, Zhu Q , Qin H",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 1,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal Cancer Patients,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",30,31,2 months,16S,3,Roche454,"T-Test,Chi-Square,Fisher's Exact Test,LEfSe",0.05,FALSE,3,"age,body mass index,sex",NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 2,"Figure 2, Figure 3",25 July 2023,Andre,"Andre,Deacme,ChiomaBlessing",Different structures of gut microbiota between healthy individuals and CRC patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|1224|28216|80840|80864|12916;2|1224|1236|2887326|468|469;2|1224|28211;2|1224|28211|204458|76892|41275;2|1224|1236|91347|543|82976;2|1224|28211|204458|76892|75;2|976|117743|200644|2762318|2782229;2|976|117743|200644|49546|237;2|1224|28216|80840|75682|29580;2|976|117747|200666|84566|84567;2|201174|1760|85009|31957|1743;2|1224|1236|72274|135621|286;2|1224|1236|2887326|468|497;2|1224|1236|91347|1903411|34037;2|976|117747|200666|84566|28453;2|1224|28211|204457|41297|13687;2|1224|1236|135614|32033|40323;2|1239|91061|1385|186820|2755;2|1224|1236|2887326|468;2|976|117743|200644|49546;2|976|117743|200644;2|1224|1236|72274|135621;2|1224;2|1224|1236;2|1224|1236|72274,Complete,Lwaldron
bsdb:633/2/1,Study 633,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z, Guo B, Gao R, Zhu Q , Qin H",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 2,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,adjacent non-cancerous tissues,cancerous tissues,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",20,31,2 months,16S,3,Roche454,"T-Test,Chi-Square,Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 1,Figure 2D,26 July 2023,Andre,"Andre,Tolulopeo",The dominant genera of group cancerous compared to non-cancerous mucosa,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|815|816;2|1239|91061|186826|1300|1357;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:633/2/2,Study 633,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z, Guo B, Gao R, Zhu Q , Qin H",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 2,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,adjacent non-cancerous tissues,cancerous tissues,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",20,31,2 months,16S,3,Roche454,"T-Test,Chi-Square,Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 2,Figure 2D,26 July 2023,Andre,"Andre,Tolulopeo",The dominant genera of group cancerous compared to non-cancerous mucosa.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,Lwaldron
bsdb:633/3/1,Study 633,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z, Guo B, Gao R, Zhu Q , Qin H",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 3,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Sigmoid neoplasm,EFO:1001181,Proximal Colon Cancer,Distal Colorectal Cancer,"Distal colon cancer tissue samples obtained from patients diagnosed with colorectal cancer (CRC), located in the sigmoid colon (25–35 cm from anus)",15,16,2 months,16S,3,Roche454,"T-Test,Chi-Square,Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,increased,Signature 1,FIGURE 4,26 July 2023,Andre,"Andre,ChiomaBlessing",Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|1236|91347|543|1940338;2|32066|203490|203491|203492|848;2|32066|203490|203491|1129771|32067,Complete,Lwaldron
bsdb:633/3/2,Study 633,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z, Guo B, Gao R, Zhu Q , Qin H",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 3,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Sigmoid neoplasm,EFO:1001181,Proximal Colon Cancer,Distal Colorectal Cancer,"Distal colon cancer tissue samples obtained from patients diagnosed with colorectal cancer (CRC), located in the sigmoid colon (25–35 cm from anus)",15,16,2 months,16S,3,Roche454,"T-Test,Chi-Square,Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,increased,Signature 2,FIGURE 4,26 July 2023,Andre,"Andre,ChiomaBlessing",Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|508458|649775|649776|3029088|638847|1943581;2|1239|909932|909929|1843491|970,Complete,Lwaldron
bsdb:634/1/1,Study 634,prospective cohort,28844190,10.1902/jop.2017.160808,NA,"Duan X, Wu T, Xu X, Chen D, Mo A, Lei Y, Cheng L, Man Y, Zhou X, Wang Y , Yuan Q",Smoking May Lead to Marginal Bone Loss Around Non-Submerged Implants During Bone Healing by Altering Salivary Microbiome: A Prospective Study,Journal of periodontology,2017,"Alveolar bone loss, dental implants, microbiota, smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,smokers,patients who have smoked >10 cigarettes a day for at least 5 years.,10,10,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Table 2",13 April 2023,Chioma,"Chioma,Fatima",Significant differences between groups using Mann-Whitney test,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__uncultured Lachnoanaerobaculum sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__uncultured Stomatobaculum sp.",2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171551|836|837;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1304;2|1239|186801|186802|543314|56774;2|1239|186801|3085636|186803|1164882|1662275;2|1239|186801|3085636|186803|1213720|1662277,Complete,Fatima
bsdb:634/1/2,Study 634,prospective cohort,28844190,10.1902/jop.2017.160808,NA,"Duan X, Wu T, Xu X, Chen D, Mo A, Lei Y, Cheng L, Man Y, Zhou X, Wang Y , Yuan Q",Smoking May Lead to Marginal Bone Loss Around Non-Submerged Implants During Bone Healing by Altering Salivary Microbiome: A Prospective Study,Journal of periodontology,2017,"Alveolar bone loss, dental implants, microbiota, smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,smokers,patients who have smoked >10 cigarettes a day for at least 5 years.,10,10,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Table 2",13 April 2023,Chioma,"Chioma,Fatima",Significant differences between groups using Mann-Whitney test,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__uncultured Selenomonas sp.",2|1239|186801|3085636|186803|43996|43997;2|1239|186801|3085636|186803|265975|1501332;2|1239|526524|526525|128827|123375|102148;2|1239|909932|909929|1843491|970;2|1239|909932|909929|1843491|970|159275,Complete,Fatima
bsdb:635/1/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Less than High school diploma,Less than High school diploma,87,65,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,13 April 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees",The relative abundance of selected species based on education level.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,2|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:635/1/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Less than High school diploma,Less than High school diploma,87,65,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species based on education level.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171551|836;2|29547|3031852|213849|72294|194;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|1239|186801|3082720|3118655|44259;2|201174|1760|85004|31953|196081;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:635/2/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Some college or associate's degree,Some college or associate's degree,87,67,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,1 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees",The relative abundance of selected species based on education level.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,2|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:635/2/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Some college or associate's degree,Some college or associate's degree,87,67,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees",The relative abundance of selected species based on education level.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85004|31953|196081;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:635/3/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Alternative smokers,Alternative smokers,86,72,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees",The relative abundance of selected species in cigarette smokers and alternate smokers,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239|909932|1843489|31977|156454;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301;2|201174|1760|85004|31953|419014;2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:635/3/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Alternative smokers,Alternative smokers,86,72,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees",The relative abundance of selected species in cigarette smokers and alternate smokers,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|32066|203490|203491|1129771|34104;2|976|200643|171549|171551|836;2|976|117743|200644|2762318|59735;2|1224|28216|80840|119060|47670;2|1224|1236|135615|868|2717;2|1239|91061|1385|539738|1378;2|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:635/4/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Former smokers,Former smokers,86,43,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees",The relative abundance of selected species in cigarette smokers and former smokers,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|1283313;2|29547|3031852|213849|72294|194;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286,Complete,Atrayees
bsdb:635/4/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Former smokers,Former smokers,86,43,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in cigarette smokers and former smokers,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|1224|28216|206351|481|482;2|976|117743|200644|2762318|59735;2|1224|28216|80840|119060|47670;2|1224|1236|135625|712|724;2|1239|186801|186802|186807|2740;2|976|117743|200644|49546|1016,Complete,Atrayees
bsdb:635/5/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Never smokers,Never smokers,86,43,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in cigarette smokers and never smokers,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|1213720;2|976|200643|171549|171552|838;2|29547|3031852|213849|72294|194;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:635/5/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Never smokers,Never smokers,86,43,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in cigarette smokers and never smokers,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",2|1224|28216|206351|481|482;2|976|117743|200644|2762318|59735;2|1239|91061|186826|1300|1301;2|976|200643|171549|171551|836;2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1357;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|201174|1760|85004|31953|1678;2|1224|1236|135625|712|713,Complete,Atrayees
bsdb:635/6/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Secondhand smokers,Secondhand smokers,86,38,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in cigarette smokers and secondhand smokers,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|33958|1578;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|156454;2|201174|1760|2037|2049|1654,Complete,Atrayees
bsdb:635/6/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Secondhand smokers,Secondhand smokers,86,38,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in cigarette smokers and secondhand smokers,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|117743|200644|2762318|59735;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|539738|1378;2|976|200643|171549|171552|1283313;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:635/7/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 7,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Asian,Asian,97,22,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in Non-Hispanic whites and Asians.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,2|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:635/8/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 8,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Hispanic,Hispanics,97,71,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in Non-Hispanic whites and Hispanics,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|29547|3031852|213849|72294|194;2|1239|186801|3082720|3118655|44259;2|203691|203692|136|2845253|157;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:635/9/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 9,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Non-Hispanic black,Non-Hispanic black,97,75,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in Non-Hispanic whites and Non-Hispanic blacks,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",2|1239|909932|1843489|31977|29465;2|1224|1236|135615|868|2717;2|32066|203490|203491|1129771|34104,Complete,Atrayees
bsdb:635/9/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 9,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Non-Hispanic black,Non-Hispanic black,97,75,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in Non-Hispanic whites and Non-Hispanic blacks,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|171552|838;2|29547|3031852|213849|72294|194;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|156454;2|201174|1760|85004|31953|1678;2|1239|186801|3082720|3118655|44259;2|976|200643|171549|171552|1283313;2|544448|31969|186329|2146|2147;2|976|200643|171549|171551|836,Complete,Atrayees
bsdb:635/10/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 10,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Males,Females,Females,132,150,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,sex,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in males and females,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|1224|1236|135625|712|713;2|203691|203692|136|2845253|157;2|976|200643|171549|171551|836,Complete,Atrayees
bsdb:635/11/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 11,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 35-64,age group 35-64,70,NA,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in age group 20-29 and age group 35-64,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",2|976|200643|171549|171551|836;2|1224|1236|72274|135621|286;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|713,Complete,Atrayees
bsdb:635/11/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 11,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 35-64,age group 35-64,70,NA,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in age group 20-29 and age group 35-64,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067,Complete,Atrayees
bsdb:635/12/1,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 12,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 65 and over,age group 65 and over,70,NA,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in age group 20-29 and age group 65 and over,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella",2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|838;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|1129771|32067;2|203691|203692|136|2845253|157;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|43996;2|1239|909932|1843489|31977|39948;2|1239|186801|3082720|186804|1257;2|1224|1236|135625|712|724;2|976|117743|200644|2762318|59735,Complete,Atrayees
bsdb:635/12/2,Study 635,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L , Dowd JB",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 12,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 65 and over,age group 65 and over,70,NA,NA,16S,4,Illumina,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,Atrayees,The relative abundance of selected species in age group 20-29 and age group 65 and over,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|91061|186826|1300|1357;2|976|117743|200644|49546|1016;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|196081;2|1239|909932|1843489|31977|156454,Complete,Atrayees
bsdb:636/1/1,Study 636,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X, Mi Q, Yang J, Guan Y, Zeng W, Xiang H, Liu X, Yang W, Yang G, Li X, Cui Y , Gao Q",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non Smokers,Tobacco smokers,The volunteers who smoked tobacco,6,14,6 months,16S,45,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 1,Figure 4 (C-F),14 March 2023,Annabelcute,"Annabelcute,Aiyshaaaa,Atrayees","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|171552;2|976|200643|171549|171551|836,Complete,Atrayees
bsdb:636/2/2,Study 636,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X, Mi Q, Yang J, Guan Y, Zeng W, Xiang H, Liu X, Yang W, Yang G, Li X, Cui Y , Gao Q",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non Smokers,E-cigarette smokers,The volunteers who smoked electronic cigarettes.,6,5,6 months,16S,45,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 4 (C-F),6 June 2023,Aiyshaaaa,Aiyshaaaa,"The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|1224|28216|206351|481|482;2|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:636/3/1,Study 636,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X, Mi Q, Yang J, Guan Y, Zeng W, Xiang H, Liu X, Yang W, Yang G, Li X, Cui Y , Gao Q",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Tobacco smokers,E-cigarette smokers,The volunteers who smoked electronic cigarettes.,14,5,6 months,16S,45,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4 (C-F),6 June 2023,Aiyshaaaa,"Atrayees,Aiyshaaaa","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,2|1224|28216|206351|481|482,Complete,Atrayees
bsdb:636/3/2,Study 636,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X, Mi Q, Yang J, Guan Y, Zeng W, Xiang H, Liu X, Yang W, Yang G, Li X, Cui Y , Gao Q",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Tobacco smokers,E-cigarette smokers,The volunteers who smoked electronic cigarettes.,14,5,6 months,16S,45,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4 (C-F),6 June 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,Atrayees
bsdb:636/5/1,Study 636,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X, Mi Q, Yang J, Guan Y, Zeng W, Xiang H, Liu X, Yang W, Yang G, Li X, Cui Y , Gao Q",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Quitting smokers,Tobacco smokers,Volunteers who are tobacco smokers,8,14,6 months.,16S,45,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 4(C-F),20 June 2023,Atrayees,Atrayees,"The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|171552;2|976|200643|171549|171551|836,Complete,Atrayees
bsdb:636/5/2,Study 636,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X, Mi Q, Yang J, Guan Y, Zeng W, Xiang H, Liu X, Yang W, Yang G, Li X, Cui Y , Gao Q",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Quitting smokers,Tobacco smokers,Volunteers who are tobacco smokers,8,14,6 months.,16S,45,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 4(C-F),21 June 2023,Atrayees,Atrayees,"The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,2|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:636/6/2,Study 636,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X, Mi Q, Yang J, Guan Y, Zeng W, Xiang H, Liu X, Yang W, Yang G, Li X, Cui Y , Gao Q",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 6,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Quitting smokers,E-cigarette smokers,Volunteers who smoke E-cigarettes,8,5,6 months.,16S,45,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4(C-F),20 June 2023,Atrayees,Atrayees,"The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,2|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:637/1/1,Study 637,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S, Kong C, Yang Y, Cai S, Li X, Cai G , Ma Y",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 1,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Individuals,CRC,Patients with colorectal cancer,58,161,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 1,Table S9 / Figure S1F,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRC cohort and controls,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Thermoflavimicrobium",2|1239|1737404|1737405|1570339|165779;2|1239|186801|3085636|186803|207244;2|201174|1760|85006|85020|43668;2|1224|28211|356|41294|374;2|976|117743|200644|2762318|501783;2|1117;2|1239|91061|1385|539738|1378;2|201174|1760|85006|1268|1269;2|1224|28216|206351|481|482;2|1224|1236|91347|1903409|53335;2|1224|1236|72274|135621|286;2|1224|1236|2887326|468|497;2|74201|134549;2|1239|91061|186826|1300|1301;2|1239|91061|1385|186824|292636,Complete,Claregrieve1
bsdb:637/1/2,Study 637,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S, Kong C, Yang Y, Cai S, Li X, Cai G , Ma Y",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 1,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Individuals,CRC,Patients with colorectal cancer,58,161,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 2,Table S9,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRC cohort and controls,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Synergistota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter",2|976;2|32066;2|201174;2|95818;2|203691;2|508458;2|1117;2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|838;2|32066|203490|203491|203492|848;2|1224|1236|135614|32033|68,Complete,Claregrieve1
bsdb:637/2/1,Study 637,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S, Kong C, Yang Y, Cai S, Li X, Cai G , Ma Y",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 2,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal adenoma,EFO:0005406,Healthy Individuals,CRA,Patients with colorectal adenoma,58,34,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 1,Table S6-7,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRA cohort and controls,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas",2|1239;2|57723;2|142182|219685;2|40117|203693|189778|189779|1234;2|200795;2|74201;2|1239|91061|186826|1300|1301;2|1117;2|1239|91061|1385|539738|1378;2|142182|219685|219686|219687|173479;2|1239|186801|186802|204475;2|74201|134549;2|1224|28211|356|41294|374;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85021;2|1224|1236|135614|32033|338,Complete,Claregrieve1
bsdb:637/2/2,Study 637,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S, Kong C, Yang Y, Cai S, Li X, Cai G , Ma Y",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 2,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal adenoma,EFO:0005406,Healthy Individuals,CRA,Patients with colorectal adenoma,58,34,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 2,Table S6-7,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRA cohort and controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Aestuariicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Synergistota,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota",2|201174|1760|2037|2049|1654;2|1224|28211|204455|31989|2054427;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|156454;2|1239|186801|3082720|3030910|109326;2|1239|91061|1385|186817|150247;2|544448|31969|186332|186333|2152;2|201174|84998|84999|1643824|1380;2|1239|186801|3085636|186803|830;2|29547|3031852|213849|72294|194;2|95818;2|976|117743|200644|49546|1016;2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|39948;2|1224|28216|80840|80864|238749;2|1239|526524|526525|2810280|1279384;2|1239|186801|186802|186806|1730;2|1239;2|508458|649775|649776|3029087|1434006;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|1164882;2|32066|203490|203491|1129771|32067;2|1224|1236|135614|32033|68;2|544448|31969|2085|2092|2093;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1224|28211|356|69277|28100;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|1239|526524|526525|128827|123375;2|1239|186801|3085636|186803|1213720;2759|33090|35493;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|1224|1236|135614|32033|338;2|95818;2|29547|3031852|213849|72294|194|205;2|976;2|32066;2|1117;2|203691;2|201174;2|508458;2|544448;2|1224,Complete,Claregrieve1
bsdb:637/3/1,Study 637,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S, Kong C, Yang Y, Cai S, Li X, Cai G , Ma Y",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 3,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,CRA,CRC,Patients with colorectal cancer,34,161,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 1,Table S4-5,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRC and CRA groups,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Formosa",2|976;2|95818;2|1224;2|32066;2|976|200643|171549|171551|836;2|1224|28216|80840|80864|238749;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1224|28211|356|69277|28100;2|1224|28216|80840|80864|283;2|1239|526524|526525|128827|123375;2|1239|1737404|1737405|1570339|165779;2|976|117743|200644|49546|1016;2|1239|186801|3082720|186804|1257;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|416916;2|1224|28216|80840|80864|28219;2|95818;2|1224|28211;2|1239|1737404|1737405|1570339|543311;2|976|117743|200644|2762318|501783;2|29547|3031852|213849|72294|194;2|1239|186801|186802|186806|1730;2|976|117743|200644|49546|225842,Complete,Claregrieve1
bsdb:637/3/2,Study 637,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S, Kong C, Yang Y, Cai S, Li X, Cai G , Ma Y",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 3,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,CRA,CRC,Patients with colorectal cancer,34,161,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 2,Table S4-5,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRC and CRA groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales",2|1239|186801|3085636|186803|572511;2|1117;2|142182|219685|219686|219687|173479;2|1239|186801|186802|204475;2|1239|909932|909929|1843491|158846;2|1239|91061|186826|1300|1301;2759|33090|35493;2|1224|1236|135614|32033|338;2|1239|186801|186802|216572;2|1239;2|57723;2|200795;2|142182|219685|219686,Complete,Claregrieve1
bsdb:638/1/1,Study 638,case-control,28750650,10.1186/s13059-017-1271-6,https://pubmed.ncbi.nlm.nih.gov/28750650/,"Wen C, Zheng Z, Shao T, Liu L, Xie Z, Le Chatelier E, He Z, Zhong W, Fan Y, Zhang L, Li H, Wu C, Hu C, Xu Q, Zhou J, Cai S, Wang D, Huang Y, Breban M, Qin N , Ehrlich SD",Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis,Genome biology,2017,"Ankylosing spondylitis, Biomarkers, Human gut microbiome, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ankylosing spondylitis,EFO:0003898,Healthy controls,Ankylosing spondylitis patients,Ankylosing spondylitis confirmed by calculating the Bath Ankylosing Spondylitis Functional Index (BASFI) and Bath Ankylosing Spondylitis Disease Activity Index (BASDAI),114,97,4 weeks,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.001,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S4,15 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Chloe,Aiyshaaaa,Atrayees",Differences of phylogenetic abundance between AS patients and healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|658087;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|207244|649756,Complete,Chloe
bsdb:638/1/2,Study 638,case-control,28750650,10.1186/s13059-017-1271-6,https://pubmed.ncbi.nlm.nih.gov/28750650/,"Wen C, Zheng Z, Shao T, Liu L, Xie Z, Le Chatelier E, He Z, Zhong W, Fan Y, Zhang L, Li H, Wu C, Hu C, Xu Q, Zhou J, Cai S, Wang D, Huang Y, Breban M, Qin N , Ehrlich SD",Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis,Genome biology,2017,"Ankylosing spondylitis, Biomarkers, Human gut microbiome, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ankylosing spondylitis,EFO:0003898,Healthy controls,Ankylosing spondylitis patients,Ankylosing spondylitis confirmed by calculating the Bath Ankylosing Spondylitis Functional Index (BASFI) and Bath Ankylosing Spondylitis Disease Activity Index (BASDAI),114,97,4 weeks,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.001,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S4,15 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Chloe,Aiyshaaaa",Differences of phylogenetic abundance between AS patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. OBRC5-5,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SS3/4,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 6_1_63FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 9_1_43BFAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_46FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_57FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2 1 46FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 3_1_53",2|1239|186801|3085636|186803|830;2|1224|1236|91347|543|544;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543|547;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|1164882|936595;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803|841;2|1239|186801|186802|384638;2|1239|186801|186802|245014;2|1239|186801|3085636|186803|658083;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803|658088;2|1239|186801|3085636|186803|665950;2|1239|186801|3085636|186803|658081;2|29547|3031852|213849|72294|194;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803|658085;2|1239|186801|3085636|186803|658086;2|1239|526524|526525|128827|2749846|31971;2|1239|186801|3085636|186803|2683689;2|1239|186801|3082720|186804|1870884|1496;2|1239|526524|526525|128827|457422;2|1239|526524|526525|128827|658659,Complete,Chloe
bsdb:639/1/1,Study 639,"cross-sectional observational, not case-control",30249275,10.1186/s40168-018-0557-6.,https://pubmed.ncbi.nlm.nih.gov/30249275/,"He Y, Wu W, Wu S, Zheng HM, Li P, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Xu JB, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Ma WJ , Zhou HW","Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis",Microbiome,2018,"16S rRNA gene sequencing, Economic status, Epidemiology, Faecal microbiome, Guangdong Gut Microbiome Project, Metabolic syndrome, Population level survey",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,NA,underdeveloped cities vs developed cities,"7009 Individuals' fecal samples from underdeveloped cities with GDP/capita of 22.1K to 25.3K CNY, and those from developed cities with GDP/capita of 149.5K to 136.1K CNY. (continuous variables)",NA,7009,Unspecified.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4a,23 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Associations between OTUs and host economic status. a Stacked plot showing the number of OTUs that are positively associated with income or spending (continuous variables).

Colors correspond to taxonomies in the legend.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|815|816;2|1224|28216;2|1239|186801|3085636|186803;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977,Complete,NA
bsdb:639/1/2,Study 639,"cross-sectional observational, not case-control",30249275,10.1186/s40168-018-0557-6.,https://pubmed.ncbi.nlm.nih.gov/30249275/,"He Y, Wu W, Wu S, Zheng HM, Li P, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Xu JB, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Ma WJ , Zhou HW","Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis",Microbiome,2018,"16S rRNA gene sequencing, Economic status, Epidemiology, Faecal microbiome, Guangdong Gut Microbiome Project, Metabolic syndrome, Population level survey",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,NA,underdeveloped cities vs developed cities,"7009 Individuals' fecal samples from underdeveloped cities with GDP/capita of 22.1K to 25.3K CNY, and those from developed cities with GDP/capita of 149.5K to 136.1K CNY. (continuous variables)",NA,7009,Unspecified.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4a,23 June 2022,Kaluifeanyi101,Kaluifeanyi101,Associations between OTUs and host economic status. A Stacked plot showing the number of OTUs that are negatively associated with income or spending (continuous variables). Colors correspond to taxonomies in the legend.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|31979;2|1224|1236;2|1239|186801|3082720|186804;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263,Complete,NA
bsdb:640/1/1,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 1,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Rheumatoid arthritis,EFO:0000685,Non Rheumatoid Arthritis,Rheumatoid Arthritis,Individual who have been diagnosed with Rheumatoid Arthritis(RA).,64,35,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3(a&b),1 April 2023,Aiyshaaaa,Aiyshaaaa,Linear discriminant analysis (LDA) effect size (LEfSe) analysis demonstrated differences in the relative abundance of some taxa between RA and non-RA controls at genus and  species level.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85006|1268|32207|43675;2|1239|909932|909929|1843491|970|135080,Complete,Atrayees
bsdb:640/1/2,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 1,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Rheumatoid arthritis,EFO:0000685,Non Rheumatoid Arthritis,Rheumatoid Arthritis,Individual who have been diagnosed with Rheumatoid Arthritis(RA).,64,35,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3(a&b),1 April 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees",Linear discriminant analysis (LDA) effect size (LEfSe) analysis demonstrated differences in the relative abundance of some taxa between RA and non-RA controls at genus and species level.,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|s__Bacteroidota bacterium",2|976|117743|200644|49546|1016;2|1224|1236|135625|712|416916;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836|28124;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|186828|117563|137732;2|32066|203490|203491|203492|848|860;2|976|200643|171549|171552|838|28132;2|976|1898104,Complete,Atrayees
bsdb:640/2/1,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 2,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),16,35,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4(a),26 July 2023,Atrayees,Atrayees,Most highly differentially abundant bacteria in RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Candidatus Absconditabacteria|s__Candidatus Absconditabacteria bacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.",2|29547|3031852|213849|72294|194|203;2|1239|909932|909929|1843491|970|671224;2|201174|1760|85007|1653|1716|61592;2|976|117743|200644|49546|1016|1019;2|221235|3018262;2|32066|203490|203491|1129771|32067|104608,Complete,Folakunmi
bsdb:640/2/2,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 2,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),16,35,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4(b),26 July 2023,Atrayees,Atrayees,Most highly differentially abundant bacteria in RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,Folakunmi
bsdb:640/3/1,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 3,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,Non-rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),64,64,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4(b),26 July 2023,Atrayees,Atrayees,Most highly differentially abundant bacteria in non-RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,decreased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,2|201174|84998|84999|1643824|2767353|1382,Complete,Folakunmi
bsdb:640/3/2,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 3,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,Non-rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),64,64,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4(b),26 July 2023,Atrayees,Atrayees,Most highly differentially abundant bacteria in non-RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum",2|976|200643|171549|171552|838|470565;2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171552|2974251|228604;2|95818;2|1239|186801|3085636|186803|43996|43997;2|1239|909932|1843489|31977|29465|423477;2|1239|186801|3085636|186803|265975|1501332,Complete,Folakunmi
bsdb:640/4/1,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 4,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,All participants carrying the AVI/AVI genotype (“non-tasters”),All participants with the homozygous PAV/PAV (“supertasters”),All participants with the homozygous PAV/PAV (“supertasters”),99,99,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4(c),26 July 2023,Atrayees,Atrayees,Most highly differentially abundant bacteria in all patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,2|1239|91061|186826|186827|46123|46125,Complete,Folakunmi
bsdb:640/4/2,Study 640,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus VC, Singh M, Schroth RJ, Chelikani P , Hitchon CA","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 4,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,All participants carrying the AVI/AVI genotype (“non-tasters”),All participants with the homozygous PAV/PAV (“supertasters”),All participants with the homozygous PAV/PAV (“supertasters”),99,99,N/A,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4(c),26 July 2023,Atrayees,Atrayees,Most highly differentially abundant bacteria in all patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,increased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,2|29547|3031852|213849|72294|194|824,Complete,Folakunmi
bsdb:641/1/1,Study 641,"cross-sectional observational, not case-control",33949151,10.1002/art.41780,NA,"Kroese JM, Brandt BW, Buijs MJ, Crielaard W, Lobbezoo F, Loos BG, van Boheemen L, van Schaardenburg D, Zaura E , Volgenant CMC",Differences in the Oral Microbiome in Patients With Early Rheumatoid Arthritis and Individuals at Risk of Rheumatoid Arthritis Compared to Healthy Individuals,"Arthritis & rheumatology (Hoboken, N.J.)",2021,NA,Experiment 1,Netherlands,Homo sapiens,Saliva,UBERON:0001836,Arthritis,EFO:0005856,healthy control,Early Rheumatoid Arthritis,Early Rheumatoid Arthritis patients (diagnosed within the previous year),50,50,3 months,16S,NA,Illumina,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary  Table 3,9 November 2022,Tislam,"Tislam,Atrayees","Saliva: a summary of the most significant zero-radius operational taxonomic units (zOTUs) that differentiated among the early rheumatoid arthritis (RA) group, at-risk group, and control group, sorted on linear discriminant analysis (LDA) score per group. Differences in relative abundance among the groups were tested with a Kruskal-Wallis test (false discovery rate corrected level of significance of 0.02), and post-hoc Mann-Whitney U tests. Results for zOTUs with a median relative abundance ≥0.01 for ≥1 group are marked with an outline.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. dentisani,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",2|976|200643|171549|171551|836|1583331;2|32066|203490|203491|203492|848|860;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|2974257|425941;2|976|200643|171549|171552|1283313;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|28449;2|1239|91061|186826|1300|1301|1303|1458253;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|28037,Complete,Atrayees
bsdb:641/1/2,Study 641,"cross-sectional observational, not case-control",33949151,10.1002/art.41780,NA,"Kroese JM, Brandt BW, Buijs MJ, Crielaard W, Lobbezoo F, Loos BG, van Boheemen L, van Schaardenburg D, Zaura E , Volgenant CMC",Differences in the Oral Microbiome in Patients With Early Rheumatoid Arthritis and Individuals at Risk of Rheumatoid Arthritis Compared to Healthy Individuals,"Arthritis & rheumatology (Hoboken, N.J.)",2021,NA,Experiment 1,Netherlands,Homo sapiens,Saliva,UBERON:0001836,Arthritis,EFO:0005856,healthy control,Early Rheumatoid Arthritis,Early Rheumatoid Arthritis patients (diagnosed within the previous year),50,50,3 months,16S,NA,Illumina,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary  Table 3,9 November 2022,Tislam,"Tislam,Atrayees","Saliva: a summary of the most significant zero-radius operational taxonomic units (zOTUs) that differentiated among the early rheumatoid arthritis (RA) group, at-risk group, and control group, sorted on linear discriminant analysis (LDA) score per group. Differences in relative abundance among the groups were tested with a Kruskal-Wallis test (false discovery rate corrected level of significance of 0.02), and post-hoc Mann-Whitney U tests. Results for zOTUs with a median relative abundance ≥0.01 for ≥1 group are marked with an outline.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus downei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus",2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|1300|1301|1305;2|976|200643|171549|171552|2974251|228604;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207|43675;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300|1301|1317;2|1239|91061|186826|1300|1301|1310,Complete,Atrayees
bsdb:642/1/NA,Study 642,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, Chin YT, Loke P , Chua KH",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Chinese Children (High SES, household income>RM500)",Malays Children (Moderate SES. house income=<RM500),"Gut microbiota from fecal samples of 24 Malays children whose household income =<RM500.

Note: Poverty line = RM 764($254).",17,24,unspecified,16S,345,NA,PERMANOVA,0.05,TRUE,NA,NA,NA,unchanged,increased,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:642/2/1,Study 642,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, Chin YT, Loke P , Chua KH",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Chinese Children (High SES, household income >RM500)","Orang Asli Children (low SES, household income<RM500)",Gut microbiota from fecal samples of 20 Orang Asli children whose household income <RM500.,17,20,unspecified,16S,345,NA,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,NA,increased,increased,Signature 1,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Chinese and Orang Asli children.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacteroidota,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|1236|135624;2|976;2|28221;2|1239|186801|186802;2|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:642/2/2,Study 642,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, Chin YT, Loke P , Chua KH",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Chinese Children (High SES, household income >RM500)","Orang Asli Children (low SES, household income<RM500)",Gut microbiota from fecal samples of 20 Orang Asli children whose household income <RM500.,17,20,unspecified,16S,345,NA,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,NA,increased,increased,Signature 2,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Chinese and Orang Asli children.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,2|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:642/3/1,Study 642,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, Chin YT, Loke P , Chua KH",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Malays children (Moderate SES, household income =>RM500)","Orang Asli children (low SES, household income <RM500)","Gut microbiota from fecal samples of 20 Orang Asli children whose household income<RM500.

45% of the households earn < RM500

Note: Poverty line = RM 764($254).",24,20,unspecified,16S,345,NA,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,increased,increased,NA,Signature 1,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Malay and Orang Asli children.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Spirochaetota,k__Bacteria,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|1236|135624;2|203691;2;2|976;2|1239|186801;2|28221;2|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:642/3/2,Study 642,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, Chin YT, Loke P , Chua KH",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Malays children (Moderate SES, household income =>RM500)","Orang Asli children (low SES, household income <RM500)","Gut microbiota from fecal samples of 20 Orang Asli children whose household income<RM500.

45% of the households earn < RM500

Note: Poverty line = RM 764($254).",24,20,unspecified,16S,345,NA,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,increased,increased,NA,Signature 2,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Malay and Orang Asli children.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales",2|976|200643|171549;2|1239|909932|909929,Complete,Claregrieve1
bsdb:643/1/1,Study 643,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y, Du L, Shi D, Kong C, Liu J, Liu G, Li X , Ma Y",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,yControl,yCRC,young-onset CRC patients (<50 years old),148,144,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,"age,sex",NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 3B,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between yCRC and yControl groups,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|946234|292800;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803;2|976|200643|171549|1853231|283168;2|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:643/1/2,Study 643,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y, Du L, Shi D, Kong C, Liu J, Liu G, Li X , Ma Y",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,yControl,yCRC,young-onset CRC patients (<50 years old),148,144,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,"age,sex",NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3B,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between yCRC and yControl groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730|39496;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1239|909932|909929|1843491|158846;2|1224|28216|80840|995019|577310;2|1239|186801|3082720|186804|1501226;2|1224|1236|91347|543|620;2|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:643/2/1,Study 643,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y, Du L, Shi D, Kong C, Liu J, Liu G, Li X , Ma Y",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,oControls,oCRC,old-onset CRC patients (50 years old or older),203,233,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3A,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between oCRC and oControl groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|207244;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|186802|3085642|580596;2|1239|186801|3082768|990719;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1492;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803;2|1239|186801|3085656|3085657|2039302;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|1160721;2|1239|186801|186802|216572|1263|1161942;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:643/2/2,Study 643,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y, Du L, Shi D, Kong C, Liu J, Liu G, Li X , Ma Y",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,oControls,oCRC,old-onset CRC patients (50 years old or older),203,233,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3A,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between oCRC and oControl groups,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Massilistercora|s__Massilistercora timonensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",2|1224|28211|204458|76892|41275;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|2719313|208479;2|1239|526524|526525|2810280|1505663;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|216851|1946507;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506553;2|1239|186801|186802|2717089|2086584;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1506553|29347,Complete,Claregrieve1
bsdb:644/1/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,colorectal adenoma,histology-proven adenoma,61,47,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Supplementary Figure 9,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between patients with colorectal adenoma and controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",2|1239|91061|1385;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|572511|1955243;2|1224|28211|356|212791|1894999;2|1224|1236|91347|543|561|562;2|1239|91061|1385|539738|1378|1966354;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|3082720|186804|1257|1262;2|976|200643|171549|171552|838|28131,Complete,Claregrieve1
bsdb:644/1/2,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,colorectal adenoma,histology-proven adenoma,61,47,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Supplementary Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between patients with colorectal adenoma and controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1239|91061|1385;2|976|200643|171549|815|816|29523;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|3085636|186803|33042|2049024;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:644/2/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 2,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (adenocarcinoma),subjects with invasive adenocarcinoma,61,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between patients with colorectal adenocarcinoma and controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii",2|1224|1236|135625|712|416916|739;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|29547|3031852|213849|72294|194|205;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378|1966354;2|1239|91061|186826|186828|117563|2049028;2|1239|186801|186802|216572|119852;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|3082720|186804|1257|1262;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|59823;2|1224|1236|72274|135621|286|76761,Complete,Claregrieve1
bsdb:644/2/2,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 2,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (adenocarcinoma),subjects with invasive adenocarcinoma,61,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between patients with colorectal adenocarcinoma and controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii",2|976|200643|171549|815|816|29523;2|1239|186801|3085636|186803|572511|1955243;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|216851|853;2|1224|1236|72274|135621|286|76761,Complete,Claregrieve1
bsdb:644/3/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 3,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma,colorectal cancer,subjects with invasive adenocarcinoma,47,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Supplementary Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|976|200643|171549|171550|239759|28117;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|29523;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|186802|1898207;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378|1966354;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288|1869337;2|1239|1737404|1737405|1570339|543311|1944660;2|976|117747|200666|84566|84567|188932;2|1239|186801|3082720|186804|1257|1262;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552|2974265|363265;2|1239|186801|186802|216572|1263|41978,Complete,Claregrieve1
bsdb:644/3/2,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 3,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma,colorectal cancer,subjects with invasive adenocarcinoma,47,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia terrae",2|1224|28211|356|212791|1894999;2|1224|1236|91347|543|561|562;2|976|117747|200666|84566|84567|188932;2|1224|1236|72274|135621|286|76761;2|201174|1760|85006|1268|32207|396015,Complete,Claregrieve1
bsdb:644/4/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,carcinoma-adjacent mucosae,carcinoma mucosae,specimens collected from adenocarcinoma tissue,52,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii",2|1239|186801|3085636|186803|572511|1955243;2|1224|1236|72274|135621|286|76761,Complete,Claregrieve1
bsdb:644/4/2,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,carcinoma-adjacent mucosae,carcinoma mucosae,specimens collected from adenocarcinoma tissue,52,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae,increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,2|32066|203490|203491|203492|848|68766,Complete,Claregrieve1
bsdb:644/5/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 5,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,adenoma-adjacent,adenocarcinoma mucosae,specimens collected from adenocarcinoma tissue,47,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia terrae",2|1239|91061|1385|186817|1386|1409;2|1224|28211|356|212791|1894999;2|1224|1236|91347|543|561|562;2|976|117747|200666|84566|84567|188932;2|1224|1236|72274|135621|286|76761;2|201174|1760|85006|1268|32207|396015,Complete,Claregrieve1
bsdb:644/5/2,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 5,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,adenoma-adjacent,adenocarcinoma mucosae,specimens collected from adenocarcinoma tissue,47,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea",2|976|200643|171549|815|816|817;2|1239|186801|3085636|186803|572511|1955243;2|29547|3031852|213849|72294|194|205;2|1239|186801|186802|1898207;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378|1966354;2|1239|91061|186826|186828|117563|2049028;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288|1869337;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|3082720|186804|1257|1262;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552|2974265|363265,Complete,Claregrieve1
bsdb:644/7/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 7,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,adenoma-adjacent,specimen collected adjacent to histology-proven adenoma,61,47,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|3085636|186803|33042|2049024;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|186802|216572|216851|853,Complete,Claregrieve1
bsdb:644/7/2,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 7,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,adenoma-adjacent,specimen collected adjacent to histology-proven adenoma,61,47,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis",2|1224|28211|356|212791|1894999;2|32066|203490|203491|203492|848|68766;2|976|117747|200666|84566|84567|188932,Complete,Claregrieve1
bsdb:644/8/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 8,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,healthy controls,carcinoma-adjacent,specimen collected from tissue adjacent to adenocarcinoma site,61,52,NA,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between healthy control tissue and adenocarcinoma-adjacent tissue,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378|1966354;2|1239|91061|186826|186828|117563|2049028;2|1239|186801|3082720|186804|1257|1262;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:644/9/1,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 9,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma tissue,carcinoma-adjacent tissue,specimens collected from tissue adjacent to adenocarcinoma,47,52,Not specified,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|976|200643|171549|171550|239759|28117;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|29523;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803|33042|2049024;2|1239|186801|186802|216572|216851|853;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378|1966354;2|1239|186801|186802|216572|119852;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|3082720|186804|1257|1262;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552|2974265|363265;2|1239|186801|186802|216572|1263|41978,Complete,Claregrieve1
bsdb:644/9/2,Study 644,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J , Sung JJ",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 9,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma tissue,carcinoma-adjacent tissue,specimens collected from tissue adjacent to adenocarcinoma,47,52,Not specified,16S,1234,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples,decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,2|1224|28211|356|212791|1894999,Complete,Claregrieve1
bsdb:645/1/1,Study 645,prospective cohort,30982856,10.1093/ajcn/nqz006,https://pubmed.ncbi.nlm.nih.gov/30982856/,"Ford SL, Lohmann P, Preidis GA, Gordon PS, O'Donnell A, Hagan J, Venkatachalam A, Balderas M, Luna RA , Hair AB",Improved feeding tolerance and growth are linked to increased gut microbial community diversity in very-low-birth-weight infants fed mother's own milk compared with donor breast milk,The American journal of clinical nutrition,2019,"breast milk, donor milk, feeding intolerance, growth, microbiota, neonate, premature infant, very low birth weight",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Maternal milk,XCO:0000415,DM (Donor's Milk),MOM (Mother's own milk),Mother's own milk group consists of infants who drank at least >50% of mother's own milk. Any less and they were placed in the other cohort.,43,74,No antibiotic exclusions were listed as infants were at a vulnerable stage in their lives.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,FIGURE 2C and FIGURE 2 D,29 June 2022,Uyokeeswaran,"Uyokeeswaran,Peace Sandy","(C) When comparing longitudinal changes across samples from all study subjects, increasing relative abundance of Proteobacteria was observed. There were no significant differences observed at the phylum level during the first 2 wk of life. By week 4, microbiota from the MOM cohort had significantly higher abundance of Actinobacteria (P = 0.032) and decreased abundance of Firmicutes (P = 0.011). (D) By week 4, microbiota from the MOM cohort had significantly increased abundance of Bacteroides (P = 0.046), Bifidobacterium (P = 0.026), and Enterococcus (P < 0.001) in comparison to the DM cohort. DM infants had significantly higher abundance of Staphylococcus (P = 0.014). DM, donor human milk; MOM, mother's own milk; PCoA, principal coordinates analysis.",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|201174;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350,Complete,Peace Sandy
bsdb:645/1/2,Study 645,prospective cohort,30982856,10.1093/ajcn/nqz006,https://pubmed.ncbi.nlm.nih.gov/30982856/,"Ford SL, Lohmann P, Preidis GA, Gordon PS, O'Donnell A, Hagan J, Venkatachalam A, Balderas M, Luna RA , Hair AB",Improved feeding tolerance and growth are linked to increased gut microbial community diversity in very-low-birth-weight infants fed mother's own milk compared with donor breast milk,The American journal of clinical nutrition,2019,"breast milk, donor milk, feeding intolerance, growth, microbiota, neonate, premature infant, very low birth weight",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Maternal milk,XCO:0000415,DM (Donor's Milk),MOM (Mother's own milk),Mother's own milk group consists of infants who drank at least >50% of mother's own milk. Any less and they were placed in the other cohort.,43,74,No antibiotic exclusions were listed as infants were at a vulnerable stage in their lives.,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2C and Figure 2D,29 June 2022,Uyokeeswaran,"Uyokeeswaran,Peace Sandy","(C) When comparing longitudinal changes across samples from all study subjects, increasing relative abundance of Proteobacteria was observed. There were no significant differences observed at the phylum level during the first 2 wk of life. By week 4, microbiota from the MOM cohort had significantly higher abundance of Actinobacteria (P = 0.032) and decreased abundance of Firmicutes (P = 0.011). (D) By week 4, microbiota from the MOM cohort had significantly increased abundance of Bacteroides (P = 0.046), Bifidobacterium (P = 0.026), and Enterococcus (P < 0.001) in comparison to the DM cohort. DM infants had significantly higher abundance of Staphylococcus (P = 0.014). DM, donor human milk; MOM, mother's own milk; PCoA, principal coordinates analysis.",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239;2|1239|91061|1385|90964|1279,Complete,Peace Sandy
bsdb:646/1/1,Study 646,case-control,27672054,10.1158/1055-9965.EPI-16-0337,NA,"Hale VL, Chen J, Johnson S, Harrington SC, Yab TC, Smyrk TC, Nelson H, Boardman LA, Druliner BR, Levin TR, Rex DK, Ahnen DJ, Lance P, Ahlquist DA , Chia N",Shifts in the Fecal Microbiota Associated with Adenomatous Polyps,"Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Non-Adenoma,Adenoma,"Patients with colorectal adenoma as identified during a screening colonoscopy. Fecal
samples from patients in which at least one adenoma > 1 cm was identified were included in the “adenoma” group.",547,233,None specified,16S,345,Illumina,Linear Regression,0.2,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,1 July 2022,Jeshudy,"Jeshudy,Suwaiba",−log(P value) of these taxa’s differential abundance.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|28216|80840|506;2|976|200643|171549;2|976;2|1224|28216;2|200940|3031449|213115|194924|35832;2|1224|28216|80840;2|28221;2|1239|186801|3082720|3030910|86331;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:646/1/2,Study 646,case-control,27672054,10.1158/1055-9965.EPI-16-0337,NA,"Hale VL, Chen J, Johnson S, Harrington SC, Yab TC, Smyrk TC, Nelson H, Boardman LA, Druliner BR, Levin TR, Rex DK, Ahnen DJ, Lance P, Ahlquist DA , Chia N",Shifts in the Fecal Microbiota Associated with Adenomatous Polyps,"Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Non-Adenoma,Adenoma,"Patients with colorectal adenoma as identified during a screening colonoscopy. Fecal
samples from patients in which at least one adenoma > 1 cm was identified were included in the “adenoma” group.",547,233,None specified,16S,345,Illumina,Linear Regression,0.2,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,1 July 2022,Jeshudy,"Jeshudy,Suwaiba",−log(P value) of these taxa’s differential abundance.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|s__unidentified Actinomycete OPB41",2|201174;2|1239|91061;2|1239;2|201174|1760|85004;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1117;2|1224|1236|135625|712|724;2|256845|1313211;2|544448|31969;2|544448;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|909932|1843489|31977|29465;2|1239|186801;2|201174|1760|68904,Complete,NA
bsdb:647/1/1,Study 647,"cross-sectional observational, not case-control",29901485,10.1097/PSY.0000000000000614.,https://pubmed.ncbi.nlm.nih.gov/29901485/,"Carson TL, Wang F, Cui X, Jackson BE, Van Der Pol WJ, Lefkowitz EJ, Morrow C , Baskin ML","Associations Between Race, Perceived Psychological Stress, and the Gut Microbiota in a Sample of Generally Healthy Black and White Women: A Pilot Study on the Role of Race and Perceived Psychological Stress",Psychosomatic medicine,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,White Women,Black Women,Healthy non-Hispanic black females (age ≥19 years),33,47,90 days,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,diet,waist circumference",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Racial comparisons of the average abundance of selected colorectal cancer-associated genera.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:648/1/1,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Gut microbiome measurement","EFO:0001799,EFO:0007874",Gut microbiome of European American children (EA),Gut microbiome of African American children (AA),"Gut microbiome of 30 African American children (18 female, 12 male; age 6 - 10 years)",30,30,unspecified,16S,345,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,household income,sex",NA,NA,NA,NA,NA,increased,Signature 1,Figure 1C,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees,Folakunmi",Differential abundance of taxa in the gut microbiota variability of AA and EA populations at 10% false discovery rate.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|186802|216572|244127;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|248744;2|1224|28216|80840|75682|846;2|976|200643|171549|171552|838;2|201174|84998|84999|84107|1473205;2|201174|84998|1643822|1643826|84108;2|508458|649775|649776;2|508458|649775;2|508458;2|1239|186801|186802|216572|707003,Complete,Atrayees
bsdb:648/2/1,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 2,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,Oral microbiota of European American children (EA),Oral microbiota of African American children (AA),"Oral microbiota of 30 African American children (18 female, 12 male; age 6 - 10 years)",30,30,unspecified,16S,345,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,household income,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2C,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Folakunmi",Genus-level differentially abundant taxa in the oral microbiota comparison between AA and EA groups at a 10% false discovery rate,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:648/2/2,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 2,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,Oral microbiota of European American children (EA),Oral microbiota of African American children (AA),"Oral microbiota of 30 African American children (18 female, 12 male; age 6 - 10 years)",30,30,unspecified,16S,345,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,household income,sex",NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2C,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Folakunmi",Genus-level differentially abundant taxa in the oral microbiota comparison between AA and EA groups at a 10% false discovery rate,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803|830;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:648/3/1,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Household income (EA & AA) =>$50,000.","Household income (EA & AA) < $50,000.","Gut microbiota of children from low-income households (EA & AA) < $50,000.",30,30,unspecified,16S,345,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 6B,30 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Both groups had an increased abundance of gut Phascolarcobacteria, with a decrease in Faecalitalea (both belonging to the phylum Firmicutes) in families with low income 
(P ≤ .05).",increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:648/3/2,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Household income (EA & AA) =>$50,000.","Household income (EA & AA) < $50,000.","Gut microbiota of children from low-income households (EA & AA) < $50,000.",30,30,unspecified,16S,345,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 6B,30 June 2022,Kaluifeanyi101,Kaluifeanyi101,"Both groups had an increased abundance of gut Phascolarcobacteria, with a decrease in Faecalitalea (both belonging to the phylum Firmicutes) in families 
with low income (P ≤ .05).",decreased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,2|1239|526524|526525|128827|1573534,Complete,Folakunmi
bsdb:648/4/1,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 4,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Socioeconomic status,EXO:0000114,"High income in European American households =>$50,000.","Low  income in European American households  < $50,000.","Oral microbiota of children from low-income EA households < $50,000.",30,30,unspecified,16S,345,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,FIGURE 6D,30 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Folakunmi","Differentially abundant taxa analysis of oral microbiota showed an increased abundance of Streptococcus in EA children from low-income families. 
No differentially abundant taxa were associated with income in AA children (not shown).",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:648/5/1,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 5,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Obesity,EFO:0001073,Non-obese EA children,Obese EA children,Obese children in the European American group,22,8,unspecified,16S,345,Illumina,PERMANOVA,0.1,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,NA,NA,NA,NA,increased,Signature 1,Figures 3E,30 January 2024,Folakunmi,Folakunmi,Oral microbial diversity was associated with obesity in EA children. Genera Aggregatibacter and Eikenella abundance was increased in obese compared to non-obese EA children.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella",2|1224|1236|135625|712|416916;2|1224|28216|206351|481|538,Complete,Folakunmi
bsdb:648/6/1,Study 648,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,https://pubmed.ncbi.nlm.nih.gov/33596768/,"Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T , Taneja V",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Non-obese African American children,Obese African American  children,NA,21,9,unspecified,16S,345,Illumina,PERMANOVA,0.1,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,increased,Signature 1,Figures 3C,31 January 2024,Folakunmi,Folakunmi,Differentially abundant taxa in obese and non-obese AA children,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|201174;2|1224;2|508458;2|1239|909932;2|201174|84998;2|1224|1236;2|1239|91061;2|508458|649775;2|1239|909932|909929;2|201174|84998|84999;2|1224|1236|91347;2|1239|91061|186826;2|508458|649775|649776;2|1224|1236|91347|543|570;2|1239|909932|1843489|31977|906,Complete,Folakunmi
bsdb:649/1/1,Study 649,randomized controlled trial,33106549,10.1038/s41598-020-75229-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589489/,"Stan TL, Soylu-Kucharz R, Burleigh S, Prykhodko O, Cao L, Franke N, Sjögren M, Haikal C, Hållenius F , Björkqvist M",Increased intestinal permeability and gut dysbiosis in the R6/2 mouse model of Huntington's disease,Scientific reports,2020,NA,Experiment 1,Sweden,Mus musculus,Feces,UBERON:0001988,Huntington disease,MONDO:0007739,Wild type,R6/2,"The CAG-repeat lengths of the R6/2 mice used in this study ranged between 242 and 257, resulting in a disease progression slower than that of the R6/2 mouse with 150 CAG repeats as described previously.",10,10,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3 Supplemental Text,9 January 2023,Jacquelynshevin,Jacquelynshevin,Relative Abundance between wildtype and R6/2,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|91061;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|526524|526525|2810280|100883;2|1224|1236|91347|543;2|1224|1236;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|1224|1236|91347;2|1239|91061|186826|33958,Complete,Fatima
bsdb:649/1/2,Study 649,randomized controlled trial,33106549,10.1038/s41598-020-75229-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589489/,"Stan TL, Soylu-Kucharz R, Burleigh S, Prykhodko O, Cao L, Franke N, Sjögren M, Haikal C, Hållenius F , Björkqvist M",Increased intestinal permeability and gut dysbiosis in the R6/2 mouse model of Huntington's disease,Scientific reports,2020,NA,Experiment 1,Sweden,Mus musculus,Feces,UBERON:0001988,Huntington disease,MONDO:0007739,Wild type,R6/2,"The CAG-repeat lengths of the R6/2 mice used in this study ranged between 242 and 257, resulting in a disease progression slower than that of the R6/2 mouse with 150 CAG repeats as described previously.",10,10,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3 Supplemental Text,9 January 2023,Jacquelynshevin,Jacquelynshevin,Relative abundance between wildtype and R6/2,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",2|201174|84998|1643822|1643826|447020;2|201174|84998|84999|84107;2|201174|84998;2|201174;2|201174|84998|84999;2|200940|3031449|213115|194924|872;2|28221;2|200940|3031449|213115;2|200940|3031449|213115|194924,Complete,Fatima
bsdb:650/1/1,Study 650,"cross-sectional observational, not case-control",32604882,10.3390/microorganisms8060961,https://pubmed.ncbi.nlm.nih.gov/32604882/,"Amaruddin AI, Hamid F, Koopman JPR, Muhammad M, Brienen EA, van Lieshout L, Geelen AR, Wahyuni S, Kuijper EJ, Sartono E, Yazdanbakhsh M , Zwittink RD","The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia",Microorganisms,2020,"gut microbiota, intestinal parasites, nutritional status, schoolchildren, socioeconomic status",Experiment 1,Indonesia,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Children of low SES,Children of high SES,"High SES school is located in the city centre and is considered of high status, with a majority of the parents working as high-skilled workers or professionals with higher education.",66,74,NA,16S,34,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 1C.,5 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy",Figure 1C. Differential abundance of bacterial taxa between high and low SES children. Taxa with Benjamini–Hochberg corrected p-value below 0.05 are shown.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|526524|526525|128827;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|28050|2049031;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|186806|1730;2|201174|84998|84999|1643824;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:650/1/2,Study 650,"cross-sectional observational, not case-control",32604882,10.3390/microorganisms8060961,https://pubmed.ncbi.nlm.nih.gov/32604882/,"Amaruddin AI, Hamid F, Koopman JPR, Muhammad M, Brienen EA, van Lieshout L, Geelen AR, Wahyuni S, Kuijper EJ, Sartono E, Yazdanbakhsh M , Zwittink RD","The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia",Microorganisms,2020,"gut microbiota, intestinal parasites, nutritional status, schoolchildren, socioeconomic status",Experiment 1,Indonesia,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Children of low SES,Children of high SES,"High SES school is located in the city centre and is considered of high status, with a majority of the parents working as high-skilled workers or professionals with higher education.",66,74,NA,16S,34,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Figure 1C.,5 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy",Figure 1C. Differential abundance of bacterial taxa between high and low SES children. Taxa with Benjamini–Hochberg corrected p-value below 0.05 are shown.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella",2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|877420;2|1239|186801|186802|543314|2137877;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|31979;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|200643|171549|2005473;2|201174|84998|1643822|1643826;2|201174|84998|1643822|1643826|580024;2|201174|84998|84999|1643824;2|201174|84998|84999|1643824|2082587,Complete,Peace Sandy
bsdb:651/1/1,Study 651,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W, Liu F, Ling Z, Tong X , Xiang C",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy volunteers (swc),CRC patients (swp),"37-88 years of age, diagnosed with colorectal cancer (swp = gut swab)",34,32,1 month,16S,123,Sanger,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4A,4 July 2022,Jeshudy,Jeshudy,Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|3085636|186803|207244;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|572511;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|28050,Complete,Atrayees
bsdb:651/1/2,Study 651,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W, Liu F, Ling Z, Tong X , Xiang C",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy volunteers (swc),CRC patients (swp),"37-88 years of age, diagnosed with colorectal cancer (swp = gut swab)",34,32,1 month,16S,123,Sanger,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4A,4 July 2022,Jeshudy,Jeshudy,Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor",2|1239|186801|3085636|186803|43996;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|91347|543|570;2|1239|186801|3082720|3030910|86331;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1239|909932|909929|1843491|970;2|1239|186801|3082720|3118655|44259,Complete,Atrayees
bsdb:651/2/1,Study 651,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W, Liu F, Ling Z, Tong X , Xiang C",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 2,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,paracancerous tissue (pa10t),cancerous tissue (cat),"37-88 years of age, colorectal cancer tissue

Note: group 0 = paracancerous tissue 10-20 cm from cancerous tissue",27,27,1 month,16S,123,Sanger,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,Table 3,3 July 2022,Jeshudy,Jeshudy,Phylotypes significantly different between cat and pa10t.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acidocella",2|1239|91061|1385|186817|1386;2|976|200643|171549|171552|577309;2|1239|909932|1843488|909930|33024;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|1224|28211;2|1224|28211|356|119045|407;2|1224|28211|204441|433|50709,Complete,Atrayees
bsdb:651/2/2,Study 651,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W, Liu F, Ling Z, Tong X , Xiang C",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 2,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,paracancerous tissue (pa10t),cancerous tissue (cat),"37-88 years of age, colorectal cancer tissue

Note: group 0 = paracancerous tissue 10-20 cm from cancerous tissue",27,27,1 month,16S,123,Sanger,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 2,Table 3,3 July 2022,Jeshudy,Jeshudy,Phylotypes significantly different between cat and pa10t.,increased,k__Bacteria|p__Bacillota|c__Bacilli,2|1239|91061,Complete,Atrayees
bsdb:651/3/1,Study 651,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W, Liu F, Ling Z, Tong X , Xiang C",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 3,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,paracancerous tissue (pa2t),cancerous tissue (cat),"37-88 years of age, cancerous tissue.

Note: Group 0 = paracancerous tissue 2-5 cm from cancerous tissue",27,27,1 month,16S,123,Sanger,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,3 July 2022,Jeshudy,Jeshudy,Phylotypes significantly different between cat and pa2t,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria",2|1224|28211|356|118882|528;2|1224|28211,Complete,Atrayees
bsdb:651/4/1,Study 651,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W, Liu F, Ling Z, Tong X , Xiang C",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy volunteers (stc),CRC patients (stp),"37-88 years of age, diagnosed with colorectal cancer (stp = stool sample)",22,21,1 month,16S,123,Sanger,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4B,4 July 2022,Jeshudy,Jeshudy,Figure 4. Relative abundance of significantly different genera between CRC patients and healthy controls. Genera differing between stp and stc.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|216572|244127;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186806|1730;2|1239|186801|3082720|3030910|86331;2|201174|84998|1643822|1643826|84108;2|976|200643|171549|171552|577309;2|200940|3031449|213115|194924|872;2|976|200643|171549|171551|836;2|1239|186801|3082720|186804|1257,Complete,Atrayees
bsdb:652/1/1,Study 652,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N , Ohkusa T",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 1,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy,Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,10,24,None Specified,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4B, Figure 7",4 July 2022,Jeshudy,"Jeshudy,Atrayees",Characterization of microbiomes in intramucosal CRC patients and healthy subjects.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium perfoetens",2|1239|909932|909929|1843491|158846;2|1224|28211|204457|41297|165695;2|32066|203490|203491|203492|848|860;2|32066|203490|203491|203492|848|852,Complete,Atrayees
bsdb:652/1/2,Study 652,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N , Ohkusa T",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 1,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy,Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,10,24,None Specified,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4B, Figure 7",4 July 2022,Jeshudy,"Jeshudy,Atrayees",Characterization of microbiomes in intramucosal CRC patients and healthy subjects.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium",2|1224|1236|135625|712|713;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|201174|1760|2037|2049|1654;2|32066|203490;2|32066|203490|203491;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848|856,Complete,Atrayees
bsdb:652/2/1,Study 652,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N , Ohkusa T",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 2,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,CRA (colorectal adenoma),Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,47,24,None Specified,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 8B,4 July 2022,Jeshudy,Jeshudy,Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",2|976|200643|171549|1853231|574697;2|201174|84998|84999|84107|102106;2|1239|909932|909929|1843491|52225;2|28221;2|200940|3031449|213115;2|508458|649775|649776|649777;2|1224|28216|80840|80864|283;2|200940|3031449|213115|194924,Complete,Atrayees
bsdb:652/2/2,Study 652,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N , Ohkusa T",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 2,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,CRA (colorectal adenoma),Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,47,24,None Specified,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 8B, Figure 9",4 July 2022,Jeshudy,"Jeshudy,Atrayees",Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|909932|909929|1843491|158846;2|1239|526524|526525|128827;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:652/3/1,Study 652,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N , Ohkusa T",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 3,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,Healthy,CRA (colorectal adenoma),"Colorectal adenoma, as diagnosed after a complete colonoscopic exampination",10,47,None Specified,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 2B, Figure 6",4 July 2022,Jeshudy,"Jeshudy,Atrayees",Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. (A) Taxonomic representation of statistically and biologically consistent differences in CRA and healthy subjects. (B) Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium",2|1239|186801|3085636|186803|140625;2|976|200643|171549|1853231|574697;2|1224|1236|91347|543|590;2|1224|28216|80840|80864|283;2|1224|1236|2887326|468;2|32066|203490|203491|203492|848|856,Complete,Atrayees
bsdb:652/3/2,Study 652,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N , Ohkusa T",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 3,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,Healthy,CRA (colorectal adenoma),"Colorectal adenoma, as diagnosed after a complete colonoscopic exampination",10,47,None Specified,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 2B, Figure 6",4 July 2022,Jeshudy,"Jeshudy,Atrayees",Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",2|201174|84998|84999|1643824|1380;2|1239|1737404|1737405|1570339|543311;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|860;2|32066|203490|203491|203492|848|851;2|32066|203490;2|32066|203490|203491;2|32066|203490|203491|203492,Complete,Atrayees
bsdb:653/1/1,Study 653,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O'Riordain M, Shanahan F , O'Toole PW",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 1,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with CRC,Individuals diagnosed with CRC,103,99,1 month,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5(B),5 July 2022,Jeshudy,"Jeshudy,Atrayees",Scatterplot of the colonic prevalence of bacterial OTUs associated with oral pathogen and biofilm CAGs.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|909932|1843489|31977|39948;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|526524|526525|128827|123375;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:653/1/2,Study 653,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O'Riordain M, Shanahan F , O'Toole PW",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 1,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with CRC,Individuals diagnosed with CRC,103,99,1 month,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5(B),5 July 2022,Jeshudy,"Jeshudy,Atrayees,Folakunmi",Scatterplot of the colonic prevalence of bacterial OTUs associated with oral pathogen and biofilm CAGs.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:653/2/1,Study 653,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O'Riordain M, Shanahan F , O'Toole PW",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 2,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with CRC,Individuals diagnosed with CRC,103,99,1 month,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplementary table 2,22 January 2024,Folakunmi,Folakunmi,Differentially abundant taxa in the oral microbiome between colorectal cancer patients and healthy controls by ANCOM,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838;2|976|200643|171549|171552|1283313;2|1239|186801|3085636|186803|1164882;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:653/3/1,Study 653,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O'Riordain M, Shanahan F , O'Toole PW",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 3,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with polyps,Individuals diagnosed with polyps,103,32,1 month,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplementary table 2,22 January 2024,Folakunmi,Folakunmi,Differentially abundant taxa in the oral microbiome between colorectal cancer patients and healthy controls by ANCOM,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1239|1737404|1737405|1570339|543311;2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|32067,Complete,Folakunmi
bsdb:654/1/1,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from the American Gut Project (AGP) data set,1237,88,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Caucasian and Asian Pacific subjects,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:654/1/2,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from the American Gut Project (AGP) data set,1237,88,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Caucasian and Asian Pacific subjects,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3082768|990719;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231;2|1239|186801|186802|186807;2|976|200643|171549|171550;2|74201|203494|48461|203557;2|256845|1313211|278082|255528;2|201174|84998|84999|84107;2|1239|186801|186802,Complete,Atrayees
bsdb:654/2/1,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanic,Hispanics sampled from the American Gut Project (AGP) data set,1237,37,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231;2|1239|186801|186802|186807;2|976|200643|171549|171550;2|1239|909932|1843489|31977|29465;2|256845|1313211|278082|255528;2|1239|186801|186802;2|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:654/2/2,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanic,Hispanics sampled from the American Gut Project (AGP) data set,1237,37,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities; f",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|186801|3082768|990719;2|74201|203494|48461|203557,Complete,ChiomaBlessing
bsdb:654/3/1,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from the American Gut Project (AGP) data set,1237,13,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities; f",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|1239|186801|186802|186807;2|1239|909932|1843489|31977|29465;2|256845|1313211|278082|255528;2|976|200643|171549|1853231;2|976|200643|171549|1853231|283168,Complete,ChiomaBlessing
bsdb:654/3/2,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from the American Gut Project (AGP) data set,1237,13,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|186801|3082768|990719;2|1239|186801|186802;2|74201|203494|48461|203557;2|976|200643|171549|171550;2|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:654/4/1,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from Human Microbiome Project (HMP) data set,211,34,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",2|1239|909932|1843489|31977|29465;2|256845|1313211|278082|255528,Complete,ChiomaBlessing
bsdb:654/4/2,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from Human Microbiome Project (HMP) data set,211,34,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|186801|186802|186807;2|1239|186801|3082768|990719;2|1239|186801|186802;2|74201|203494|48461|203557;2|976|200643|171549|1853231;2|976|200643|171549|1853231|283168;2|976|200643|171549|171550;2|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:654/5/1,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanics,Hispanics sampled from Human Microbiome Project (HMP) data set,211,43,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 4,8 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",2|1239|186801|186802|186807;2|1239|186801|3082768|990719;2|1239|909932|1843489|31977|29465;2|256845|1313211|278082|255528,Complete,ChiomaBlessing
bsdb:654/5/2,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanics,Hispanics sampled from Human Microbiome Project (HMP) data set,211,43,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 4,8 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|186801|186802;2|74201|203494|48461|203557;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231;2|976|200643|171549|171550;2|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:654/6/1,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from Human Microbiome Project (HMP) data set,211,10,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,8 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|909932|1843489|31977|29465;2|976|200643|171549|1853231;2|976|200643|171549|1853231|283168;2|976|200643|171549|171550;2|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:654/6/2,Study 654,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks AW, Priya S, Blekhman R , Bordenstein SR",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from Human Microbiome Project (HMP) data set,211,10,NA,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,8 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",2|1239|186801|186802|186807;2|1239|186801|3082768|990719;2|1239|186801|186802;2|74201|203494|48461|203557;2|256845|1313211|278082|255528,Complete,ChiomaBlessing
bsdb:655/1/1,Study 655,prospective cohort,31771977,10.1128/mSystems.00639-19,https://pubmed.ncbi.nlm.nih.gov/31771977/,"Yang Y, Zheng W, Cai Q, Shrubsole MJ, Pei Z, Brucker R, Steinwandel M, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Racial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European Ancestry,mSystems,2019,"oral microbiome, racial difference",Experiment 1,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,European Americans (EA),African Americans (AA),"Mouth rinse samples of 1,058 African Americans, with about 57% population with low SES of annual household income < $15,000.",558,1058,12 Months,16S,1234,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,household income,sex,smoking status",NA,NA,NA,NA,NA,increased,Signature 1,Table 2; Figure 3,11 July 2022,Kaluifeanyi101,Kaluifeanyi101,"TABLE 2 Significantly higher abundance of Bacteroidetes and lower abundance of Actinobacteria and Firmicutes among African-Americans
FIG 3 Thirteen common bacterial taxa showing a significant differential abundance between AAs and EAs in linear regression analyses.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|28129;2|1239|186801|3082720|186804,Complete,NA
bsdb:655/1/2,Study 655,prospective cohort,31771977,10.1128/mSystems.00639-19,https://pubmed.ncbi.nlm.nih.gov/31771977/,"Yang Y, Zheng W, Cai Q, Shrubsole MJ, Pei Z, Brucker R, Steinwandel M, Bordenstein SR, Li Z, Blot WJ, Shu XO , Long J",Racial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European Ancestry,mSystems,2019,"oral microbiome, racial difference",Experiment 1,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,European Americans (EA),African Americans (AA),"Mouth rinse samples of 1,058 African Americans, with about 57% population with low SES of annual household income < $15,000.",558,1058,12 Months,16S,1234,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,household income,sex,smoking status",NA,NA,NA,NA,NA,increased,Signature 2,Table 2; Figure 3,11 July 2022,Kaluifeanyi101,Kaluifeanyi101,"TABLE 2 Significantly higher abundance of Bacteroidetes and lower abundance of Actinobacteria and Firmicutes among African-Americans 
FIG 3 Thirteen common bacterial taxa showing a significant differential abundance between AAs and EAs in linear regression analyses.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057",2|201174;2|1239|91061|186826|186828;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186828|117563|46124;2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|45634;2|1239|91061|186826|1300|1301|712621,Complete,NA
bsdb:656/1/1,Study 656,"cross-sectional observational, not case-control",26982745,10.1097/MPG.0000000000001186,https://pubmed.ncbi.nlm.nih.gov/26982745/,"Mello CS, Carmo-Rodrigues MS, Filho HB, Melli LC, Tahan S, Pignatari AC , de Morais MB",Gut Microbiota Differences in Children From Distinct Socioeconomic Levels Living in the Same Urban Area in Brazil,Journal of pediatric gastroenterology and nutrition,2016,NA,Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Private school children (High SES),Children living in slum (Low SES),"Children between 5 and 11 years old living in slums in Sao Paulo State, Brazil.",30,100,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,11 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between the slum children and children from the private school,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Bacteroidota",2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806|1730;2|1239;2|1239|91061|186826|33958|1578|1591;2157|28890|183925|2158|2159|2172|2173;2|976,Complete,Claregrieve1
bsdb:656/1/2,Study 656,"cross-sectional observational, not case-control",26982745,10.1097/MPG.0000000000001186,https://pubmed.ncbi.nlm.nih.gov/26982745/,"Mello CS, Carmo-Rodrigues MS, Filho HB, Melli LC, Tahan S, Pignatari AC , de Morais MB",Gut Microbiota Differences in Children From Distinct Socioeconomic Levels Living in the Same Urban Area in Brazil,Journal of pediatric gastroenterology and nutrition,2016,NA,Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Private school children (High SES),Children living in slum (Low SES),"Children between 5 and 11 years old living in slums in Sao Paulo State, Brazil.",30,100,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,11 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between the slum children and children from the private school,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.",2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|186802|31979|1485|1502;2|1224|1236|91347|543|590|599,Complete,Claregrieve1
bsdb:657/1/1,Study 657,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen AI, Pappalardo VY, Buijs MJ, Brandt BW, Mäkitie AA, Meurman JH , Zaura E",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 1,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,Healthy controls,pre-treatment oral squamous cell carcinoma patients,"Patients diagnosed with Oral Squamous Cell Carcinoma (OSCC), prior to receiving cancer treatment",101,99,Not mentioned,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2 A,8 August 2023,Andre,Andre,Discriminatory zero-radius operational taxonomic units (zOTUs) between oral squamous cell carcinoma (OSCC) patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis",2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|186827|46123|46125;2|976|117743|200644|49546|1016|327575;2|1239|91061|186826|1300|1301|1328;2|32066|203490|203491|203492|848|76859;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1303,Complete,Peace Sandy
bsdb:657/1/2,Study 657,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen AI, Pappalardo VY, Buijs MJ, Brandt BW, Mäkitie AA, Meurman JH , Zaura E",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 1,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,Healthy controls,pre-treatment oral squamous cell carcinoma patients,"Patients diagnosed with Oral Squamous Cell Carcinoma (OSCC), prior to receiving cancer treatment",101,99,Not mentioned,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2 A,8 August 2023,Andre,Andre,Discriminatory zero-radius operational taxonomic units (zOTUs) between oral squamous cell carcinoma (OSCC) patients and healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens",2|976|200643|171549|171552|838|28132;2|1239|91061|186826|1300|1301|1304;2|1224|28216|206351|481|482|484;2|1224|1236|135625|712|724|729;2|1239|909932|1843489|31977|29465|39778;2|1239|91061|186826|1300|1301|113107;2|1239|909932|1843489|31977|29465|29466;2|201174|1760|85006|1268|32207|43675;2|201174|1760|2037|2049|1654|712118;2|32066|203490|203491|203492|848|860;2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|838|60133,Complete,Peace Sandy
bsdb:657/2/1,Study 657,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen AI, Pappalardo VY, Buijs MJ, Brandt BW, Mäkitie AA, Meurman JH , Zaura E",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 2,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,"Nonsmoking, nondrinking, and dentate healthy controls","Nonsmoking, nondrinking, and dentate pre-treatment OSCC patients","OSCC patients who have not received any cancer treatment yet and who do not smoke tobacco or drink alcohol, and have at least one remaining tooth in their mouth.",34,24,Not mentioned,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Figure 2 B,8 August 2023,Andre,Andre,Discriminatory zOTUs between OSCC patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 134,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 351,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 392,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp. oral taxon 203,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis",2|1239|909932|909929|1843491|970|712530;2|95818|713053;2|32066|203490|203491|1129771|32067|712364;2|1239|91061|186826|1300|1357|1358;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|186828|117563|137732;2|1239|91061|186826|186827|46123|46125;2|1224|1236|135625|712|416916|732;2|32066|203490|203491|203492|848|671211;2|32066|203490|203491|1129771|32067|157691;2|1224|28216|206351|481|482|34026;2|1239|91061|1385|539738|1378|84135;2|1239|91061|186826|1300|1301|1303,Complete,Peace Sandy
bsdb:657/2/2,Study 657,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen AI, Pappalardo VY, Buijs MJ, Brandt BW, Mäkitie AA, Meurman JH , Zaura E",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 2,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,"Nonsmoking, nondrinking, and dentate healthy controls","Nonsmoking, nondrinking, and dentate pre-treatment OSCC patients","OSCC patients who have not received any cancer treatment yet and who do not smoke tobacco or drink alcohol, and have at least one remaining tooth in their mouth.",34,24,Not mentioned,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Figure 2 B,9 August 2023,Andre,Andre,Discriminatory zOTUs between OSCC patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 221",2|1239|909932|1843489|31977|29465|39778;2|1239|91061|186826|1300|1301|113107;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|28137;2|201174|1760|2037|2049|1654|712118;2|976|200643|171549|171552|2974251|28136;2|32066|203490|203491|1129771|32067|712362,Complete,Peace Sandy
bsdb:657/3/1,Study 657,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen AI, Pappalardo VY, Buijs MJ, Brandt BW, Mäkitie AA, Meurman JH , Zaura E",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 3,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,pre-treatment OSCC patients,post-treatment OSCC patients,"OSCC patients who received cancer treatment, and seen after a mean follow-up of 47.8 months.",28,28,Not mentioned,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 4,9 August 2023,Andre,Andre,Discriminatory zOTUs between baseline and post-therapy samples in 28 OSCC patients (output of LEfSe analysis).,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Bacteria|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 511,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 417,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. dentisani",2|1239|526524|526525|128827|123375|102148;2|1239|186801|3082720|3030910|86331|114527;2|1239|91061|186826|1300|1301|1306;2|32066|203490|203491|1129771|32067|104608;2|203691|203692|136|2845253|157|166;2|976|117743|200644|2762318|59735|712187;2|976|712911;2|976|200643|171549|171551|836|28124;2|201174|84998|84999|1643824|2767353|1382;2|1224|28216|80840|119060|47670|47671;2|32066|203490|203491|1129771|32067|712365;2|1239|186801|3082720|186804|1257|341694;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|171552|838|652722;2|32066|203490|203491|1129771|32067|554406;2|976|117743|200644|49546|1016|327575;2|32066|203490|203491|203492|848|155615;2|1239|909932|1843489|31977|29465|423477;2|976|200643|171549|171552|838|28137;2|1239|91061|186826|186827|46123|46125;2|201174|1760|2037|2049|1654|651609;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1303|1458253,Complete,Peace Sandy
bsdb:657/3/2,Study 657,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen AI, Pappalardo VY, Buijs MJ, Brandt BW, Mäkitie AA, Meurman JH , Zaura E",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 3,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,pre-treatment OSCC patients,post-treatment OSCC patients,"OSCC patients who received cancer treatment, and seen after a mean follow-up of 47.8 months.",28,28,Not mentioned,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,4,9 August 2023,Andre,Andre,Discriminatory zOTUs between baseline and post-therapy samples in 28 OSCC patients (output of LEfSe analysis),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae",2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|33958|2759736|1597;2|1239|91061|186826|33958|2759736|47715;2|201174|1760|2037|2049|1654|52769,Complete,Peace Sandy
bsdb:658/1/1,Study 658,randomized controlled trial,34622226,https://doi.org/10.1016/j.xcrm.2021.100383,https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(21)00237-8,"Wang F, He MM, Yao YC, Zhao X, Wang ZQ, Jin Y, Luo HY, Li JB, Wang FH, Qiu MZ, Lv ZD, Wang DS, Li YH, Zhang DS , Xu RH",Regorafenib plus toripalimab in patients with metastatic colorectal cancer: a phase Ib/II clinical trial and gut microbiome analysis,Cell reports. Medicine,2021,"colorectal cancer, immunotherapy, microbiome, programmed cell death protein 1, regorafenib, toripalimab",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (Progressive Disease),Responders (Partial Response or Stable Disease),"Patients with histologically confirmed metastatic or unresectable MSS/MSI-L/pMMR colorectal cancer treated with 80 mg, or 120 mg regorafenib, plus toripalimab resulting in stable disease or partial response.",21,11,Any condition requiring ongoing systemic antibiotic therapy,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supp table S3,9 October 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Peace Sandy","Linear discriminant analysis effect size (LDA) from phylum to species level shows 
differentially enriched taxa in NR and R groups. Related to Figure 4. R, response; NR, non-response.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|1239|909932|1843489|31977|39948|2161821;2|1239|909932|909929;2|1239|909932|1843489;2|976|200643|171549|171552|577309,Complete,Peace Sandy
bsdb:658/1/2,Study 658,randomized controlled trial,34622226,https://doi.org/10.1016/j.xcrm.2021.100383,https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(21)00237-8,"Wang F, He MM, Yao YC, Zhao X, Wang ZQ, Jin Y, Luo HY, Li JB, Wang FH, Qiu MZ, Lv ZD, Wang DS, Li YH, Zhang DS , Xu RH",Regorafenib plus toripalimab in patients with metastatic colorectal cancer: a phase Ib/II clinical trial and gut microbiome analysis,Cell reports. Medicine,2021,"colorectal cancer, immunotherapy, microbiome, programmed cell death protein 1, regorafenib, toripalimab",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (Progressive Disease),Responders (Partial Response or Stable Disease),"Patients with histologically confirmed metastatic or unresectable MSS/MSI-L/pMMR colorectal cancer treated with 80 mg, or 120 mg regorafenib, plus toripalimab resulting in stable disease or partial response.",21,11,Any condition requiring ongoing systemic antibiotic therapy,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supp table S3,9 October 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Peace Sandy","Linear discriminant analysis effect size (LDA) from phylum to species level shows differentially enriched taxa in NR and R groups. Related to Figure 4. R, response; NR, non-response.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__uncultured Bilophila sp.",2|1239|909932|1843488|909930;2|1239|909932|1843488;2|1239|909932|1843488|909930|904;2|976|200643|171549|171550|239759;2|200940|3031449|213115|194924|35832;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|200940|3031449;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|68766;2|1239|186801|3085636|186803|1506553;2|976|200643|1970189|1573805;2|1239|186801|186802|216572;2|976|200643|171549|171550;2|2904303;2|1239|909932|1843488|909930|904;2|976|200643|171549|171550|239759;2|200940|3031449|213115|194924|35832|529385,Complete,Peace Sandy
bsdb:659/1/1,Study 659,case-control,33435800,10.1080/19490976.2020.1869504,NA,"Harry Cheuk Hay Lau, Joseph Jao-Yiu Sung",Gut microbiota: impacts on gastrointestinal cancer immunotherapy,Gut microbes,2021,"CpG- oligodeoxynucleotide therapy, Gut microbiota, adoptive cell transfer, blockade-induced adverse events, gastrointestinal cancer, immune checkpoint blockade, probiotics",Experiment 1,United States of America,Mus musculus,Wall of small intestine,UBERON:0001168,Gastric cancer,MONDO:0001056,Mice quarantined to a different breeding environment,Mice kept in original breeding environment,Mature mice from a distinct strain,6,6,4 weeks,16S,NA,RT-qPCR,Kruskall-Wallis,NA,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,20 March 2023,Ellajessica,Ellajessica,All animals were housed in environment A until 8 weeks of age. Samples obtained during this period are designated by blue symbols. Red symbols represent fecal samples obtained from animals that remained in the original environment (A) (sampled in the animals over 8 weeks of age); open symbols represent animals relocated to environment B. Numbers indentify individual animals; numbers in parenthesis give the age of animal in weeks.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,2|976|200643|171549|815,Complete,ChiomaBlessing
bsdb:659/1/2,Study 659,case-control,33435800,10.1080/19490976.2020.1869504,NA,"Harry Cheuk Hay Lau, Joseph Jao-Yiu Sung",Gut microbiota: impacts on gastrointestinal cancer immunotherapy,Gut microbes,2021,"CpG- oligodeoxynucleotide therapy, Gut microbiota, adoptive cell transfer, blockade-induced adverse events, gastrointestinal cancer, immune checkpoint blockade, probiotics",Experiment 1,United States of America,Mus musculus,Wall of small intestine,UBERON:0001168,Gastric cancer,MONDO:0001056,Mice quarantined to a different breeding environment,Mice kept in original breeding environment,Mature mice from a distinct strain,6,6,4 weeks,16S,NA,RT-qPCR,Kruskall-Wallis,NA,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,23 March 2023,Ellajessica,Ellajessica,Samples obtained from mice relocated at 4 weeks of age are represented by open symbols; red symbols represent animals relocated to environment B at over 8 weeks of age. Numbers identify individual animals; numbers in parenthesis give the age of animal in weeks and (b) UPLC-MS PCA results from the analysis of urine samples from these animals showing the effect of relocation on metabolite profiles.,decreased,k__Bacteria|p__Bacillota|s__Firmicutes bacterium AM10-47,2|1239|2292890,Complete,NA
bsdb:660/1/1,Study 660,case-control,34123872,https://doi.org/10.3389/fcimb.2021.658203,https://pubmed.ncbi.nlm.nih.gov/34123872/,"Jia YJ, Liao Y, He YQ, Zheng MQ, Tong XT, Xue WQ, Zhang JB, Yuan LL, Zhang WL , Jia WH",Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, China, cigarette smoking, oral microbiota, saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Never smokers,Smokers,"Subjects who smoked at least one cigarette every one to three days in the past year, or who smoked at least one cigarette every one to three days but had quit smoking for at least a year (ever smokers + current smokers groups combined)",150,166,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 1, text",15 April 2023,Atrayees,"Atrayees,Claregrieve1",Differentially abundant genera and species between smokers and non-smokers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1239|526524|526525|128827|118747;2|29547|3031852|213849|72294|194;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|437755;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|60133;2|201174|1760|85006|1268|32207|2047;2|1239|526524|526525|128827|123375|102148;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:660/1/2,Study 660,case-control,34123872,https://doi.org/10.3389/fcimb.2021.658203,https://pubmed.ncbi.nlm.nih.gov/34123872/,"Jia YJ, Liao Y, He YQ, Zheng MQ, Tong XT, Xue WQ, Zhang JB, Yuan LL, Zhang WL , Jia WH",Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, China, cigarette smoking, oral microbiota, saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Never smokers,Smokers,"Subjects who smoked at least one cigarette every one to three days in the past year, or who smoked at least one cigarette every one to three days but had quit smoking for at least a year (ever smokers + current smokers groups combined)",150,166,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Table 1, text",15 April 2023,Atrayees,"Atrayees,Claregrieve1",Differentially abundant genera and species between smokers and non-smokers,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus",2|1224|1236|135625|712|416916;2|1224|1236|135615|868|2717;2|1224|28216|206351|481|538;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|32257;2|1224|28216|80840|119060|47670;2|1224|1236|2887326|468|475;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|1107316;2|1224|28216|206351|481|482|28449;2|1239|186801|186802|186807|2740;2|201174|1760|85006|1268|32207|172042;2|1224|1236|135625|712|724|735,Complete,Claregrieve1
bsdb:661/1/1,Study 661,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S, Guo J, Liu R, Zhang F, Wen S, Liu Y, Ren W, Zhang X, Shang Y, Gao M, Lu J , Pang Y",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM).,9,9,"proof of extensive antibiotic therapy for 1+ week in previous 6 months. 
also, prior treatment of systemic antituberculous therapy for more than 1 week.",16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure. 1 and 2(A),8 June 2023,Aiyshaaaa,Aiyshaaaa,The Welch’s t-test was used to analyze phylum and genus level differences in microbiota compositions between pairs of groups: HC and TBM,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1224;2|1224|1236|91347|543|1940338,Complete,Aiyshaaaa
bsdb:661/1/2,Study 661,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S, Guo J, Liu R, Zhang F, Wen S, Liu Y, Ren W, Zhang X, Shang Y, Gao M, Lu J , Pang Y",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM).,9,9,"proof of extensive antibiotic therapy for 1+ week in previous 6 months. 
also, prior treatment of systemic antituberculous therapy for more than 1 week.",16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure. 1 and 2(A),8 June 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees",The Welch’s t-test was used to analyze phylum and genus level differences in microbiota compositions between pairs of groups: HC and TBM,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",2|201174;2|1239;2|1239|186801|3085636|186803|572511;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|1407607;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|841;2|1239|186801|3082720|186804|1501226,Complete,Aiyshaaaa
bsdb:661/2/1,Study 661,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S, Guo J, Liu R, Zhang F, Wen S, Liu Y, Ren W, Zhang X, Shang Y, Gao M, Lu J , Pang Y",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Pulmonary tuberculosis (PTB),The  patients who have been diagnosed from Pulmonary tuberculosis (PTB).,9,13,"therapy for 1+ week in previous 6 months.
also, prior treatment of systemic antituberculous therapy for more than 1 week.",16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure. 1 and 2(B),8 June 2023,Aiyshaaaa,Aiyshaaaa,"Welch’s t-test was used to analyze phylum-level differences in microbiota compositions
between pairs of groups: HC and PTB",increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1224;2|976|200643;2|976|200643|171549|815|816;2|1224|1236|91347|543|1940338,Complete,Aiyshaaaa
bsdb:661/2/2,Study 661,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S, Guo J, Liu R, Zhang F, Wen S, Liu Y, Ren W, Zhang X, Shang Y, Gao M, Lu J , Pang Y",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Pulmonary tuberculosis (PTB),The  patients who have been diagnosed from Pulmonary tuberculosis (PTB).,9,13,"therapy for 1+ week in previous 6 months.
also, prior treatment of systemic antituberculous therapy for more than 1 week.",16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure. 1 and 2(B),8 June 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees",Welch’s t-test was used to analyze phylum-level differences in microbiota compositions between pairs of groups: HC and PTB,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|189330;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|33042,Complete,Aiyshaaaa
bsdb:661/3/1,Study 661,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S, Guo J, Liu R, Zhang F, Wen S, Liu Y, Ren W, Zhang X, Shang Y, Gao M, Lu J , Pang Y",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Pulmonary tuberculosis (PTB),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM),13,9,"proof of extensive antibiotic therapy for 1+ week in previous 6 months.
also, prior treatment of systemic antituberculous therapy for more than 1 week.",16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure. 1 and 2(C),8 June 2023,Aiyshaaaa,Aiyshaaaa,"Welch’s t-test was used to analyze phylum-level differences in microbiota compositions
between pairs of groups: TBM and PTB",increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1224;2|1224|1236|91347|543|1940338,Complete,Aiyshaaaa
bsdb:661/3/2,Study 661,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S, Guo J, Liu R, Zhang F, Wen S, Liu Y, Ren W, Zhang X, Shang Y, Gao M, Lu J , Pang Y",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Pulmonary tuberculosis (PTB),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM),13,9,"proof of extensive antibiotic therapy for 1+ week in previous 6 months.
also, prior treatment of systemic antituberculous therapy for more than 1 week.",16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure. 1 and 2(C),8 June 2023,Aiyshaaaa,Aiyshaaaa,Welch’s t-test was used to analyze phylum-level differences in microbiota compositions between pairs of groups: TBM and PTB,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota",2|1239|186801|3085636|186803|572511;2|976|200643|171549|815|816;2|201174;2|976|200643;2|1239,Complete,Aiyshaaaa
bsdb:662/1/1,Study 662,"cross-sectional observational, not case-control",25658868,10.1371/journal.pone.0117427,https://pubmed.ncbi.nlm.nih.gov/25658868/,"Greenhill AR, Tsuji H, Ogata K, Natsuhara K, Morita A, Soli K, Larkins JA, Tadokoro K, Odani S, Baba J, Naito Y, Tomitsuka E, Nomoto K, Siba PM, Horwood PF , Umezaki M",Characterization of the gut microbiota of Papua New Guineans using reverse transcription quantitative PCR,PloS one,2015,NA,Experiment 1,Papua New Guinea,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High SES (low land region),Low SES (high land region),Participants living a subsistence lifestyle in the high-land rural areas of Papua New Guinea,29,86,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Comparison of population numbers of selected microbial groups in the highland and lowland study participants.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174;2|976;2|1224|1236|91347|543;2|1239;2|1239|91061|186826|33958|1578,Complete,Fatima
bsdb:663/1/1,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Malay,Malay ethnic group living in the  Segamat Malaysian community.,65,46,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 4.,12 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Fatima
bsdb:663/1/2,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Malay,Malay ethnic group living in the  Segamat Malaysian community.,65,46,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4, text",12 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Fatima","Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Fatima
bsdb:663/2/1,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,India,India ethnic group living in the  Segamat Malaysian community.,65,49,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,13 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Fatima
bsdb:663/2/2,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,India,India ethnic group living in the  Segamat Malaysian community.,65,49,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,13 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Fatima
bsdb:663/3/1,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Jakun,Jakun ethnic group living in the  Segamat Malaysian community.,65,54,Unspecified,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,13 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Fatima
bsdb:663/3/2,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Jakun,Jakun ethnic group living in the  Segamat Malaysian community.,65,54,Unspecified,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,13 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Fatima
bsdb:663/4/1,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 4,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,India,Malay,Malay ethnic group living in the  Segamat Malaysian community.,49,46,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"demographics,diet,health,hygiene",unchanged,unchanged,NA,NA,NA,NA,Signature 1,FIGURE 5,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Fatima","Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description: IM Indian–Malay, JI Jakun–Indian.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|186802|216572;2|1239|186801|186802,Complete,Fatima
bsdb:663/5/1,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 5,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Jakun,India,India ethnic group living in the  Segamat Malaysian community.,54,49,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"demographics,diet,health,hygiene",unchanged,unchanged,NA,NA,NA,NA,Signature 1,FIGURE 5,13 July 2022,Kaluifeanyi101,Kaluifeanyi101,Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description:  JI Jakun–Indian.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|1686,Complete,Fatima
bsdb:663/5/2,Study 663,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW , Rahman S",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 5,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Jakun,India,India ethnic group living in the  Segamat Malaysian community.,54,49,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"demographics,diet,health,hygiene",unchanged,unchanged,NA,NA,NA,NA,Signature 2,FIGURE 5,13 July 2022,Kaluifeanyi101,Kaluifeanyi101,Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description: JI Jakun–Indian.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,2|1224|1236|91347|543|570|1463165,Complete,Fatima
bsdb:664/1/1,Study 664,case-control,28506555,10.1016/j.brainres.2017.04.019,NA,"Hopfner F, Künstner A, Müller SH, Künzel S, Zeuner KE, Margraf NG, Deuschl G, Baines JF , Kuhlenbäumer G",Gut microbiota in Parkinson disease in a northern German cohort,Brain research,2017,"Gut microbiota, Parkinson disease, Stool",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Participants with Parkinson's Disease.,Participants diagnosed with Parkinson's Disease by a movement disorder specialist in the clinic according to the UK Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.,29,29,Antibiotic use within the last three months and COMT inhibitors.,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 1.,24 April 2023,Fcuevas3,"Fcuevas3,Aiyshaaaa,Atrayees",Comparison of p-values of bacteria associated with PD in this study or in previous studies.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|976|200643|171549|2005519;2|1239|91061|186826|81852;2|1239|91061|186826|33958,Complete,Atrayees
bsdb:665/1/1,Study 665,prospective cohort,28368458,10.1093/annonc/mdx108,https://pubmed.ncbi.nlm.nih.gov/28368458/,"Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K, Monot C, Boselli L, Routier E, Cassard L, Collins M, Vaysse T, Marthey L, Eggermont A, Asvatourian V, Lanoy E, Mateus C, Robert C , Carbonnel F",Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab,Annals of oncology : official journal of the European Society for Medical Oncology,2017,"colitis, ipilimumab, melanoma, microbiota",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Resistance, Non responders, No colitis","Responders, Colitis",MM patients that developed an immune-mediated colitis following ipilimumab treatment,19,7,NA,16S,34,Illumina,LEfSe,0.05,NA,3.5,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,24 August 2022,Fatima,Fatima,Gut microbiota composition at baseline predicts ipilimumab-induced colitis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",2|976|200643|171549|815|816|28116;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|204475|745368;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|186801|3085636|186803|841|360807,Complete,Fatima
bsdb:665/1/2,Study 665,prospective cohort,28368458,10.1093/annonc/mdx108,https://pubmed.ncbi.nlm.nih.gov/28368458/,"Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K, Monot C, Boselli L, Routier E, Cassard L, Collins M, Vaysse T, Marthey L, Eggermont A, Asvatourian V, Lanoy E, Mateus C, Robert C , Carbonnel F",Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab,Annals of oncology : official journal of the European Society for Medical Oncology,2017,"colitis, ipilimumab, melanoma, microbiota",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Resistance, Non responders, No colitis","Responders, Colitis",MM patients that developed an immune-mediated colitis following ipilimumab treatment,19,7,NA,16S,34,Illumina,LEfSe,0.05,NA,3.5,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,24 August 2022,Fatima,Fatima,Gut microbiota composition at baseline predicts ipilimumab-induced colitis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",2|976|200643|171549|171552|838|59823;2|976|200643|171549|815|816|29523;2|976|200643|171549|815|816|820;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|815|816|2778071;2|976|200643|171549|2005525|375288|823,Complete,Fatima
bsdb:666/1/1,Study 666,"cross-sectional observational, not case-control",22228076,10.1097/MPG.0b013e318249039c.,https://pubmed.ncbi.nlm.nih.gov/22228076/,"Grześkowiak Ł, Collado MC, Mangani C, Maleta K, Laitinen K, Ashorn P, Isolauri E , Salminen S",Distinct gut microbiota in southeastern African and northern European infants,Journal of pediatric gastroenterology and nutrition,2012,NA,Experiment 1,"Finland,Malawi",Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High-Income country (Finland),Low-income country (Malawi),44 healthy 6-month-old rural infants from Malawi,31,44,6 months,WMS,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Finnish and Malawian infants,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:666/1/2,Study 666,"cross-sectional observational, not case-control",22228076,10.1097/MPG.0b013e318249039c.,https://pubmed.ncbi.nlm.nih.gov/22228076/,"Grześkowiak Ł, Collado MC, Mangani C, Maleta K, Laitinen K, Ashorn P, Isolauri E , Salminen S",Distinct gut microbiota in southeastern African and northern European infants,Journal of pediatric gastroenterology and nutrition,2012,NA,Experiment 1,"Finland,Malawi",Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High-Income country (Finland),Low-income country (Malawi),44 healthy 6-month-old rural infants from Malawi,31,44,6 months,WMS,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Finnish and Malawian infants,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",2|74201|203494|48461|1647988|239934|239935;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1686;2|1239|186801|3085636|186803|572511|1532;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|186802|31979|1485|1502;2|1239|91061|1385|90964|1279|1280;2|1239|186801|186802|216572|1535,Complete,Claregrieve1
bsdb:667/1/1,Study 667,prospective cohort,32925716,10.1097/MD.0000000000021788,https://pubmed.ncbi.nlm.nih.gov/32925716/,"Li L , Ye J",Characterization of gut microbiota in patients with primary hepatocellular carcinoma received immune checkpoint inhibitors: A Chinese population-based study,Medicine,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Patients in the clinical response group treated by immune checkpoint inhibitors therapy (defined by radiographic evidence of complete response, partial response or stable disease per RECIST 1.1 criteria for at least 6 months)",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1b,15 July 2022,Sharmilac,"Sharmilac,Fatima",Compositional differences in the gut microbiome are associated with responses to anti-PD-1 immunotherapy.,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium hungatei,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239;2|201174|1760|85006|1268;2|544448|31969;2|1239|186801|186802|216572;2|1239|1737404|1737405|1570339|162289;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|171551|836|1583331;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|1508657|48256;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40518;2|1239|909932|1843489|31977;2|1239|186801|186802,Complete,Fatima
bsdb:667/1/2,Study 667,prospective cohort,32925716,10.1097/MD.0000000000021788,https://pubmed.ncbi.nlm.nih.gov/32925716/,"Li L , Ye J",Characterization of gut microbiota in patients with primary hepatocellular carcinoma received immune checkpoint inhibitors: A Chinese population-based study,Medicine,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Patients in the clinical response group treated by immune checkpoint inhibitors therapy (defined by radiographic evidence of complete response, partial response or stable disease per RECIST 1.1 criteria for at least 6 months)",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 1b,21 July 2022,Sharmilac,"Sharmilac,Fatima",Compositional differences in the gut microbiome are associated with responses to anti-PD-1 immunotherapy.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides mediterraneensis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio alaskensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|976|200643|171549;2|976;2|976|200643;2|201174|84998|84999|84107|102106|147206;2|976|200643|171549|815|816|1841856;2|200940|3031449|213115|194924|2909705|58180;2|976|200643|171549|171552|838|470565;2|201174|1760|85004|31953|2701|2702;2|201174|1760|85004|31953|2701,Complete,Fatima
bsdb:667/2/NA,Study 667,prospective cohort,32925716,10.1097/MD.0000000000021788,https://pubmed.ncbi.nlm.nih.gov/32925716/,"Li L , Ye J",Characterization of gut microbiota in patients with primary hepatocellular carcinoma received immune checkpoint inhibitors: A Chinese population-based study,Medicine,2020,NA,Experiment 2,China,Homo sapiens,Buccal mucosa,UBERON:0006956,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Patients in the clinical response group treated by immune checkpoint inhibitors therapy (defined by radiographic evidence of complete response, partial response or stable disease per RECIST 1.1 criteria for at least 6 months)",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:668/1/1,Study 668,"cross-sectional observational, not case-control",32236123,10.1371/journal.pone.0228574,NA,"Stennett CA, Dyer TV, He X, Robinson CK, Ravel J, Ghanem KG , Brotman RM",A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women,PloS one,2020,NA,Experiment 1,United States of America,Homo sapiens,Vaginal fluid,UBERON:0036243,Bacterial vaginosis,EFO:0003932,vaginal delivery,cesarean section,women reported birth by C-section,117,27,women reported birth by vaginal delivery,PCR,NA,Illumina,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,1 June 2023,Danyab56,Danyab56,"The bacterial taxa with the highest effect sizes (linear discriminant analysis [LDA] scores > 4) reflect marked abundance in one birth mode group and not in the other. Three taxa were differentially abundant at this level, with P. bivia being more abundant in C-section-delivered group and L. jensenii and L. iners being more abundant in the vaginally-delivered group. However, these differences were not statistically significant (0.05 < p < 0.30).",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,2|976|200643|171549|171552|838|28125,Complete,Fatima
bsdb:668/1/2,Study 668,"cross-sectional observational, not case-control",32236123,10.1371/journal.pone.0228574,NA,"Stennett CA, Dyer TV, He X, Robinson CK, Ravel J, Ghanem KG , Brotman RM",A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women,PloS one,2020,NA,Experiment 1,United States of America,Homo sapiens,Vaginal fluid,UBERON:0036243,Bacterial vaginosis,EFO:0003932,vaginal delivery,cesarean section,women reported birth by C-section,117,27,women reported birth by vaginal delivery,PCR,NA,Illumina,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,1 June 2023,Danyab56,Danyab56,"The bacterial taxa with the highest effect sizes (linear discriminant analysis [LDA] scores > 4) reflect marked abundance in one birth mode group and not in the other. Three taxa were differentially abundant at this level, with P. bivia being more abundant in C-section-delivered group and L. jensenii and L. iners being more abundant in the vaginally-delivered group. However, these differences were not statistically significant (0.05 < p < 0.30).",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|1239|91061|186826|33958|1578|109790;2|1239|91061|186826|33958|1578|147802,Complete,Fatima
bsdb:669/1/1,Study 669,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G , Lionetti P",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 1,"Italy,Burkina Faso",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Place of residence measurement","EFO:0001799,EFO:0009583",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Supporting Info. Table S5 + Fig. S2,17 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees,ChiomaBlessing",Report of the species assignment for BF and EU populations relative to the most abundant bacterial genera found by the RDP classifier,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Aegyptianella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales str. KB11,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales str. KB13,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. TP-5,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis|s__Bifidobacterium animalis subsp. lactis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium simiae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium thermophilum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Budvicia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Cytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aff. ruminicola Tc2-24,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aurantiaca,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella paludivivens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter brevis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter oryzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium M21/2,k__Bacteria|s__butyrate-producing bacterium PH07AY5,k__Bacteria|s__butyrate-producing bacterium PH07BY04",2|1224|28211|766|942|203861;2|1239|186801|186802|216572|52784;2|976|200643|171549|185297;2|976|200643|171549|185299;2|976|200643|171549|815|816|28113;2|976|200643|171549|815|816|643958;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|28025;2|201174|1760|85004|31953|1678|28025|302911;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|201174|1760|85004|31953|1678|78448;2|201174|1760|85004|31953|1678|78346;2|201174|1760|85004|31953|1678|180216;2|201174|1760|85004|31953|1678|33905;2|1224|1236|91347|1903416|82978;2|1239|186801|3085636|186803|830;2|29547|3031852|213849|72294|194;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|33870;2|976|768503|768507|89373|978;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|52228;2|1239|186801|3085636|186803|140625;2|1239|91061|186826|33958|1243;2|976|200643|171549|171552|2974265|363265;2|1239|909932|909929|1843491|52225;2|1224|1236|91347|1903414|581;2|976|200643|171549|2005523|346096;2|976|200643|171549|171552|838|81582;2|976|200643|171549|171552|838|596085;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|59823;2|1224|1236|135624|83763|866;2|1239|186801|186802|31979|1266;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552|2974251|185294;2|201174|84998|1643822|1643826|84108;2|1224|1236|135624|83763|83768;2|1224|1236|135624|83763|83770;2|203691|203692|136|2845253|157;2|203691|203692|136|2845253|157|166;2|1224|28216|206351|481|299568;2|1239|91061|186826|33958|46255;2|976|200643|171549|171552|558436|83231;2|976|200643|171549|171552|558436|185293;2|976|200643|171549|171552|558436|839;2|1239|186801|186802|245005;2|340481;2|340484,Complete,ChiomaBlessing
bsdb:669/1/2,Study 669,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G , Lionetti P",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 1,"Italy,Burkina Faso",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Place of residence measurement","EFO:0001799,EFO:0009583",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Supporting Info. Table S5 + Fig. S2,17 July 2022,Kaluifeanyi101,"Kaluifeanyi101,ChiomaBlessing",Report of the species assignment for BF and EU populations relative to the most abundant bacterial genera found by the RDP classifier,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. AR20,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. XO77B42,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp. PL1,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp. h12,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. DJF_VR33k2,k__Bacteria|s__bacterium ic1395,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium M21/2,k__Bacteria|s__butyrate-producing bacterium PH07AY5,k__Bacteria|s__butyrate-producing bacterium PH07BY04,k__Bacteria|s__swine fecal bacterium RF3E-Xyl1,k__Bacteria|s__swine fecal bacterium RF3G-Cel1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Propionispira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Seinonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Thermobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Chitinibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Lawsonia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Orientia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Phocoenobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Telluria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Thalassobacter",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|626932;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|93974;2|976|200643|171549|815|816|371598;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|201174|1760|85004|31953|1678|78346;2|201174|1760|85004|31953|1678|138809;2|201174|1760|85004|31953|1678|308029;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|204516;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|1239|186801|186802|216572|292632|537421;2|330061;2|1239|186801|186802|245005;2|340481;2|340484;2|621345;2|621352;2|1239|186801|186802|216572|244127;2|1239|186801|186802|541019|342658;2|1239|186801|186802|543313|228923;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|31979|44261;2|1239|909932|909929|1843491|84034;2|1239|186801|186802|186806|113286;2|1239|91061|1385|186824|292637;2|1239|91061|1385|186822|76632;2|32066|203490|203491|203492|848;2|201174|84998|1643822|1643826|84111;2|200940|3031449|213115|194924|35832;2|1224|1236|91347|543|158483;2|1224|28216|206351|2897177|230666;2|1224|1236|91347|543|544;2|1224|1236|91347|543|547;2|1224|1236|91347|543|579;2|200940|3031449|213115|194924|41707;2|1224|28216|80840|75682|149698;2|1224|28211|766|775|69474;2|1224|1236|135625|712|146805;2|1224|1236|91347|543|590;2|1224|1236|91347|543|620;2|1224|28216|80840|995019|40544;2|1224|28216|80840|75682|34069;2|1224|28211|204455|2854170|266808,Complete,ChiomaBlessing
bsdb:669/2/1,Study 669,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G , Lionetti P",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 2,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Place of residence measurement","EFO:0001799,EFO:0009583",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3B,11 July 2023,Atrayees,"Atrayees,ChiomaBlessing","Number of sequences relative to principal Enterobacteriaceae genera, in BF and EU children microbiota.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,ChiomaBlessing
bsdb:669/3/1,Study 669,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G , Lionetti P",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 3,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Place of residence measurement","EFO:0001799,EFO:0009583",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Supporting Info. Fig. S1,22 January 2024,ChiomaBlessing,ChiomaBlessing,Boxplots (percentage of sequences) of the four most represented phyla in the BF compared to EU children.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|201174;2|976|200643,Complete,ChiomaBlessing
bsdb:669/3/2,Study 669,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G , Lionetti P",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 3,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Place of residence measurement","EFO:0001799,EFO:0009583",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Supporting Info. Fig. S1,22 January 2024,ChiomaBlessing,ChiomaBlessing,Boxplots (percentage of sequences) of the four most represented phyla in the BF compared to EU children.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|1239;2|1224,Complete,ChiomaBlessing
bsdb:670/1/1,Study 670,"cross-sectional observational, not case-control",23349750,10.1371/journal.pone.0053838,https://pubmed.ncbi.nlm.nih.gov/23349750/,"Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA , Singh U",Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States,PloS one,2013,NA,Experiment 1,"United States of America,Bangladesh",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Socioeconomic status","EFO:0001799,EXO:0000114",US children,Bangladesh Children (Household income < $61),"Fecal specimens from 6 Bangladeshi children (ages 8–13), in low socioeconomic conditions with an average monthly income per family of,5,000 takas (the U.S. $61).",4,6,3 months,16S,123,Roche454,ANOSIM,0.1,TRUE,NA,NA,"age,sex",NA,increased,increased,NA,NA,NA,Signature 1,Table 3,19 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Bangladeshi children and US children,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3085636|186803|830;2|1239|186801|186802,Complete,Claregrieve1
bsdb:670/1/2,Study 670,"cross-sectional observational, not case-control",23349750,10.1371/journal.pone.0053838,https://pubmed.ncbi.nlm.nih.gov/23349750/,"Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA , Singh U",Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States,PloS one,2013,NA,Experiment 1,"United States of America,Bangladesh",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Socioeconomic status","EFO:0001799,EXO:0000114",US children,Bangladesh Children (Household income < $61),"Fecal specimens from 6 Bangladeshi children (ages 8–13), in low socioeconomic conditions with an average monthly income per family of,5,000 takas (the U.S. $61).",4,6,3 months,16S,123,Roche454,ANOSIM,0.1,TRUE,NA,NA,"age,sex",NA,increased,increased,NA,NA,NA,Signature 2,Table 3,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential microbial abundance between Bangladeshi children and US children,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|976|200643|171549|815|816|818;2|1239|186801|186802|216572|216851|853,Complete,Claregrieve1
bsdb:671/1/1,Study 671,prospective cohort,32011017,10.1111/ppe.12623,https://pubmed.ncbi.nlm.nih.gov/32011017/,"Kortekangas E, Kamng'ona AW, Fan YM, Cheung YB, Ashorn U, Matchado A, Poelman B, Maleta K, Dewey KG , Ashorn P",Environmental exposures and child and maternal gut microbiota in rural Malawi,Paediatric and perinatal epidemiology,2020,"child health, environment, gut microbiota, seasons, socio-economic factors",Experiment 1,Malawi,Homo sapiens,Feces,UBERON:0001988,Seasonal gut microbiome measurement,EFO:0007753,samples taken in dry/hot or rainy season,samples taken in dry/cold season,samples taken in the dry/cold season,NA,NA,NA,16S,4,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,"antibiotic exposure,delivery procedure,education level,marital status,maternal age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential abundance between samples from dry/cold season vs samples from dry/hot or rainy season,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus porcinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301|1340;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|541000;2|1239|186801|186802|31979|1485;2|1239|186801|186802|1898207;2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:671/1/2,Study 671,prospective cohort,32011017,10.1111/ppe.12623,https://pubmed.ncbi.nlm.nih.gov/32011017/,"Kortekangas E, Kamng'ona AW, Fan YM, Cheung YB, Ashorn U, Matchado A, Poelman B, Maleta K, Dewey KG , Ashorn P",Environmental exposures and child and maternal gut microbiota in rural Malawi,Paediatric and perinatal epidemiology,2020,"child health, environment, gut microbiota, seasons, socio-economic factors",Experiment 1,Malawi,Homo sapiens,Feces,UBERON:0001988,Seasonal gut microbiome measurement,EFO:0007753,samples taken in dry/hot or rainy season,samples taken in dry/cold season,samples taken in the dry/cold season,NA,NA,NA,16S,4,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,"antibiotic exposure,delivery procedure,education level,marital status,maternal age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1",Differential abundance between samples from dry/cold season vs samples from dry/hot or rainy season,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",2|1224|1236|91347|543|547;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485;2|1239|91061|186826|186828|117563|46124;2|1224|28216|206351|481|482;2|976|200643|171549|815|816|817;2|1239|186801|186802|216572|1263;2|1224|1236|91347|543;2|976|200643|171549|815|816|818,Complete,Claregrieve1
bsdb:672/1/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Day-10 (D10) (chronological age),4-months corrected age (4M),Faecal samples collected from moderate–late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management at 4-months corrected age (4M).,207,118,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Text (page 5),18 March 2024,Scholastica,Scholastica,Significantly abundant taxa between the two time points; day-10 (D10) (chronological age) and at 4-months corrected age (4M).,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|909932|1843489|31977;2|1239|526524|526525|128827;2|1239|186801|3082720|186804;2|1239|91061|186826|33958;2|201174|1760|85004|31953;2|201174|84998|1643822|1643826;2|201174|84998|84999|84107;2|201174|1760|2037|2049;2|201174|84998|84999|1643824;2|1224|1236|91347|543;2|976|200643|171549|815;2|1239|186801|186802|216572,Complete,NA
bsdb:672/1/2,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Day-10 (D10) (chronological age),4-months corrected age (4M),Faecal samples collected from moderate–late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management at 4-months corrected age (4M).,207,118,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Text (page 5),18 March 2024,Scholastica,Scholastica,Significantly abundant taxa between the two time points; day-10 (D10) (chronological age) and at 4-months corrected age (4M).,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|1239|91061|1385|90964;2|201174|1760|85007|1653;2|1224|1236|135625|712,Complete,NA
bsdb:672/2/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 2,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Higher SES (D10),Lower SES (D10),Moderate–late preterm (MLPT) babies at Day-10 (D10) whose families lived in the lower SES (socioeconomic status) areas,59,80,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Text (page 5),18 March 2024,Scholastica,Scholastica,Significantly abundant taxa in MLPT babies from lower socioeconomic status (SES) group compared to the higher SES group at D10,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
bsdb:672/3/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 3,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Higher SES (4M),Lower SES (4M),Moderate–Late Preterm (MLPT) babies at 4-months corrected-age (4M) whose families lived in the lower SES (socioeconomic status) areas,59,80,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Text (page 5),18 March 2024,Scholastica,Scholastica,Significantly abundant taxa in MLPT babies from lower socioeconomic status (SES) group compared to the higher SES group at 4M,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,2|1239|909932|1843489|31977|906,Complete,NA
bsdb:672/4/NA,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 4,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,European (D10),Maori (D10),Moderate–Late Preterm (MLPT) Babies at D10 born to mothers self-reporting as Maori,77,24,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:672/5/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 5,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Asian (4M),Maori (4M),Moderate–Late Preterm (MLPT) babies at 4M born to mothers self-reporting as Maori,72,24,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text (page 5),18 March 2024,Scholastica,"Scholastica,MyleeeA",Significantly abundant taxa in MLPT Babies at 4M born to mothers self-reporting as Maori compared to Asian,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85006|1268|32207;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:672/6/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 6,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Asian (4M),Pacifica (4M),Moderate–Late Preterm (MLPT) babies at 4-months born to mothers self-reporting as Pacifica,72,36,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text (page 5),18 March 2024,Scholastica,"Scholastica,MyleeeA",Significantly abundant taxa in MLPT Babies at 4-months born to mothers self-reporting as Pacifica compared to Asian,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
bsdb:672/7/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 7,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No University (4M),University (4M),Moderate–late preterm (MLPT) babies at 4-months whose mothers have a university degree,108,105,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,30 March 2024,MyleeeA,MyleeeA,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data. Only results with Q-value<0.25 are shown.",decreased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,2|201174|84998|1643822|1643826|84111,Complete,NA
bsdb:672/8/NA,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 8,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Mix feeding (4M),Breastmilk feeding (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,95,36,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:672/9/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 9,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only formula (4M),Breastmilk feeding (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,42,36,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text (page 6),18 March 2024,Scholastica,Scholastica,Significantly abundant taxa in MLPT Babies at 4-months corrected age who were breastmilk fed compared to babies that were fed only formula,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,2|1239|909932|1843489|31977|906,Complete,NA
bsdb:672/10/NA,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 10,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only formula (4M),Mixed feeding (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were mix fed,42,95,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:672/11/NA,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 11,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No maternal antibiotics,Yes maternal antibiotics,Maternal use of antibiotics within the four-week period before the D10 fecal sample collection,69,130,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:672/12/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 12,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No maternal probiotics,Yes maternal probiotics,Maternal use of probiotics within the four-week period before the D10 fecal sample collection,147,19,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,MyleeeA,"Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,NA
bsdb:672/13/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 13,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No infant probiotics,Yes infant probiotics,D10 fecal samples of infants who themselves received probiotics during their admission,159,40,None,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Text (page 6),19 March 2024,Scholastica,Scholastica,Significantly abundant taxa in  samples of MLPT infants at D10 who themselves received probiotics during their admission,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
bsdb:672/14/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 14,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Antibiotics,Yes Antibiotics,Infant who received antibiotic within the month immediately preceding the 4-month follow-up appointment,5,108,N/A,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S4 and Text (Page 7),31 March 2024,MyleeeA,MyleeeA,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,NA
bsdb:672/15/NA,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 15,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only Formula (4M),Breast Milk (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,42,36,N/A,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:672/16/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 16,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only Formula (D10),Breast Milk (D10),Moderate–late preterm (MLPT) babies at Day 10 who were breastmilk fed,42,36,N/A,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,MyleeeA,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
bsdb:672/17/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 17,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Mixed Feeding (4M),Breast Milk (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,95,36,N/A,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,MyleeeA,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by shotgun metagenomics data.",increased,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,2|200940|3031449|213115|194924|35832,Complete,NA
bsdb:672/18/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 18,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Mixed Feeding (D10),Only Formula (D10),Moderate–late preterm (MLPT) babies at Day 10 who were fed with only formula,95,42,N/A,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,MyleeeA,"Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data.",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
bsdb:672/19/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 19,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Antibiotics (4M),Yes Antibiotics (4M),Maternal use of antibiotics within the one month preceding the four-month follow-up period,69,130,N/A,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,MyleeeA,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",2|1239|186801|3085636|186803|1506553;2|1239|186801|3082720|186804|1505657,Complete,NA
bsdb:672/20/NA,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 20,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Infant Antibiotics (4M),Yes Infant Antibiotics (4M),Infant use of antibiotics within the one month preceding the 4-month follow-up appointment,89,4,N/A,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:672/21/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 21,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Infant Antibiotics (D10),Yes Infant Antibiotics (D10),Infants who themselves use antibiotic during neonatal admission at D10,97,102,N/A,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S4,1 April 2024,Scholastica,Scholastica,"Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
bsdb:672/22/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 22,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Caesarean section (D10),Vaginal delivery (D10),D10 fecal samples of MLPT babies born vaginally,136,77,N/A,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (page 8), Supplementary Table S4",1 April 2024,Scholastica,Scholastica,"Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
bsdb:672/23/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 23,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Singletons (4M),Twins (4M),Fecal samples of MLPT babies born as twins at 4-month corrected age,63,31,N/A,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S4,1 April 2024,Scholastica,Scholastica,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data. Only results with Q-value<0.25 are shown.",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,2|1239|186801|186802|216572|1508657,Complete,NA
bsdb:672/24/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 24,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Singletons (4M),Twins (4M),Fecal samples of MLPT babies born as twins at 4-month corrected age,63,31,N/A,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (page 8), Supplementary Table S4",1 April 2024,Scholastica,Scholastica,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data. Only results with Q-value<0.25 are shown.",increased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,2|201174|84998|1643822|1643826|84111|84112,Complete,NA
bsdb:672/25/1,Study 672,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong CYL, Vatanen T, Alexander T, Bloomfield FH , O'Sullivan JM",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 25,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Auckland city hospital (4M),Middlemore Hospital (4M),MLPT babies born at Middlemore Hospital at 4-month corrected age,83,80,N/A,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (page 8), Supplementary Table S4",1 April 2024,Scholastica,Scholastica,"Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by shotgun metagenomics data, (Q-value<0.25).",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,NA
bsdb:673/1/1,Study 673,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar JS, Klotz B, Valdes BE , Agudelo GM","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 1,"United States of America,Colombia,South Korea,Japan,Spain,France,Denmark",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Colombia data,"30 healthy Colombia adults of both genders from the general population living in Medellin, Colombia South America.",13,30,4 Months,16S,123,Roche454,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",increased,k__Bacteria|p__Bacillota,2|1239,Complete,Peace Sandy
bsdb:673/1/2,Study 673,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar JS, Klotz B, Valdes BE , Agudelo GM","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 1,"United States of America,Colombia,South Korea,Japan,Spain,France,Denmark",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Colombia data,"30 healthy Colombia adults of both genders from the general population living in Medellin, Colombia South America.",13,30,4 Months,16S,123,Roche454,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference; NA = not available.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Peace Sandy
bsdb:673/2/2,Study 673,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar JS, Klotz B, Valdes BE , Agudelo GM","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 2,"Colombia,Denmark,France,Spain,United States of America,South Korea,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Europe data,"The European dataset consisted of the subset of 13 healthy volunteers (three women and 10 men) among Spanish, French, and Danish inhabitants whose microbiomes were published by the MetaHIT Consortium",13,13,4 Months,16S,123,Roche454,PERMANOVA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference; NA = not available.",decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Peace Sandy
bsdb:673/3/2,Study 673,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar JS, Klotz B, Valdes BE , Agudelo GM","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 3,"Colombia,Denmark,France,Spain,United States of America,South Korea,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,South Korea data,The Korean dataset consisted of 14 lean and four overweight individuals (six women and 12 men),54,14,4 months,16S,123,Roche454,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Taxonomic composition of the gut microbiota in the different datasets

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Peace Sandy
bsdb:673/4/1,Study 673,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar JS, Klotz B, Valdes BE , Agudelo GM","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 4,"Colombia,Denmark,France,South Korea,Spain,United States of America,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Japan data,The Japanese dataset consisted of 454-generated V1 and V2 16S rDNA sequences of 10 lean and one overweight adult (six females and five males) that participated in an intervention with probiotics,54,11,4 months,16S,12,Roche454,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2022,Kaluifeanyi101,Kaluifeanyi101,"Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Peace Sandy
bsdb:673/4/2,Study 673,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar JS, Klotz B, Valdes BE , Agudelo GM","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 4,"Colombia,Denmark,France,South Korea,Spain,United States of America,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Japan data,The Japanese dataset consisted of 454-generated V1 and V2 16S rDNA sequences of 10 lean and one overweight adult (six females and five males) that participated in an intervention with probiotics,54,11,4 months,16S,12,Roche454,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Taxonomic composition of the gut microbiota in the different datasets

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Peace Sandy
bsdb:674/1/1,Study 674,"cross-sectional observational, not case-control",34444813,10.3390/nu13082645,https://pubmed.ncbi.nlm.nih.gov/34444813/,"Lapidot Y, Reshef L, Goldsmith R, Na'amnih W, Kassem E, Ornoy A, Gophna U , Muhsen K",The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence,Nutrients,2021,"dietary intake, microbiome, obesity, school age, socioeconomic status",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Low SES,High SES,"Children from the higher SES village (A)
SES scores below the median score of 6.4 based on (a) residential SES rank; (b) the number of paternal schooling years; and (c) household crowding index.",69,70,NA,16S,4,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,diet,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 2D;,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Figure 2D. A heatmap of the multivariable model describing
the top 50 associations between the independent variables and bacterial features. Positive associations are colored in red, while inverse associations are colored in blue. The color gradient represents the strength of the association (the effect
size), with darker colors representing the stronger associations. The effect size was calculated by the following formula: (−log(qval)*SIGN (coeff)).",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1224|28216|80840|80864|80865;2|976|200643|171549|171550;2|976|200643|171549|2005519;2|1239|186801|186802|31979|1485;2|1239|526524|526525|128827;2|976|200643|171549|2005525|375288;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|1263,Complete,Peace Sandy
bsdb:674/1/2,Study 674,"cross-sectional observational, not case-control",34444813,10.3390/nu13082645,https://pubmed.ncbi.nlm.nih.gov/34444813/,"Lapidot Y, Reshef L, Goldsmith R, Na'amnih W, Kassem E, Ornoy A, Gophna U , Muhsen K",The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence,Nutrients,2021,"dietary intake, microbiome, obesity, school age, socioeconomic status",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Low SES,High SES,"Children from the higher SES village (A)
SES scores below the median score of 6.4 based on (a) residential SES rank; (b) the number of paternal schooling years; and (c) household crowding index.",69,70,NA,16S,4,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,diet,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 2D,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy","Figure 2D. A heatmap of the multivariable model describing the top 50 associations between the independent variables and bacterial features. Positive associations are colored in red, while inverse associations are colored in blue. The color gradient represents the strength of the association (the effect size), with darker colors representing the stronger associations. The effect size was calculated by the following formula: (−log(qval)*SIGN (coeff)).",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107;2|1239|526524|526525|128827|118747;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|171552|838;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|189330;2|201174|84998|1643822|1643826|447020,Complete,Peace Sandy
bsdb:675/1/1,Study 675,"cross-sectional observational, not case-control",31973685,10.1080/19490976.2020.1712985,https://pubmed.ncbi.nlm.nih.gov/31973685/,"Moran-Ramos S, Lopez-Contreras BE, Villarruel-Vazquez R, Ocampo-Medina E, Macias-Kauffer L, Martinez-Medina JN, Villamil-Ramirez H, León-Mimila P, Del Rio-Navarro BE, Ibarra-Gonzalez I, Vela-Amieva M, Gomez-Perez FJ, Velazquez-Cruz R, Salmeron J, Reyes-Castillo Z, Aguilar-Salinas C , Canizales-Quinteros S",Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study,Gut microbes,2020,"adolescents, children, co-abundance groups, diversity, enterotypes, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower monthly household income,higher monthly household income,higher monthly household income,NA,NA,6 months,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,antibiotic exposure,household income,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table  1, text",23 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees",Taxa significantly associated with monthly household income.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",2|201174|84998|1643822|1643826|84111|84112;2|976|200643|171549|815|816|817;2|976|200643|171549|171550;2|1239|526524|526525|128827|61170;2|1239|186801|186802|216572|119852;2|1239|526524|526525|128827|2749846|31971,Complete,Atrayees
bsdb:675/1/2,Study 675,"cross-sectional observational, not case-control",31973685,10.1080/19490976.2020.1712985,https://pubmed.ncbi.nlm.nih.gov/31973685/,"Moran-Ramos S, Lopez-Contreras BE, Villarruel-Vazquez R, Ocampo-Medina E, Macias-Kauffer L, Martinez-Medina JN, Villamil-Ramirez H, León-Mimila P, Del Rio-Navarro BE, Ibarra-Gonzalez I, Vela-Amieva M, Gomez-Perez FJ, Velazquez-Cruz R, Salmeron J, Reyes-Castillo Z, Aguilar-Salinas C , Canizales-Quinteros S",Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study,Gut microbes,2020,"adolescents, children, co-abundance groups, diversity, enterotypes, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower monthly household income,higher monthly household income,higher monthly household income,NA,NA,6 months,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,"age,antibiotic exposure,household income,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table 1, text",23 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees",taxa significantly associated with monthly household income.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977,Complete,Atrayees
bsdb:676/1/1,Study 676,prospective cohort,31026576,10.1016/j.jtho.2019.04.007,"https://pubmed.ncbi.nlm.nih.gov/31026576/#:~:text=Patients_With_NSCLC-,The_Diversity_of_Gut_Microbiome_is_Associated_With_Favorable_Responses,(8):1378-1389.","Jin Y, Dong H, Xia L, Yang Y, Zhu Y, Shen Y, Zheng H, Yao C, Wang Y , Lu S",The Diversity of Gut Microbiome is Associated With Favorable Responses to Anti-Programmed Death 1 Immunotherapy in Chinese Patients With NSCLC,Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer,2019,"Advanced NSCLC, Clinical benefit, Gut microbiota, Nivolumab, Systemic immune signatures",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients in this study were defined as responder (R) (with partial response or stable disease),14,23,NA,16S,34,Illumina,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 1,"Figures 3a,b & c",25 July 2022,Sharmilac,Sharmilac,"Comparison of gut microbiota composition between responders (R) and non responders (NR). (A) Heatmap of seven bacterial genera with statistically differential abundance in R (n ¼ 13) and NR (n ¼ 12) at baseline. (B) Histogram of two representative differentially abundant genera at baseline. (C) Histogram of Bifidobacterium longum and Prevotella copri at baseline (left) and T1 timepoint (right). Statistical analysis was performed by Mann-Whitney test. **p < 0.01, * p < 0.05.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|976|200643|171549|171550|239759|28117;2|201174|1760|85004|31953|1678|216816;2|1239|186801|3085636|186803|140625;2|1239|186801|3085636|186803;2|976|200643|171549|171552|2974251|165179;2|1224|1236|91347|543|620,Complete,Fatima
bsdb:676/1/2,Study 676,prospective cohort,31026576,10.1016/j.jtho.2019.04.007,"https://pubmed.ncbi.nlm.nih.gov/31026576/#:~:text=Patients_With_NSCLC-,The_Diversity_of_Gut_Microbiome_is_Associated_With_Favorable_Responses,(8):1378-1389.","Jin Y, Dong H, Xia L, Yang Y, Zhu Y, Shen Y, Zheng H, Yao C, Wang Y , Lu S",The Diversity of Gut Microbiome is Associated With Favorable Responses to Anti-Programmed Death 1 Immunotherapy in Chinese Patients With NSCLC,Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer,2019,"Advanced NSCLC, Clinical benefit, Gut microbiota, Nivolumab, Systemic immune signatures",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients in this study were defined as responder (R) (with partial response or stable disease),14,23,NA,16S,34,Illumina,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 2,"Figure 3a,b,c",25 July 2022,Sharmilac,Sharmilac,"Comparison of gut microbiota composition between responders (R) and non responders (NR). (A) Heatmap of seven bacterial genera with statistically differential abundance in R (n ¼ 13) and NR (n ¼ 12) at baseline. (B) Histogram of two representative differentially abundant genera at baseline. (C) Histogram of Bifidobacterium longum and Prevotella copri at baseline (left) and T1 timepoint (right). Statistical analysis was performed by Mann-Whitney test. **p < 0.01, * p < 0.05.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:677/1/1,Study 677,prospective cohort,33619320,10.1038/s42003-021-01741-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7900251/pdf/42003_2021_Article_1741.pdf,"Sims TT, El Alam MB, Karpinets TV, Dorta-Estremera S, Hegde VL, Nookala S, Yoshida-Court K, Wu X, Biegert GWG, Delgado Medrano AY, Solley T, Ahmed-Kaddar M, Chapman BV, Sastry KJ, Mezzari MP, Petrosino JF, Lin LL, Ramondetta L, Jhingran A, Schmeler KM, Ajami NJ, Wargo J, Colbert LE , Klopp AH",Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation,Communications biology,2021,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Survival time,EFO:0000714,Long-term survivors,Short-term surviviors,Cervical Cancer patients that had a follow-up of one year or less because of death,48,7,None,16S,4,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a,16 March 2023,BLESSING123,"BLESSING123,Chloe","The different abundance of bacterial taxa between the two
groups were identified by LEfSe. It was significantly different when alpha value of the factorial Kruskal–Wallis test was <0.05 and the logarithmic LDA score was
>3.5. The left histogram showed the LDA scores of taxa differentially abundant between the two groups. The taxonomy was listed, followed by its core group.
Putative species (Specific OTUs) identified as significantly more enriched/depleted (Fisher/Wilcoxon test p value < 0.05) in patients with short-term vs longterm in baseline samples",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|29547;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1224|1236|135625|712|724;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3085636|186803|1506577;2|1239|909932|1843489|31977|29465,Complete,Chloe
bsdb:677/1/2,Study 677,prospective cohort,33619320,10.1038/s42003-021-01741-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7900251/pdf/42003_2021_Article_1741.pdf,"Sims TT, El Alam MB, Karpinets TV, Dorta-Estremera S, Hegde VL, Nookala S, Yoshida-Court K, Wu X, Biegert GWG, Delgado Medrano AY, Solley T, Ahmed-Kaddar M, Chapman BV, Sastry KJ, Mezzari MP, Petrosino JF, Lin LL, Ramondetta L, Jhingran A, Schmeler KM, Ajami NJ, Wargo J, Colbert LE , Klopp AH",Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation,Communications biology,2021,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Survival time,EFO:0000714,Long-term survivors,Short-term surviviors,Cervical Cancer patients that had a follow-up of one year or less because of death,48,7,None,16S,4,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,16 March 2023,BLESSING123,"BLESSING123,Chloe","The different abundance of bacterial taxa between the two
groups were identified by LEfSe. It was significantly different when alpha value of the factorial Kruskal–Wallis test was <0.05 and the logarithmic LDA score was
>3.5. The left histogram showed the LDA scores of taxa differentially abundant between the two groups. The taxonomy was listed, followed by its core group.
Putative species (Specific OTUs) identified as significantly more enriched/depleted (Fisher/Wilcoxon test p value < 0.05) in patients with short-term vs longterm in baseline samples",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|1239|909932|1843489|31977|39948;2|976|200643|171549|171551;2|976|200643|171549|171551|836,Complete,Chloe
bsdb:678/1/1,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 1,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Cigarette Smokers,People consuming tobacco in the form of cigarettes (CS),225,33,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,increased,NA,increased,Signature 1,Table 2,17 March 2023,Adi13,"Adi13,ChiomaBlessing","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.",2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|29547|3031852|213849|72294|194;2|1239|909932|1843489|31977|39948;2|1224|28211|356|212791;2|1239|909932|1843489|31977|906;2|544448|31969|2085|2092|2093;2|976|200643|171549|2005523|346096;2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|508458|649775|649776|649777|2753|290252,Complete,Claregrieve1
bsdb:678/1/2,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 1,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Cigarette Smokers,People consuming tobacco in the form of cigarettes (CS),225,33,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,increased,NA,increased,Signature 2,Table 2,17 March 2023,Adi13,Adi13,"Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|976|200643|171549|171551|836;2|976|117743|200644|49546|1016;2|1239|91061|1385|539738|1378;2|1239|91061|186826|81852|2737;2|1239|186801|3082720|186804|1257;2|32066|203490|203491|203492|848;2|32066|203490|203491|1129771|32067;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|538;2|1224|28216|206351|481|482;2|1224|1236|135615|868|2717;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:678/2/1,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 2,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Dokha Smokers,People consuming tobacco in the form of dokha (DS),225,16,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:678/2/2,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 2,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Dokha Smokers,People consuming tobacco in the form of dokha (DS),225,16,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|1224|28216|80840|119060|47670;2|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:678/3/2,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 3,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Shisha Smokers,People consuming tobacco in the form of shisha (SS),225,15,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"k__Bacteria|p__Candidatus Gracilibacteria|s__Candidatus Gracilibacteria bacterium GN02-872,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Candidatus Absconditabacteria|s__candidate division SR1 bacterium",2|363464|1912928;2|1117;2|221235|2044938,Complete,Claregrieve1
bsdb:678/4/1,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 4,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Mutiple Smokers,"People consuming tobacco in multiple forms out of cigarettes (CS), dokha (DS) and shisha (SS)",225,41,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.",2|29547|3031852|213849|72294|194;2|1224|28211|356|212791;2|544448|31969|2085|2092|2093;2|976|200643|171549|2005523|346096;2|203691|203692|136|2845253|157;2|508458|649775|649776|649777|2753|290252,Complete,Claregrieve1
bsdb:678/4/2,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 4,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Mutiple Smokers,"People consuming tobacco in multiple forms out of cigarettes (CS), dokha (DS) and shisha (SS)",225,41,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus",2|1224|1236|135625|712|713;2|1224|28216|206351|481|538;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1239|91061|186826|81852|2737,Complete,Claregrieve1
bsdb:678/5/1,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 5,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Cotinine measurement,EFO:0007813,Cotinine negative,Cotinine positive,Subjects with positive cotinine result,225,22,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S4,5 December 2023,ChiomaBlessing,ChiomaBlessing,Differentially abundant taxa at all taxonomical levels in the contrasts between cotinine positive versus cotinine negative.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Candidatus Gracilibacteria|s__Candidatus Gracilibacteria bacterium GN02-872,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Candidatus Absconditabacteria|s__candidate division SR1 bacterium",2|1224|1236|135625|712|416916;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|1224|28216|206351|481|538;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|201174|1760|85006|1268|32207;2|976|117743|200644|2762318;2|1117;2|363464|1912928;2|1224;2|221235|2044938,Complete,ChiomaBlessing
bsdb:678/5/2,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 5,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Cotinine measurement,EFO:0007813,Cotinine negative,Cotinine positive,Subjects with positive cotinine result,225,22,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S4,5 December 2023,ChiomaBlessing,ChiomaBlessing,Differentially abundant taxa at all taxonomical levels in the contrasts between cotinine positive versus cotinine negative.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia",2|201174|1760|85004|31953|1678;2|29547|3031852|213849|72294|194;2|200940|3031451|3024411|213121|893;2|1239|186801|3082720|3118655|44259;2|1239|909932|1843489|31977|906;2|544448|31969|2085|2092|2093;2|976|200643|171549|2005523|346096;2|203691|203692|136|2845253|157;2|508458|649775|649776|649777|2753|290252;2|976|200643|171549|171552|577309;2|203691|203692,Complete,ChiomaBlessing
bsdb:678/6/NA,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 6,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,"People consuming tobacco (in any form; cigarettes, dokha, shisha)",225,105,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:678/7/NA,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 7,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Dokha,CIigarettes,People consuming tobacco in the form of cigarettes (CS),16,33,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:678/8/1,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 8,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Shisha,CIigarettes,People consuming tobacco in the form of cigarettes (CS),15,33,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S3,11 December 2023,ChiomaBlessing,ChiomaBlessing,Differentially abundant taxa at all taxonomical levels between Cigarettes and Shisha,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",2|1224|1236|135625|712|713;2|1239|186801|3085636|186803|830;2|976|117743|200644|49546|1016;2|1224|28216|80840|80864;2|32066|203490;2|1239|91061|1385|539738;2|976|117743|200644|2762318,Complete,ChiomaBlessing
bsdb:678/8/2,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 8,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Shisha,CIigarettes,People consuming tobacco in the form of cigarettes (CS),15,33,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S3,11 December 2023,ChiomaBlessing,ChiomaBlessing,Differentially abundant taxa at all taxonomical levels between Cigarettes and Shisha,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",2|976|200643|171549|2005523|346096;2|203691|203692|136|2845253|157;2|508458|649775|649776|649777|2753|290252;2|544448|31969|2085|2092|2093,Complete,ChiomaBlessing
bsdb:678/9/1,Study 678,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y, Inman CK, Peters BA, Ali R, Wareth LA, Abdulle A, Alsafar H, Anouti FA, Dhaheri AA, Galani D, Haji M, Hamiz AA, Hosani AA, Houqani MA, Junaibi AA, Kazim M, Kirchhoff T, Mahmeed WA, Maskari FA, Alnaeemi A, Oumeziane N, Ramasamy R, Schmidt AM, Weitzman M, Zaabi EA, Sherman S, Hayes RB , Ahn J",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 9,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Shisha,Dokha,People consuming tobacco in the form of Dokha,15,16,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S3,11 December 2023,ChiomaBlessing,ChiomaBlessing,Differentially abundant taxa at all taxonomical levels between Dokha and Shisha,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae",2|1224|1236|135625|712|713;2|976|117743|200644|2762318;2|1239|91061|1385|539738,Complete,ChiomaBlessing
bsdb:679/1/1,Study 679,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ , Gajewski TF",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,NA,26,16,NA,16S,4,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, text",28 July 2022,Sharmilac,"Sharmilac,Fatima",Relative abundance of differentially abundant taxa in responders versus nonresponders;,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,Fatima
bsdb:679/2/1,Study 679,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ , Gajewski TF",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,NA,26,16,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"text, Figure 2",24 August 2022,Fatima,Fatima,Quantitative PCR score representing aggregate data for the relative abundances of 10 species,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",2|976|200643|171549|2005525|375288;2|1239|91061|186826|81852|1350|1352;2|201174|84998|84999|84107|102106|74426;2|201174|1760|85004|31953|1678|1680;2|1224|1236|91347|543|570|573;2|1239|909932|1843489|31977|29465|29466;2|976|200643|171549|2005525|375288|46503;2|1239|91061|186826|33958|1578|1591;2|201174|1760|85004|31953|1678|216816,Complete,Fatima
bsdb:679/2/2,Study 679,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ , Gajewski TF",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,NA,26,16,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"text, Figure 2",24 August 2022,Fatima,Fatima,Quantitative PCR score representing aggregate data for the relative abundances of 10 species,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|841|166486,Complete,Fatima
bsdb:679/3/1,Study 679,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ , Gajewski TF",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Non-responders, group B","Responders, group A",Mouse with 16.SIY melanoma tumor growth,3,3,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,24 August 2022,Fatima,Fatima,Relative abundance in mouse groups A and b of key species validated for quantitative PCR,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",2|201174|84998|84999|84107|102106|74426;2|201174|1760|85004|31953|1678|216816;2|1239|91061|186826|33958|1578|1591;2|1224|1236|91347|543|570|573;2|976|200643|171549|2005525|375288|46503,Complete,Fatima
bsdb:679/3/2,Study 679,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ , Gajewski TF",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Non-responders, group B","Responders, group A",Mouse with 16.SIY melanoma tumor growth,3,3,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,24 August 2022,Fatima,Fatima,Relative abundance in mouse groups A an B of key species validated for quantitative PCR scoring.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,2|1239|186801|3085636|186803|841|166486,Complete,Fatima
bsdb:680/1/1,Study 680,prospective cohort,32733788,10.3389/fonc.2020.00902,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358584/,"Guan X, Ma F, Sun X, Li C, Li L, Liang F, Li S, Yi Z, Liu B , Xu B",Gut Microbiota Profiling in Patients With HER2-Negative Metastatic Breast Cancer Receiving Metronomic Chemotherapy of Capecitabine Compared to Those Under Conventional Dosage,Frontiers in oncology,2020,"breast cancer, capecitabine, gut microbiota, maintenance chemotherapy, metronomic chemotherapy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,non-responders (patients treated with conventional dose),responders (patients treated with metronomic dose of capecitabine),Patients with HER2-negative metastatic breast cancer who receive metronomic capecitabine as maintenance treatment.,16,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2B, text",29 August 2022,Sharmilac,"Sharmilac,Merit","Comparison of the distribution of gut microbiota between the metronomic group and the routine group at different levels. 
(B) Distribution of the gut microbiota composition in the metronomic group and the routine group at the genus level.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|1926307;2|1239|909932|1843489;2|1239|909932|909929|1843491|158846|2049033;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Fatima
bsdb:680/1/2,Study 680,prospective cohort,32733788,10.3389/fonc.2020.00902,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358584/,"Guan X, Ma F, Sun X, Li C, Li L, Liang F, Li S, Yi Z, Liu B , Xu B",Gut Microbiota Profiling in Patients With HER2-Negative Metastatic Breast Cancer Receiving Metronomic Chemotherapy of Capecitabine Compared to Those Under Conventional Dosage,Frontiers in oncology,2020,"breast cancer, capecitabine, gut microbiota, maintenance chemotherapy, metronomic chemotherapy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,non-responders (patients treated with conventional dose),responders (patients treated with metronomic dose of capecitabine),Patients with HER2-negative metastatic breast cancer who receive metronomic capecitabine as maintenance treatment.,16,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2B, text",30 August 2022,Sharmilac,"Sharmilac,Merit",Comparison of the distribution of gut microbiota between the metronomic group and the routine group at different levels.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Cyanobacteriota,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.",2|1239|186801|3085636|186803|572511;2|1117;2759|33090|35493;2|1239|186801|3085636|186803|572511|1955243,Complete,Fatima
bsdb:681/1/1,Study 681,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS , Ram JL",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Healthy Controls(HC),Colorectal cancer,colorectal cancer; 24% of the colorectal cancer cases were current smokers. 16% habitual alcohol drinkers,122,68,None specified,16S,34,Illumina,"Zero-Inflated Beta Regression,Negative Binomial Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,4 April 2023,Aiyshaaaa,Aiyshaaaa,"The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative
bacterial count at each taxonomic level based on negative binomial models",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota",2|201174|1760|2037;2|201174;2|1239|91061;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239,Complete,Lwaldron
bsdb:681/1/2,Study 681,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS , Ram JL",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Healthy Controls(HC),Colorectal cancer,colorectal cancer; 24% of the colorectal cancer cases were current smokers. 16% habitual alcohol drinkers,122,68,None specified,16S,34,Illumina,"Zero-Inflated Beta Regression,Negative Binomial Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,4 April 2023,Aiyshaaaa,Aiyshaaaa,"The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative
bacterial count at each taxonomic level based on negative binomial models",decreased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|1224;2|976|200643;2|32066|203490,Complete,Lwaldron
bsdb:681/3/1,Study 681,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS , Ram JL",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Young,Old (≥ 65 yrs),“Advanced age” was defined as 65 years or older.,103,87,None specified,16S,34,Illumina,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,29 July 2022,Jeshudy,"Jeshudy,Aiyshaaaa","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171551|836|837;2|1239|91061|186826|1300|1301|1302;2|1239;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:681/3/2,Study 681,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS , Ram JL",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Young,Old (≥ 65 yrs),“Advanced age” was defined as 65 years or older.,103,87,None specified,16S,34,Illumina,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,4 April 2023,Aiyshaaaa,Aiyshaaaa,"The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative
bacterial count at each taxonomic level based on negative binomial models",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|976|200643;2|976|200643|171549;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|201174|1760|2037;2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|201174;2|1224;2|32066|203490,Complete,Lwaldron
bsdb:681/4/1,Study 681,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS , Ram JL",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Non Smokers,Current Smokers,"Current smokers, where defined as ever smokers who smoked at least one cigarette per day for six months or longer and were smoking within 2 year prior to interview.",138,52,None specified,16S,34,Illumina,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,29 July 2022,Jeshudy,"Jeshudy,Aiyshaaaa","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota",2|1239;2|1239|186801;2|1239|186801|186802|1898207;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39777;2|976|200643;2|201174,Complete,Lwaldron
bsdb:681/4/2,Study 681,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS , Ram JL",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Non Smokers,Current Smokers,"Current smokers, where defined as ever smokers who smoked at least one cigarette per day for six months or longer and were smoking within 2 year prior to interview.",138,52,None specified,16S,34,Illumina,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,29 July 2022,Jeshudy,"Jeshudy,Aiyshaaaa","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models",decreased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|1224;2|1224|28216;2|1224|28216|206351;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|488;2|32066|203490,Complete,Lwaldron
bsdb:682/1/1,Study 682,case-control,31674052,10.1111/jgh.14910,NA,"Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J , Hou X",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,duodenal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria with SIBO,43,34,3 months; also includes probiotics and proton-pump inhibitors,16S,123,Roche454,LEfSe,0.05,NA,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Figure S3,30 July 2022,Jeshudy,Jeshudy,Enriched genera in duodenal mucosa obtained from LEfSe.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae|g__Nevskia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|201174|1760|85006|1268|1663;2|1239|91061|186826|186828|2747;2|1239|91061|186826|33958|1243;2|1224|28211|356|41294|374;2|1224|1236|1775403|568386|64001;2|1239|91061|186826|1300|1357;2|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:682/1/2,Study 682,case-control,31674052,10.1111/jgh.14910,NA,"Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J , Hou X",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,duodenal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria with SIBO,43,34,3 months; also includes probiotics and proton-pump inhibitors,16S,123,Roche454,LEfSe,0.05,NA,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,Figure S3B,30 July 2022,Jeshudy,"Jeshudy,Folakunmi",Enriched genera in duodenal mucosa obtained from LEfSe.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces purpurascens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|1224|28216|80840|506|222;2|1224|28211|356|82115|357;2|201174|1760|85006|85019|1696;2|1224|28211|204458|76892|41275;2|201174|1760|85006|85023|33882;2|201174|1760|85006|1268|1269;2|1224|28211|356|118882|528;2|1239|91061|1385|186822|44249;2|201174|1760|85009|31957|1743;2|1224|28211|356|82115|379;2|976|117747|200666|84566|28453;2|1224|28211|204457|41297|165695;2|201174|1760|85011|2062|1883|1924;2|201174|1760|85007|1653|1716,Complete,Folakunmi
bsdb:682/3/1,Study 682,case-control,31674052,10.1111/jgh.14910,NA,"Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J , Hou X",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,rectal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO,43,34,3 months; also includes probiotics and proton-pump inhibitors,16S,123,Roche454,LEfSe,0.05,NA,2,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,Signature 1,figure 3B,8 February 2024,Folakunmi,Folakunmi,Differentially abundant taxa in rectal mucosa between SIBO- IBS-D patients and  SIBO+ IBS-D patients.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus",2|1239|909932|909929|1843491|82373;2|1239|91061|186826|186828|2747;2|1239|91061|186826|81852|1350;2|201174|1760|1643682|85030|88138;2|1239|91061|1385|186817|129337;2|201174|1760|85004|31953|1678;2|201174|1760|85009|31957|1743;2|1239|1737404|1737405|1570339|31983,Complete,Folakunmi
bsdb:682/3/2,Study 682,case-control,31674052,10.1111/jgh.14910,NA,"Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J , Hou X",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,rectal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO,43,34,3 months; also includes probiotics and proton-pump inhibitors,16S,123,Roche454,LEfSe,0.05,NA,2,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,Signature 2,figure 3B,8 February 2024,Folakunmi,Folakunmi,Differentially abundant taxa in rectal mucosa between SIBO- IBS-D patients and SIBO+ IBS-D patients.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|572511;2|1239|91061|1385|90964|1279;2|201174|1760|85006|85021|53457;2|1224|1236|91347|543|544;2|976|200643|171549|1853231|283168;2|1224|28211|356|119045|407;2|1297|188787|118964|183710|1298;2|1224|28211|356|82115|357;2|976|117747|200666|84566|28453,Complete,Folakunmi
bsdb:682/4/1,Study 682,case-control,31674052,10.1111/jgh.14910,NA,"Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J , Hou X",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 4,China,Homo sapiens,Duodenum,UBERON:0002114,Small intestine enteropathy,EFO:0009705,HC.sibo-,HC.sibo+,duodenal fluid samples of healthy controls (with no IBS) with SIBO,12,7,3 months; also includes probiotics and proton-pump inhibitors,16S,123,Roche454,Chi-Square,0.05,NA,NA,NA,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,Signature 1,Table S1,30 July 2022,Jeshudy,Jeshudy,Comparisons of microbial composition at the phylum level between SIBO+ and SIBO- IBS-D patients and healthy individuals.,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,Folakunmi
bsdb:682/5/1,Study 682,case-control,31674052,10.1111/jgh.14910,NA,"Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J , Hou X",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,Feces samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO,43,34,3 months; also includes probiotics and proton-pump inhibitors,16S,123,Roche454,Chi-Square,0.05,NA,NA,NA,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,Signature 1,Table S1,30 July 2022,Jeshudy,Jeshudy,Comparisons of microbial composition at the phylum level between SIBO+ and SIBO- IBS-D patients and healthy individuals.,increased,k__Bacteria|p__Bacillota,2|1239,Complete,Folakunmi
bsdb:683/1/1,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 1,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
PRIOR to polypectomy.",32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,2,NA,2,"age,body mass index,smoking behavior",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,31 July 2022,Jeshudy,Jeshudy,Distribution of selected taxa for adenomas versus controls at baseline,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|135858;2|1224|28216|80840|995019|40544,Complete,Atrayees
bsdb:683/1/2,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 1,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
PRIOR to polypectomy.",32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,2,NA,2,"age,body mass index,smoking behavior",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2,31 July 2022,Jeshudy,Jeshudy,Distribution of selected taxa for adenomas versus controls at baseline,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|1573534;2|1798710|1906119,Complete,Atrayees
bsdb:683/2/NA,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 2,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].",19,19,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,0.05,NA,2,"age,body mass index,smoking status",NA,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:683/3/1,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 3,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
POST polypectomy.",32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,31 July 2022,Jeshudy,Jeshudy,Distribution of selected taxa for adenomas versus controls at follow-up.,decreased,"k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1798710|1906119;2|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:683/3/2,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 3,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
POST polypectomy.",32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2,31 July 2022,Jeshudy,Jeshudy,Distribution of selected taxa for adenomas versus controls at follow-up.,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,2|1224|28216|80840|995019|40544,Complete,Atrayees
bsdb:683/4/1,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 4,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,adenoma group pre-polypectomy,adenoma group post-polypectomy,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].",32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,31 July 2022,Jeshudy,Jeshudy,Distribution of selected taxa for baseline versus follow-up.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|2569097|39488;2|544448|1912503;2|1224|1236|91347|543;2|74201|414999|415001|415002;2|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:683/4/2,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 4,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,adenoma group pre-polypectomy,adenoma group post-polypectomy,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].",32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,31 July 2022,Jeshudy,Jeshudy,Distribution of selected taxa for adenomas at baseline and follow-up.,increased,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,2|1798710|1906119,Complete,Atrayees
bsdb:683/5/1,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 5,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,control group pre-endoscopy,control group post-endoscopy,Patients with a successful endoscopy.,32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, 3",31 July 2022,Jeshudy,"Jeshudy,Atrayees",Distribution of selected taxa for baseline versus follow-up,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",2|1239|186801|3085636|186803|2569097|39488;2|200940|3031449|213115|194924|872;2|1239|909932|1843489|31977|39948;2|1239|91061|186826|1300|1301;2|256845|1313211|278082|255528|172900;2|544448|1912503;2|74201|414999|415001|415002;2|1239|186801|186802|31979|1485;2|1798710|1906119,Complete,Atrayees
bsdb:683/5/2,Study 683,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG , de Boer NK",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 5,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,control group pre-endoscopy,control group post-endoscopy,Patients with a successful endoscopy.,32,32,3 months prior to study inclusion and 3 months prior to second sample,16S,4,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,31 July 2022,Jeshudy,Jeshudy,Distribution of selected taxa for baseline versus follow-up,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:684/1/3,Study 684,"cross-sectional observational, not case-control",31719139,https://doi.org/10.1128/msystems.00438-19,https://pubmed.ncbi.nlm.nih.gov/31719139/,"Gupta A, Dhakan DB, Maji A, Saxena R, P K VP, Mahajan S, Pulikkan J, Kurian J, Gomez AM, Scaria J, Amato KR, Sharma AK , Sharma VK","Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India",mSystems,2019,"Flavonifractor plautii, biomarkers, colorectal cancer, gut microbiome",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy control,Colorectal cancer patients,Indians who are colorectial cancer patients,30,30,Recent use of antibiotics.,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 3,"Text, Figure 2, Table S3",27 March 2023,Atrayees,"Atrayees,Claregrieve1",Species observed to be significantly associated with CRC or healthy samples.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|28111;2|29547|3031852|213849|72294|194|76517;2|1224|1236|91347|543|544|545;2|1239|91061|186826|81852|1350|1353;2|1239|91061|1385|539738|1378|29391;2|1224|1236|91347|543|570|571;2|1239|91061|186826|33958|2742598|1633;2157|28890|183925|2158|2159|2172|2173;2|976|200643|171549|1853231|283168|28118;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28125;2|1239|186801|3085636|186803|841|360807;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1305;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|946234|292800;2|976|200643|171549|2005525|375288|823;2|1239|1737404|1737405|1570339|543311|33033;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|3082720|186804|1257|341694,Complete,Claregrieve1
bsdb:684/1/4,Study 684,"cross-sectional observational, not case-control",31719139,https://doi.org/10.1128/msystems.00438-19,https://pubmed.ncbi.nlm.nih.gov/31719139/,"Gupta A, Dhakan DB, Maji A, Saxena R, P K VP, Mahajan S, Pulikkan J, Kurian J, Gomez AM, Scaria J, Amato KR, Sharma AK , Sharma VK","Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India",mSystems,2019,"Flavonifractor plautii, biomarkers, colorectal cancer, gut microbiome",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy control,Colorectal cancer patients,Indians who are colorectial cancer patients,30,30,Recent use of antibiotics.,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 4,"Text, Figure 2, Table S3",27 March 2023,Atrayees,"Atrayees,Claregrieve1",Species observed to be significantly associated with CRC or healthy samples,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|909932|1843488|909930|904|905;2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|2569097|39488;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|820;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1689;2|1239|186801|3085636|186803|3342669|45851;2|1224|28216|80840|80864|283|285;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330|88431;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|186806|1730|39496;2|32066|203490|203491|203492|848|856;2|1224|1236|135625|712|724|249188;2|1239|91061|186826|33958|1578|1604;2|1239|909932|909929|1843491|52225|52226;2|976|200643|171549|171552|2974251|165179;2|1239|186801|3085636|186803|841|166486;2|1239|91061|186826|1300|1301|68892;2|203691|203692|136|2845253|157|167;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|216851|853;2|1239|91061|186826|33958|2767887|1623;2|1239|909932|1843489|31977|906|907;2|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:685/1/1,Study 685,case-control,33050883,10.1186/s12866-020-01938-w,NA,"Zhang Q, Zhao H, Wu D, Cao D , Ma W",A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer,BMC microbiology,2020,"Colorectal cancer, Gene expression, Gut microflora, Pathways enrichment, Survival analysis",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Control,CRC,Tumor specimens taken from patients with colorectal cancer,19,19,None specified,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text,1 August 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRC and control samples,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|201174;2|32066;2|32066|203490|203491|203492|848;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511,Complete,Claregrieve1
bsdb:685/1/2,Study 685,case-control,33050883,10.1186/s12866-020-01938-w,NA,"Zhang Q, Zhao H, Wu D, Cao D , Ma W",A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer,BMC microbiology,2020,"Colorectal cancer, Gene expression, Gut microflora, Pathways enrichment, Survival analysis",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Control,CRC,Tumor specimens taken from patients with colorectal cancer,19,19,None specified,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Text,1 August 2022,Jeshudy,"Jeshudy,Claregrieve1",Differential microbial abundance between CRC and control samples,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|1239;2|1224,Complete,Claregrieve1
bsdb:686/1/1,Study 686,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A , Cordero F",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC),Patients diagnosed with colorectal carcinoma,24,29,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,ChiomaBlessing,Differences in fecal microbiome among healthy and carcinoma (CRC) patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",2|976|200643|171549|815|816|329854;2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|186802|216572|292632;2|201174|1760|85004|31953|1678|216816,Complete,ChiomaBlessing
bsdb:686/1/2,Study 686,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A , Cordero F",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC),Patients diagnosed with colorectal carcinoma,24,29,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,ChiomaBlessing,Differences in fecal microbiome among healthy and carcinoma (CRC) patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|1224|1236|91347|1903414|581|582;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|561|562;2|976|200643|171549|171552|2974265|363265;2|1239|186801|3085636|186803|1506553|1512,Complete,ChiomaBlessing
bsdb:686/2/1,Study 686,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A , Cordero F",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Adenomas,Patients diagnosed with colorectal adenomas,24,27,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S1B,1 August 2022,Jeshudy,"Jeshudy,ChiomaBlessing",Differences in fecal microbiome among healthy and adenoma patients,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|186803|28050|39485,Complete,ChiomaBlessing
bsdb:686/3/1,Study 686,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A , Cordero F",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma (CRC),Patients diagnosed with colorectal carcinoma,27,29,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,ChiomaBlessing,Differences in fecal microbiome among adenoma and carcinoma (CRC) patients,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,2|976|200643|171549|1853231|283168|28118,Complete,ChiomaBlessing
bsdb:686/3/2,Study 686,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A , Cordero F",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma (CRC),Patients diagnosed with colorectal carcinoma,27,29,None specified,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,ChiomaBlessing,Differences in fecal microbiome among adenoma and carcinoma (CRC) patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",2|201174|1760|85004|31953|1678|1686;2|201174|84998|84999|84107|102106|74426,Complete,ChiomaBlessing
bsdb:687/1/1,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,healthy controls,colorectal cancer patients,diagnosed of colorectal cancer by colonoscopy and histopathology,20,44,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figures 4b,29 August 2022,Mary Bearkland,Mary Bearkland,"Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed
from features differentially abundant in CRC and HC fecal samples.
The criteria for feature selection were LDA score > 4, p < 0.05,
Green and red represent the HC group and CRC group, respectively.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|620;2|1224|1236|91347|543|561,Complete,Fatima
bsdb:687/1/2,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,healthy controls,colorectal cancer patients,diagnosed of colorectal cancer by colonoscopy and histopathology,20,44,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figures 4b,29 August 2022,Mary Bearkland,"Mary Bearkland,Fatima","Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed
from features differentially abundant in CRC and HC fecal samples.
The criteria for feature selection were LDA score > 4, p < 0.05,
Green and red represent the HC group and CRC group, respectively.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",2|201174|84998|84999|84107|102106;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|186804|1501226;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1766253,Complete,Fatima
bsdb:687/2/1,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without KRAS mutation,colorectal cancer patients with KRAS mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,21,18,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5a,31 August 2022,Mary Bearkland,"Mary Bearkland,Fatima,Merit",LEfSe was used to compare the microbial variation of the KRAS,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. 11SE38,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter|s__uncultured Gracilibacter sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.",2|1239|909932|1843488|909930;2|976|200643|171549|171550|239759|1872444;2|1239|186801|3085636|186803|2569097|39488;2|1239;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|3082771|1738645;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|186802|216572|216851;2|1239|186801|186802|541019|342658;2|1239|186801|186802|216572|1892380;2|1239|186801|186802|216572|1892380|1849041;2|1239|526524|526525|128827|61170|61171;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|1506553|1926283;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|1224|28211|204457|41297|165696;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|583272;2|1224|28211|204457|41297;2|1224|28211|204457;2|1239|186801|3085636|186803|2569097;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|3082771|1738645;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|909932|909929|1843491|158846;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186806|1730|165185;2|1239|186801|186802|541019|342658|517604;2|976|200643|171549|171552|838|159272,Complete,Fatima
bsdb:687/2/2,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without KRAS mutation,colorectal cancer patients with KRAS mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,21,18,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5a,31 August 2022,Mary Bearkland,"Mary Bearkland,Fatima",LEfSe was used to compare the microbial variation of the KRAS,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. T17/4F,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense",2|201174;2;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1689;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|33958|1578|765944;2|201174|1760|85004|31953|1678|165187;2|201174|1760|85004|31953|1678|1686|630129,Complete,Fatima
bsdb:687/3/1,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without TP53 mutation,colorectal cancer patients with TP53 mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,11,28,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5b,2 September 2022,Mary Bearkland,Mary Bearkland,LEfSe was used to compare the microbial variation of the TP53,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,2|1239|186801|186802|186806|1730|290054,Complete,Atrayees
bsdb:687/3/2,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without TP53 mutation,colorectal cancer patients with TP53 mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,11,28,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5b,2 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees",LEfSe was used to compare the microbial variation of the TP53,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|186802|216572;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:687/4/1,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without APC mutation,colorectal cancer patients with APC mutation,diagnosed with colorectal cancer by colonoscopy and histopathology,9,30,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5c,3 September 2022,Mary Bearkland,Mary Bearkland,LEfSe was used to compare the microbial variation of the  APC groups.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037,Complete,Atrayees
bsdb:687/5/1,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without PIK3CA mutation,colorectal cancer patients with PIK3CA mutation,diagnosed with colorectal cancer by colonoscopy and histopathology,33,6,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d,3 September 2022,Mary Bearkland,Mary Bearkland,LEfSe was used to compare the microbial variation of the PIK3CA groups.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174|1760|2037;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654,Complete,Atrayees
bsdb:687/5/2,Study 687,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S , Yu Z",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without PIK3CA mutation,colorectal cancer patients with PIK3CA mutation,diagnosed with colorectal cancer by colonoscopy and histopathology,33,6,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5d,3 September 2022,Mary Bearkland,"Mary Bearkland,Fatima",LEfSe was used to compare the microbial variation of the PIK3CA groups.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. LNB2,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. enrichment culture clone HSL70,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__uncultured Selenomonas sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|976|200643|171549|171550|239759;2|201174|1760|85004|31953|1678|1686;2|200940|3031449|213115|194924|872|281992;2|1224|1236|91347|543|547|887631;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|437755|371674;2|1239|909932;2|1224|28216|80840|119060|48736;2|1239|909932|909929;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|906;2|1224|28216|80840|119060|48736;2|1239|909932|909929|1843491|970|159275;2|1239|91061|186826|33958,Complete,Atrayees
bsdb:688/2/1,Study 688,prospective cohort,29097493,10.1126/science.aan4236,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827966/,"Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC, Cogdill AP, Zhao L, Hudgens CW, Hutchinson DS, Manzo T, Petaccia de Macedo M, Cotechini T, Kumar T, Chen WS, Reddy SM, Szczepaniak Sloane R, Galloway-Pena J, Jiang H, Chen PL, Shpall EJ, Rezvani K, Alousi AM, Chemaly RF, Shelburne S, Vence LM, Okhuysen PC, Jensen VB, Swennes AG, McAllister F, Marcelo Riquelme Sanchez E, Zhang Y, Le Chatelier E, Zitvogel L, Pons N, Austin-Breneman JL, Haydu LE, Burton EM, Gardner JM, Sirmans E, Hu J, Lazar AJ, Tsujikawa T, Diab A, Tawbi H, Glitza IC, Hwu WJ, Patel SP, Woodman SE, Amaria RN, Davies MA, Gershenwald JE, Hwu P, Lee JE, Zhang J, Coussens LM, Cooper ZA, Futreal PA, Daniel CR, Ajami NJ, Petrosino JF, Tetzlaff MT, Sharma P, Allison JP, Jenq RR , Wargo JA",Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients were classified as R if they achieved an objective response (complete or partial response or stable disease lasting at least 6 months),35,54,NA,16S,NA,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Figure 2D,30 August 2022,Sharmilac,Sharmilac,"(D) LDA scores computed for differentially-abundant taxa in the fecal microbiomes of R
(blue) and NR (red). Length indicates effect size associated with a taxon. p=0.05 for the
Kruskal-Wallis test; LDA score > 3.",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium hungatei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239;2|1239|186801;2|1239|186801|186802|1898207;2|1239|186801|186802|216572;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263;2|976|200643|171549|171551|836|1583331;2|1239|909932|1843489|31977;2|1239|186801|186802|216572|1508657|48256;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930|33024|33025;2|1239|1737404|1737405|1570339|162289;2|201174|1760|85006|1268;2|544448|31969;2|201174|1760|85006|1268|32207,Complete,Fatima
bsdb:688/2/2,Study 688,prospective cohort,29097493,10.1126/science.aan4236,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827966/,"Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC, Cogdill AP, Zhao L, Hudgens CW, Hutchinson DS, Manzo T, Petaccia de Macedo M, Cotechini T, Kumar T, Chen WS, Reddy SM, Szczepaniak Sloane R, Galloway-Pena J, Jiang H, Chen PL, Shpall EJ, Rezvani K, Alousi AM, Chemaly RF, Shelburne S, Vence LM, Okhuysen PC, Jensen VB, Swennes AG, McAllister F, Marcelo Riquelme Sanchez E, Zhang Y, Le Chatelier E, Zitvogel L, Pons N, Austin-Breneman JL, Haydu LE, Burton EM, Gardner JM, Sirmans E, Hu J, Lazar AJ, Tsujikawa T, Diab A, Tawbi H, Glitza IC, Hwu WJ, Patel SP, Woodman SE, Amaria RN, Davies MA, Gershenwald JE, Hwu P, Lee JE, Zhang J, Coussens LM, Cooper ZA, Futreal PA, Daniel CR, Ajami NJ, Petrosino JF, Tetzlaff MT, Sharma P, Allison JP, Jenq RR , Wargo JA",Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients were classified as R if they achieved an objective response (complete or partial response or stable disease lasting at least 6 months),35,54,NA,16S,NA,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Figure 2D,30 August 2022,Sharmilac,Sharmilac,"(D) LDA scores computed for differentially-abundant taxa in the fecal microbiomes of R
(blue) and NR (red). Length indicates effect size associated with a taxon. p=0.05 for the
Kruskal-Wallis test; LDA score > 3.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio alaskensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides mediterraneensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|201174|84998|84999|84107|102106|147206;2|200940|3031449|213115|194924|2909705|58180;2|976|200643|171549|815|816|1841856;2|976|200643|171549|171552|838|470565;2|201174|1760|85004|31953|2701|2702;2|201174|1760|85004|31953|2701;2|976;2|976|200643|171549;2|976|200643,Complete,Fatima
bsdb:689/1/1,Study 689,prospective cohort,28923537,10.1016/j.neo.2017.08.004,https://pubmed.ncbi.nlm.nih.gov/28923537/,"Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP , Koh AY",Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients,"Neoplasia (New York, N.Y.)",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non responders (Progressive disease),Responders,"Twenty-four patients showed RECIST response (19, 49%) or stable (5, 13%) disease to ICT, what we classify as responders in this study",16,23,NA,WMS,NA,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",30 August 2022,Sharmilac,"Sharmilac,Aiyshaaaa","MSS identifies specific bacterial species that are enriched in the gut microbiomes of melanoma patients who are responding to ICT therapy. Relative abundance of gut bacterial taxa as determined by MetaPhlAn analysis of MSS data generated from fecal specimens collected from melanoma patients prior to receiving ipilimumab/nivolumab, pembrolizumab, ipilimumab alone, or nivolumab alone.Differential taxonomic abundance was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe) projected as a histogram (A, C and E) or cladrogram (B, D and F). All listed bacterial groups were significantly (P b .05, Kruskal-Wallis test) enriched for their respective groups (responder versus progressive).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|818;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802|216572|216851|853;2|1239|526524|526525|128827|61170|61171;2|1239|91061|186826|1300|1301|1318,Complete,Peace Sandy
bsdb:689/1/2,Study 689,prospective cohort,28923537,10.1016/j.neo.2017.08.004,https://pubmed.ncbi.nlm.nih.gov/28923537/,"Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP , Koh AY",Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients,"Neoplasia (New York, N.Y.)",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non responders (Progressive disease),Responders,"Twenty-four patients showed RECIST response (19, 49%) or stable (5, 13%) disease to ICT, what we classify as responders in this study",16,23,NA,WMS,NA,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, text",16 April 2023,Sharmilac,"Sharmilac,Peace Sandy","MSS identifies specific bacterial species that are enriched in the gut microbiomes of melanoma patients who are responding to ICT therapy. Relative abundance of gut bacterial taxa as determined by MetaPhlAn analysis of MSS data generated from fecal specimens collected from melanoma patients prior to receiving ipilimumab/nivolumab, pembrolizumab, ipilimumab alone, or nivolumab alone.Differential taxonomic abundance was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe) projected as a histogram (A, C and E) or cladrogram (B, D and F). All listed bacterial groups were significantly (P b .05, Kruskal-Wallis test) enriched for their respective groups (responder versus progressive).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc gasicomitatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc mesenteroides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|201174|1760|2037|2049|1654|1656;2|1239|1737404|1737405|1570339|165779|33037;2|976|200643|171549|815|816|28111;2|1239|91061|186826|33958|1578|1596;2|201174|84998|84999|1643824|2767353|1382;2|1239|91061|186826|33958|1243|115778;2|1239|91061|186826|33958|1243|1245;2|1239|1737404|1737405|1570339|162289;2|201174|1760|2037|2049|2529408|1660;2|201174|84998|1643822|1643826|84108|84109;2|1239|91061|186826|1300|1301|102684;2|1239|91061|186826|1300|1301|1309;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|909932|1843488|909930;2|201174|84998|84999|1643824|1380;2|201174|1760|2037;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|201174|1760|2037|2049|1654;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:690/1/1,Study 690,prospective cohort,32010563,10.21037/tlcr.2019.10.23,NA,"Katayama Y, Yamada T, Shimamoto T, Iwasaku M, Kaneko Y, Uchino J , Takayama K",The role of the gut microbiome on the efficacy of immune checkpoint inhibitors in Japanese responder patients with advanced non-small cell lung cancer,Translational lung cancer research,2019,"Immunotherapy, gut microbiome, non-small cell lung cancer (NSCLC), retrospective analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,We defined responder (R) (partial response to ICI treatment) or non-responder (NR) (stable or progressive disease after ICI treatment at the time of first clinical evaluation) according to the RECIST 1.1 evaluation.,11,6,NA,16S,12,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,2 September 2022,Sharmilac,"Sharmilac,Fatima",The differential abundant taxa in the gut microbiomes of R (green) and NR (red) was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|84036;2|1239|91061|186826|33958,Complete,Fatima
bsdb:690/1/2,Study 690,prospective cohort,32010563,10.21037/tlcr.2019.10.23,NA,"Katayama Y, Yamada T, Shimamoto T, Iwasaku M, Kaneko Y, Uchino J , Takayama K",The role of the gut microbiome on the efficacy of immune checkpoint inhibitors in Japanese responder patients with advanced non-small cell lung cancer,Translational lung cancer research,2019,"Immunotherapy, gut microbiome, non-small cell lung cancer (NSCLC), retrospective analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,We defined responder (R) (partial response to ICI treatment) or non-responder (NR) (stable or progressive disease after ICI treatment at the time of first clinical evaluation) according to the RECIST 1.1 evaluation.,11,6,NA,16S,12,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,2 September 2022,Sharmilac,"Sharmilac,Fatima",The differential abundant taxa in the gut microbiomes of R (green) and NR (red) was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe),decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|200940|3031449|213115|194924|35832;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|40544;2|1224|28211;2|1224|28216|80840|506;2|1224|28216;2|1224|28216|80840;2|976|200643|171549|171551,Complete,Fatima
bsdb:691/1/1,Study 691,prospective cohort,31990790,10.1097/CMR.0000000000000656,https://journals.lww.com/melanomaresearch/Fulltext/2020/06000/Gut_microbial_species_and_metabolic_pathways.2.aspx,"Wind TT, Gacesa R, Vich Vila A, de Haan JJ, Jalving M, Weersma RK , Hospers GAP",Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma,Melanoma research,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Melanoma patients with a confirmed response, defined as a complete response, partial response (PR) or stable disease (SD) according to RECIST 12 weeks after start of therapy that was ongoing at the next radiological evaluation, were labelled ‘responder’. In order to include late responders in our analysis, patients with progressive disease (PD) on the first radiological evaluation but a response at the second radiological evaluation compared to baseline were also labelled ‘responder’.",13,12,NA,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,1 September 2022,Sharmilac,"Sharmilac,Claregrieve1",Differentially abundant taxa in responders vs non-responders (FDR cut-off = 0.05),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171550|239759|328814;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|818;2|200940|3031449|213115|194924|872|901;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806|1730|39496;2|1224|1236|135625|712|724|729;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|3085636|186803|658082;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|815|909656|204516;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|39492;2|1239|186801|3085636|186803|2316020|33038;2|200940|3031449|213115|194924|35832;2|1224|1236;2|1224|1236|91347|543|561;2|1224|1236|91347|543;2|1239|909932|1843488|909930;2|1239|909932|1843489|31977|39948;2|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:691/1/2,Study 691,prospective cohort,31990790,10.1097/CMR.0000000000000656,https://journals.lww.com/melanomaresearch/Fulltext/2020/06000/Gut_microbial_species_and_metabolic_pathways.2.aspx,"Wind TT, Gacesa R, Vich Vila A, de Haan JJ, Jalving M, Weersma RK , Hospers GAP",Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma,Melanoma research,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Melanoma patients with a confirmed response, defined as a complete response, partial response (PR) or stable disease (SD) according to RECIST 12 weeks after start of therapy that was ongoing at the next radiological evaluation, were labelled ‘responder’. In order to include late responders in our analysis, patients with progressive disease (PD) on the first radiological evaluation but a response at the second radiological evaluation compared to baseline were also labelled ‘responder’.",13,12,NA,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,1 September 2022,Sharmilac,"Sharmilac,Claregrieve1",Differentially abundant taxa in responders vs non-responders (FDR cut-off = 0.05),decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|1288121;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|371601;2|976|200643|171549|2005519|397864|487174;2|201174|1760|85004|31953|1678|216816;2|1239|186801|3085636|186803|33042|751585;2|1239|526524|526525|128827|658657;2|1239|526524|526525|128827|457422;2|1239|186801|186802|186806|1730|39490;2|1239|526524|526525|128827|61170|61171;2|1239|186801|3085636|186803|658087;2|1239|186801|3085636|186803|665951;2|976|200643|171549|171552|577309|454154;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|2974251|165179;2|1239|186801|186802|216572|1263|40519;2|201174|1760|2037|2049|2529408|1660;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1343;2|1239|186801|3085636|186803|2316020|46228;2|201174|84998|1643822|1643826|84111;2|201174|84998|84999|1643824|133925;2|1239|186801|3082720|186804;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|1300;2|976|200643|171549|171552,Complete,Claregrieve1
bsdb:692/1/1,Study 692,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X, He Y, Li H, Yu D, Na L, Sun T, Zhang D, Shi X, Xia Y, Jiang T, Rong S, Yang S, Ma X , Xu G",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who didn't take prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (preoperative fecal sample),"Patients with radiologic and pathologic diagnosis of CRC (preoperatively). Patients in the intervention group (prebiotic group) received a daily oral dose of 30 g prebiotic supplement (Hangzhou Niuqu Biotech Co., Hainengbo, China) containing fructooligosaccharide (25%), xylooligosaccharide (25%), polydextrose (25%), and resistant dextrin (25%) for 7 d from hospitalization to the day before the operation.",20,18,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 4; Table 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between patients who took prebiotics and patients who did not,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|976|200643|171549|815|816;2|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:692/1/2,Study 692,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X, He Y, Li H, Yu D, Na L, Sun T, Zhang D, Shi X, Xia Y, Jiang T, Rong S, Yang S, Ma X , Xu G",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who didn't take prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (preoperative fecal sample),"Patients with radiologic and pathologic diagnosis of CRC (preoperatively). Patients in the intervention group (prebiotic group) received a daily oral dose of 30 g prebiotic supplement (Hangzhou Niuqu Biotech Co., Hainengbo, China) containing fructooligosaccharide (25%), xylooligosaccharide (25%), polydextrose (25%), and resistant dextrin (25%) for 7 d from hospitalization to the day before the operation.",20,18,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table 4; Table 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between patients who took prebiotics and patients who did not,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:692/2/1,Study 692,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X, He Y, Li H, Yu D, Na L, Sun T, Zhang D, Shi X, Xia Y, Jiang T, Rong S, Yang S, Ma X , Xu G",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients non-prebiotic (preoperative),colorectal cancer patients non-prebiotic (postoperative),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and did not take prebiotics pre-surgery.,20,20,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 5,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the pre- and postoperative timepoints in patients who did not take prebiotics,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:692/2/2,Study 692,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X, He Y, Li H, Yu D, Na L, Sun T, Zhang D, Shi X, Xia Y, Jiang T, Rong S, Yang S, Ma X , Xu G",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients non-prebiotic (preoperative),colorectal cancer patients non-prebiotic (postoperative),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and did not take prebiotics pre-surgery.,20,20,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 5,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the pre- and postoperative timepoints in patients who did not take prebiotics,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|1385|186817|1386;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:692/3/1,Study 692,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X, He Y, Li H, Yu D, Na L, Sun T, Zhang D, Shi X, Xia Y, Jiang T, Rong S, Yang S, Ma X , Xu G",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who took prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (postoperative fecal sample),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and took prebiotics pre-surgery.,18,18,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 5; Figure 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the pre- and postoperative timepoints in patients who took prebiotics,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|91061|1385|186817|1386;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338,Complete,Claregrieve1
bsdb:692/3/2,Study 692,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X, He Y, Li H, Yu D, Na L, Sun T, Zhang D, Shi X, Xia Y, Jiang T, Rong S, Yang S, Ma X , Xu G",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who took prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (postoperative fecal sample),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and took prebiotics pre-surgery.,18,18,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 5; Figure 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the pre- and postoperative timepoints in patients who took prebiotics,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:693/1/1,Study 693,prospective cohort,31337439,10.1186/s40425-019-0650-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651993/,"Zheng Y, Wang T, Tu X, Huang Y, Zhang H, Tan D, Jiang W, Cai S, Zhao P, Song R, Li P, Qin N , Fang W",Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma,Journal for immunotherapy of cancer,2019,"Anti-PD-1 immunotherapy, Gut microbiome, Hepatocellular carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Responders (R, n = 3) were defined by radiographic evidence as complete or partial response, or stable disease lasting for at least six months.",5,3,NA,WMS,NA,BGISEQ-500 Sequencing,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"text, Figure 2A, Figure S4",3 September 2022,Sharmilac,"Sharmilac,Fatima","Meta-analysis of the bacteria significantly enriched in R and NR. a Heatmap showing the relative abundance of R-enriched and NR-enriched bacterial species, as identified by LEfSe.
Differentially abundant genera (a) and species (b) between R and NR, identified by LEfSe.",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Liberibacter|s__Candidatus Liberibacter brunswickensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Salinibacteraceae|g__Salinibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|186802|216572|244127|169435;2|976|200643|171549|815|816|246787;2|201174|1760|85004|31953|1678|1689;2|1239|186801|3085636|186803|572511|40520;2|1224|28211|356|82115|34019|1968796;2|1239|186801|3085636|186803|33042|410072;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|3085636|186803|189330|39486;2|32066|203490|203491|203492|848|861;2|1239|186801|3085636|186803|658087;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|2742598|97478;2|1239|91061|186826|33958|2742598|1632;2|1239|91061|186826|33958|2742598|1633;2|1239|909932|1843489|31977|906|187326;2|1239|186801|186802|216572|1263|40518;2|1853220|1853222|1853224|1853225|146918;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|216572|292632;2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|1263;2|74201|203494|48461|1647988|239934;2|1239|909932|1843489|31977|39948;2|201174|1760|85004|31953|196081,Complete,Fatima
bsdb:693/1/2,Study 693,prospective cohort,31337439,10.1186/s40425-019-0650-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651993/,"Zheng Y, Wang T, Tu X, Huang Y, Zhang H, Tan D, Jiang W, Cai S, Zhao P, Song R, Li P, Qin N , Fang W",Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma,Journal for immunotherapy of cancer,2019,"Anti-PD-1 immunotherapy, Gut microbiome, Hepatocellular carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Responders (R, n = 3) were defined by radiographic evidence as complete or partial response, or stable disease lasting for at least six months.",5,3,NA,WMS,NA,BGISEQ-500 Sequencing,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"text, Figure 2A",3 September 2022,Sharmilac,"Sharmilac,Fatima,Aiyshaaaa","Meta-analysis of the bacteria significantly enriched in R and NR. a Heatmap showing the relative abundance of R-enriched and NR-enriched bacterial species, as identified by LEfSe.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio",2|1224|1236|135625|712|416916|732;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|626930;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|816|820;2|1224|28211|356|772|773;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1681;2|1224|28216|80840|506|517;2|1224|1236|91347|543|561|208962;2|32066|203490|203491|203492|848|856;2|1224|1236|135625|712|724|249188;2|1224|1236|91347|543|570|548;2|1239|91061|186826|33958|2767887|1624;2|1239|909932|1843489|31977|906|907;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|85009|31957;2|1224|1236|1706369|1706371|10,Complete,Fatima
bsdb:694/1/1,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were
orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously
into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3c,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on the Wilcoxon rank-sum test.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 012,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",2|1239|526524|526525|128827|1470349;2|1239|186801|186802|1159214;2|1239|91061|186826|33958|1578;2|1224|1236|91347|1903414|583|584;2|1239|526524|526525|128827|1522;2|1239|526524|526525|128827;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|841;2|95818|2093818|2093825|2171986|1331051,Complete,Claregrieve1
bsdb:694/1/2,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were
orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously
into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3c,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on the Wilcoxon rank-sum test.,decreased,"k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__uncultured Oscillibacter sp.",2|95818|2093818|2093825|2171986|1331051;2|1239|186801|186802|186807;2|1239|91061|1385|90964|1279|29387;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803|1506577;2|1239|186801|186802|216572|459786|876091,Complete,Claregrieve1
bsdb:694/2/1,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally lavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3d,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2),increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 012,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.",2|1239|526524|526525|128827|1470349;2|1239|186801|186802|1159214;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|91061|186826|33958|2767887|1622;2|1224|1236|91347|1903414|583;2|1224|1236|91347|1903414|583|584;2|1239|526524|526525|128827|1522;2|1239|526524|526525|128827;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|841|512314,Complete,Claregrieve1
bsdb:694/2/2,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally lavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3D,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.",2|976|200643|171549|194843;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|186802|186807;2|1239|91061|1385;2|1239|91061|1385|90964|1279;2|95818|2093818|2093825|2171986|1331051;2|95818;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803|1506577;2|1239|186801|186802|216572|459786|1945593,Complete,Claregrieve1
bsdb:694/3/1,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg) + PD-1,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4f,13 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between the GQD (300 mg/kg) + PD-1 group vs. the control group based on the Wilcoxon rank-sum test.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Mycoplasmatota|c__Mollicutes",2|976|200643|171549|171550|239759;2|976|200643|171549;2|976|200643|171549|815|816|85831;2|1239|526524|526525|128827|1470349;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803|1898203;2|1239|186801|186802|186807;2|976|200643|171549|171552;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|186806|1730|165185;2|1239|186801|186802|216572|707003;2|1239|186801|186802|186806|1730|39497;2|544448|31969,Complete,Claregrieve1
bsdb:694/3/2,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg) + PD-1,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig 4f,14 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between GQD(300mg/kg)+PD-1 group and control group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas|s__uncultured Candidatus Saccharimonas sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__uncultured Coprococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239|186801|186802|216572|244127|1872531;2|201174|1760|85004|31953|1678|28025;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|3085636|186803|841|2049040;2|1239|186801|3085636|186803;2|976|200643|171549|194843;2|95818|2093818|2093825|2171986|1331051|1983405;2|1239|186801|3085636|186803|33042|458253;2|1239|186801|186802|172733;2|1239|186801|186802|216572|1508657|1757166;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:694/4/1,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Supp fig S6D,15 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between GQD(300mg/kg) treated mice and controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|186802|186806|1730|39497;2|1239|186801|3085636|186803|1649459;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:694/4/2,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,supp fig S6,15 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance between GQD(300mg/kg) treated mice and controls,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Archaea|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|201174;2|544448|31969|186332|186333|2086;2|544448|31969|186332|186333;2|544448|31969|186332;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3082768|990719;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|201174|84998|84999;2|28221;2|200940|3031449|213115|194924|872;2|200940|3031449|213115;2157|28889|183924|114380|2272;2|201174|84998|1643822|1643826|580024;2|1239|186801|3085636|186803|1506577;2|1239|186801|186802|543314|35517;2|976|200643|171549;2|1239|186801|3082768|990719;2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:694/5/1,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,9,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,supp fig S6,17 September 2022,Mary Bearkland,Mary Bearkland,Supplementary Figure S6:  (E) LDA scores computed for differentially abundant taxa in the faecal microbiomes of mice from each group.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota",2|201174|84998|1643822|1643826|447020;2|544448|31969|186332|186333|2086;2|544448|31969|186332|186333;2|544448|31969|186332;2|1239|526524|526525|2810280|1505663;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|1649459;2|544448|31969;2|544448,Complete,Claregrieve1
bsdb:694/5/2,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,9,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,supp fig S6,17 September 2022,Mary Bearkland,Mary Bearkland,Supplementary Figure S6:  (E) LDA scores computed for differentially abundant taxa in the faecal microbiomes of mice from each group.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota",2|1239|186801|186802|216572|459786;2|1239,Complete,Claregrieve1
bsdb:694/6/1,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low dose 300 mg/kg GQD + PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig S6,17 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differentially abundant taxa between control mice and mice treated with 300mg/kg GQD + PD-1,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|171550|239759;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|526524|526525|128827|1470349;2|976|200643|171549|171552;2|976|200643|171549|171550;2|1239|186801|186802|216572|1508657;2|976|200643|171549|171552;2|1239|186801|186802|541000,Complete,Claregrieve1
bsdb:694/6/2,Study 694,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J, Jia Y, Li J, Kuai W, Li Y, Guo F, Xu X, Zhao Z, Lv J , Li Z",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low dose 300 mg/kg GQD + PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supp fig S6,17 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differentially abundant taxa between control mice and mice treated with 300mg/kg GQD + PD-1,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Candidatus Saccharibacteria",2|1239|186801|186802|216572|244127;2|976|200643|171549;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|95818,Complete,Claregrieve1
bsdb:695/1/1,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,13,14,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees",Supplementary Figure 1.Compositional differences in the gut microbiome are associated with responses to PD-1 antibody immunotherapy  (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|815|816;2|1239|186801|186802|216572|1508657;2|976|200643|171549|2005525|375288;2|1239|526524|526525|128827,Complete,Atrayees
bsdb:695/1/2,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,13,14,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees",Supplementary Figure 1.Compositional differences in the gut microbiome are associated with responses to PD-1 antibody immunotherapy  (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803;2|976|200643|171549;2|1224|28216|80840|995019|577310;2|1239|186801|186802,Complete,Atrayees
bsdb:695/2/1,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",13,14,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees",Supplementary Figure 1(B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543|1940338;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1224|1236|91347|543;2|1239|91061|186826;2|1239|186801|186802,Complete,Atrayees
bsdb:695/2/2,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",13,14,NA,16S,4,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees",Supplementary Figure 1(B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803;2|976|200643|171549;2|1239|526524|526525|128827,Complete,Atrayees
bsdb:695/3/1,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Coli,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",14,14,NA,16S,4,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,supp fig 1B,18 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees",Supplementary Figure 1 (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543|1940338;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1224|1236|91347|543;2|1239|186801|186802|216572|1508657,Complete,Atrayees
bsdb:695/3/2,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Coli,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",14,14,NA,16S,4,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,supp fig 1B,18 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees",Supplementary Figure 1 (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|815|816;2|1239|526524|526525|128827;2|1239|186801|186802|216572|1508657;2|200940|3031449|213115|194924|872;2|976|200643|171549;2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:695/4/1,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 2,18 September 2022,Mary Bearkland,Mary Bearkland,Bar plot of compositional differences at species level in the Control vs. Coli,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,s__uncultured prokaryote",2|976|200643|171549|815|2212467;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|371601;2|976|200643|171549|2005525|375288|1869337;2|976|200643|171549;198431,Complete,Atrayees
bsdb:695/4/2,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 2,18 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees",Bar plot of compositional differences at species level in the Control vs. Coli,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides oleiciplenus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:530,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:633,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:462",2|976|200643|171549|815|816|626931;2|976|200643|171549|815|816|1262741;2|976|200643|171549|815|816|1262744;2|976|200643|171549|2005525|375288|328812;2|976|200643|171549|815|909656|204516;2|976|200643|171549|815|909656|671267;2|77133;2|976|200643|171549|815|816|1262740,Complete,Atrayees
bsdb:695/5/1,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 2,20 September 2022,Mary Bearkland,Mary Bearkland,Bar plot of compositional differences at species level in the Control vs. Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 2_1_33B,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter rarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|74201|203494|48461|1647988|239934|239935;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|469589;2|976|200643|171549|815|816|820;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171552|558436|1676614;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288,Complete,Atrayees
bsdb:695/5/2,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 2,21 September 2022,Mary Bearkland,Mary Bearkland,Bar plot of compositional differences at species level in the  Control vs. Vanc group of mice before PD-1 antibody treatment by one-way ANOVA.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:927,k__Bacteria|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873",2|976|200643|171549|815|816|1262753;2|1239|1378168;2|1239|186801|3085636|186803|397291;2|976|200643|171549|815|909656|204516;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|1262936,Complete,Atrayees
bsdb:695/6/1,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,coli,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,7,7,NA,WMS,NA,Illumina,ANOVA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 2,21 September 2022,Mary Bearkland,Mary Bearkland,Bar plot of compositional differences at species level in the  Vanc vs.Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis",2|976|200643|171549|171552|838|1262927;2|976|200643|171549|2005525|375288|823;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549;2|976|200643|171549|815|816|820;2|976|200643|171549|2005525|375288;2|74201|203494|48461|1647988|239934|239935;2|1224|28216|80840|995019|577310|487175,Complete,Atrayees
bsdb:695/6/2,Study 695,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X, Lv J, Guo F, Li J, Jia Y, Jiang D, Wang N, Zhang C, Kong L, Liu Y, Zhang Y, Lv J , Li Z",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,coli,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,7,7,NA,WMS,NA,Illumina,ANOVA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 2,21 September 2022,Mary Bearkland,Mary Bearkland,Bar plot of compositional differences at species level in the Vanc vs.Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:927,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacteria|p__Bacillota|s__Firmicutes bacterium ASF500",2|976|200643|171549|815|816|1262753;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|1262936;2|976|200643|171549|171552|838|1262924;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|397291;2|1239|1378168,Complete,Atrayees
bsdb:696/1/1,Study 696,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z, Guo B, Gao R, Zhu Q, Wu W , Qin H",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 1,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,CGT group - colorectal cancer patients perioperative placebo,PGT group - colorectal cancer patients perioperative probiotics,"Patients in the PGT group received an encapsulated probiotics preparation (Shanghai Xinyi Pharmaceutical Co., Ltd., Shanghai, China) containing live combined Bifidobacterium longum, Lactobacillus acidophilus and Enterococcus faecalis (1:1:1) with no less than 1.0x107 CFU/g viable cells, three times/day, with a total daily dose of 6.0x107 CFU for five days",11,11,Received antibiotics for the past 3 months prior to surgery,16S,3,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Fig 4,29 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1224|1236|91347|543|1940338;2|1224|28211|356|82115;2|1224|28211|356;2|1224|28211|356|82115|379;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|28211;2|976|200643|171549|171552,Complete,Peace Sandy
bsdb:696/1/2,Study 696,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z, Guo B, Gao R, Zhu Q, Wu W , Qin H",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 1,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,CGT group - colorectal cancer patients perioperative placebo,PGT group - colorectal cancer patients perioperative probiotics,"Patients in the PGT group received an encapsulated probiotics preparation (Shanghai Xinyi Pharmaceutical Co., Ltd., Shanghai, China) containing live combined Bifidobacterium longum, Lactobacillus acidophilus and Enterococcus faecalis (1:1:1) with no less than 1.0x107 CFU/g viable cells, three times/day, with a total daily dose of 6.0x107 CFU for five days",11,11,Received antibiotics for the past 3 months prior to surgery,16S,3,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter",2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539003;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|653683,Complete,Peace Sandy
bsdb:696/2/1,Study 696,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z, Guo B, Gao R, Zhu Q, Wu W , Qin H",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 2,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT Group - Healthy controls,PGT group - colorectal cancer patients perioperative probiotics,PGT group - colorectal cancer patients that received perioperative probiotics,11,11,Received antibiotics for the past 3 months prior to surgery,16S,3,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 1,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1224|1236|91347|543|1940338;2|1224|28211|356|82115|379;2|1224|28211|356|82115;2|1224|28211|356;2|1224|28211|356|82115|379|391;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|28211;2|976|200643|171549|171552,Complete,Peace Sandy
bsdb:696/2/2,Study 696,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z, Guo B, Gao R, Zhu Q, Wu W , Qin H",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 2,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT Group - Healthy controls,PGT group - colorectal cancer patients perioperative probiotics,PGT group - colorectal cancer patients that received perioperative probiotics,11,11,Received antibiotics for the past 3 months prior to surgery,16S,3,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 2,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter",2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539003;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|653683,Complete,Peace Sandy
bsdb:696/3/1,Study 696,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z, Guo B, Gao R, Zhu Q, Wu W , Qin H",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 3,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT- Healthy controls,CGT- colorectal cancer patients that received perioperative placebo,Patients that received perioperative placebos,11,11,Received antibiotics for the past 3 months prior to surgery,16S,3,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter",2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539003;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|653683,Complete,Peace Sandy
bsdb:696/3/2,Study 696,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z, Guo B, Gao R, Zhu Q, Wu W , Qin H",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 3,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT- Healthy controls,CGT- colorectal cancer patients that received perioperative placebo,Patients that received perioperative placebos,11,11,Received antibiotics for the past 3 months prior to surgery,16S,3,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Peace Sandy","Figure 4. Different structures of the gut microbiota in the CGT, PGT, and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",2|1224|1236|72274;2|1224;2|1224|1236;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621;2|976|117743|200644;2|976|117743|200644|49546;2|1224|1236|2887326|468,Complete,Peace Sandy
bsdb:697/1/1,Study 697,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen YC, Lee PC, Kuo YL, Wu WK, Chen CC, Lei CH, Yeh CP, Hsu C, Hsu CH, Lin ZZ, Shao YY, Lu LC, Liu TH, Chen CH, Wu MS, Huang YH , Cheng AL",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-responders to Immune checkpoint inhibitors,Responders to Immune checkpoint inhibitors,"Patients who responded to ICI therapy, defined as complete or partial response per Response
Evaluation Criteria in Solid Tumors (RECIST) v.1.1.",26,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3a,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance in baseline gut microbiome between responders and nonresponders,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2|1224|1236|135624|83763|83770;2|1239|186801|3085636|186803|1506577,Complete,Claregrieve1
bsdb:697/1/2,Study 697,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen YC, Lee PC, Kuo YL, Wu WK, Chen CC, Lei CH, Yeh CP, Hsu C, Hsu CH, Lin ZZ, Shao YY, Lu LC, Liu TH, Chen CH, Wu MS, Huang YH , Cheng AL",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-responders to Immune checkpoint inhibitors,Responders to Immune checkpoint inhibitors,"Patients who responded to ICI therapy, defined as complete or partial response per Response
Evaluation Criteria in Solid Tumors (RECIST) v.1.1.",26,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3a,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance in baseline gut microbiome between responders and nonresponders,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|1239|186801|3082720|186804;2|74201|203494;2|74201|203494|48461;2|74201,Complete,Claregrieve1
bsdb:697/2/1,Study 697,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen YC, Lee PC, Kuo YL, Wu WK, Chen CC, Lei CH, Yeh CP, Hsu C, Hsu CH, Lin ZZ, Shao YY, Lu LC, Liu TH, Chen CH, Wu MS, Huang YH , Cheng AL",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-Disease control with Immune checkpoint inhibitors,Disease control with Immune checkpoint inhibitors,“disease control” was defined as objective response or stable disease lasting =16 weeks.” Objective response was defined as complete or partial response per Response Evaluation Criteria in Solid Tumors (RECIST) v.1.1.,17,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3b,12 October 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Claregrieve1",Differential microbial abundance in baseline gut microbiome between patients whose disease was not controlled and patients whose disease was controlled,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",2|1239|909932|1843488|909930|904;2|201174;2|1224|1236|135624;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|33042;2|201174|84998|84999;2|201174|84998;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|3085636|186803|28050;2|1239|909932|1843489|31977|906;2|1224|1236|135624|83763|674963;2|1224|1236|135624|83763;2|1239|186801|3085636|186803|1506577;2|1239|186801|3085636|186803|1506553|29347,Complete,Claregrieve1
bsdb:697/2/2,Study 697,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen YC, Lee PC, Kuo YL, Wu WK, Chen CC, Lei CH, Yeh CP, Hsu C, Hsu CH, Lin ZZ, Shao YY, Lu LC, Liu TH, Chen CH, Wu MS, Huang YH , Cheng AL",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-Disease control with Immune checkpoint inhibitors,Disease control with Immune checkpoint inhibitors,“disease control” was defined as objective response or stable disease lasting =16 weeks.” Objective response was defined as complete or partial response per Response Evaluation Criteria in Solid Tumors (RECIST) v.1.1.,17,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3b,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance in baseline gut microbiome between patients whose disease was not controlled and patients whose disease was controlled,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:697/3/1,Study 697,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen YC, Lee PC, Kuo YL, Wu WK, Chen CC, Lei CH, Yeh CP, Hsu C, Hsu CH, Lin ZZ, Shao YY, Lu LC, Liu TH, Chen CH, Wu MS, Huang YH , Cheng AL",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-responders to Immune checkpoint inhibitors,Responders to Immune checkpoint inhibitors,"“Objective response” was defined as complete or partial response per Response
Evaluation Criteria in Solid Tumors (RECIST) v.1.1.",12,6,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3a,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1",Differential microbial abundance in baseline gut microbiome between responders and nonresponders,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.",2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|1283313|1872471,Complete,Claregrieve1
bsdb:698/1/1,Study 698,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma HQ, Yu TT, Zhao XJ, Zhang Y , Zhang HJ",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,Patients with Crohn's disease,"Patients with Crohn's disease (11 with as active disease defined by CDAI > 150, 4 with inactive disease)",29,15,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,Suwaiba",Differential microbial abundance between Crohn's patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|s__unidentified rumen bacterium RFN20",2|1239|91061|186826|186827|46123;2|1224|1236|91347|543|561;2|1224;2|1239|186801|186802|186806|113286;2|70463,Complete,Claregrieve1
bsdb:698/1/2,Study 698,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma HQ, Yu TT, Zhao XJ, Zhang Y , Zhang HJ",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,Patients with Crohn's disease,"Patients with Crohn's disease (11 with as active disease defined by CDAI > 150, 4 with inactive disease)",29,15,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Table 2,20 October 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between Crohn's patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",2|1239|186801|186802|3085642|580596;2|1239|909932|909929|1843491|52225;2|1224|1236|135625|712|724;2|256845|1313211|278082|255528|172900,Complete,Claregrieve1
bsdb:698/2/1,Study 698,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma HQ, Yu TT, Zhao XJ, Zhang Y , Zhang HJ",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Patients with ulcerative colitis,29,14,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2,20 October 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between ulcerative colitis patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Spirochaetota",2|1239|91061|186826|186828|117563;2|1239|186801|3082720|186804|1257;2|1239|909932|909929|1843491|55506;2|976|117743|200644|49546|1016;2|1224;2|1224|1236|91347|543|561;2|1224|28216|80840|75682|29580;2|29547|3031852|213849|72294|194;2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|201174|1760|85007|1653|1716;2|203691,Complete,Claregrieve1
bsdb:698/2/2,Study 698,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma HQ, Yu TT, Zhao XJ, Zhang Y , Zhang HJ",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Patients with ulcerative colitis,29,14,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,Merit",Differential microbial abundance between ulcerative colitis patients and healthy controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|976|200643|171549|171550|239759;2|976|200643|171549|1853231|574697;2|200940|3031449|213115|194924|872;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|140625;2|256845;2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491|52225;2|1224|28216|80840|75682|846;2|976|200643|171549|171552|838;2|508458|649775|649776|3029088|638847;2|508458|649775|649776|649777|2753;2|256845|1313211|278082|255528|172900;2|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:698/3/1,Study 698,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma HQ, Yu TT, Zhao XJ, Zhang Y , Zhang HJ",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Patients with ulcerative colitis,Patients with Crohn's disease,Patients with Crohn's disease,14,15,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,Suwaiba,Merit",Differential abundance between patients with ulcerative colitis vs Crohn's disease,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",2|1239|91061|186826|186827|46123|46125;2|200940|3031449|213115|194924|872;2|1239|186801|186802|186806|113286;2|201174|84998|1643822|1643826|84108,Complete,Claregrieve1
bsdb:698/3/2,Study 698,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma HQ, Yu TT, Zhao XJ, Zhang Y , Zhang HJ",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Patients with ulcerative colitis,Patients with Crohn's disease,Patients with Crohn's disease,14,15,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,20 October 2022,Claregrieve1,Claregrieve1,Differential abundance between patients with ulcerative colitis vs Crohn's disease,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniferax|s__Propioniferax innocua,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|437755;2|1239|91061|1385|90964|1279;2|976|117743|200644|49546|1016;2|1224|1236|135625|712|724;2|1224|28216|80840|75682|29580;2|1224|1236|135615|868|2717;2|1224|28216|80840|119060|47670;2|201174|1760|85009|31957|53456|1753;2|1224|1236|135622|267890|22;2|201174|1760|85007|1653|1716,Complete,Claregrieve1
bsdb:699/1/1,Study 699,case-control,35440670,https://doi.org/10.1038/s41598-022-07995-7,NA,"Zuo W, Wang B, Bai X, Luan Y, Fan Y, Michail S , Sun F",16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis,Scientific reports,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Children aged 7-21 with mild to moderate ulcerative colitis,23,19,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table S4,20 October 2022,Claregrieve1,"Claregrieve1,Lwaldron,Suwaiba",Differential microbial abundance between controls and UC subjects,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__uncultured Oscillospira sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|186802|216572|244127;2|1239;2|976|200643|171549|2005519|397864;2|1239|186801|3082720|186804|1870884;2|201174|84998|84999;2|1239|186801|186802|186806|1730|290054;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572;2|201174|84998|1643822|1643826|84108;2|976|200643|171549|2005525|195950;2|74201|203494|48461;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|39492;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|119852|512316;2|1239|91061|186826|81852|423410,Complete,Claregrieve1
bsdb:699/1/2,Study 699,case-control,35440670,https://doi.org/10.1038/s41598-022-07995-7,NA,"Zuo W, Wang B, Bai X, Luan Y, Fan Y, Michail S , Sun F",16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis,Scientific reports,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Children aged 7-21 with mild to moderate ulcerative colitis,23,19,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table S4,20 October 2022,Claregrieve1,Claregrieve1,Differential microbial abundance between controls and UC subjects,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|28123;2|1239|91061|186826|1300|1301;2|1239|186801|186802|31979|1485|1502;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|1506553;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1257;2|1239|1737404|1737405;2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|29465;2|32066;2|32066|203490|203491;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1224;2|1224|1236;2|1224|28216|206351|481;2|1224|28216|206351|481|538;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:700/1/1,Study 700,case-control,22170749,10.1002/ibd.22860,NA,"Michail S, Durbin M, Turner D, Griffiths AM, Mack DR, Hyams J, Leleiko N, Kenche H, Stolfi A , Wine E",Alterations in the gut microbiome of children with severe ulcerative colitis,Inflammatory bowel diseases,2012,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,children with ulcerative colitis,Children hospitalized for intravenous corticosteroid therapy for acute UC,26,27,1 month,16S,NA,RT-qPCR,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 2,20 October 2022,Fatima,Fatima,Phylum and Class comparisons for healthy children and children with ulcerative colitis (UC).,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia",2|201174;2|201174|1760;2|1224|28211;2|1239|91061;2|976|200643;2|1224|28216;2|1239|186801;2|28221;2|29547;2|1239|526524;2|1239;2|32066;2|1224|1236;2|256845|1313211|278081|566277|256846;2|1224;2|203691;2|74201|203494;2|201174|84998,Complete,Fatima
bsdb:701/1/1,Study 701,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y , Andoh A",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Non-IBD,CD,Patients with Crohn's disease activity index <150,14,26,Current,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 5(a),23 November 2022,Fatima,"Fatima,Aiyshaaaa",Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota",2|1224|1236|135625|712|713;2|32066|203490|203491|203492|180162;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803|2316020|33038;2|976,Complete,Atrayees
bsdb:701/1/2,Study 701,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y , Andoh A",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Non-IBD,CD,Patients with Crohn's disease activity index <150,14,26,Current,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 5(a),20 March 2023,Aiyshaaaa,Aiyshaaaa,Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|186802|204475;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263|40518;2|1224|1236|72274|135621|286,Complete,Atrayees
bsdb:701/2/1,Study 701,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y , Andoh A",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,NON-IBD controls,UC,The patient who is diagnosed from ulcerative colitis(UC).,14,43,Current,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5(b),20 March 2023,Aiyshaaaa,Aiyshaaaa,Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota",2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|544;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465;2|1239,Complete,Atrayees
bsdb:701/2/2,Study 701,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y , Andoh A",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,NON-IBD controls,UC,The patient who is diagnosed from ulcerative colitis(UC).,14,43,Current,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5(b),21 March 2023,Aiyshaaaa,Aiyshaaaa,Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|203691|203692|1643686|143786|29521;2|29547|3031852|213849|72293|209;2|976|200643|171549|1853231|283168;2|976|200643|171549|171550|239759;2|1239|186801|186802|204475;2|1224|1236|72274|135621|286;2|1239|186801|3085636|186803|33042;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:701/3/1,Study 701,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y , Andoh A",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,UC,CD,The patient who is diagnosed from Crohn's disease(CD).,43,26,Current,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5(c),21 March 2023,Aiyshaaaa,Aiyshaaaa,Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|32066|203490|203491|203492|180162;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543|561;2|1224|1236|91347|1903414|581;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|2316020|33038,Complete,Atrayees
bsdb:701/3/2,Study 701,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y , Andoh A",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,UC,CD,The patient who is diagnosed from Crohn's disease(CD).,43,26,Current,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5(c),21 March 2023,Aiyshaaaa,Aiyshaaaa,Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|204475;2|1224|1236|91347|543|544;2|1239|186801|3085636|186803|841;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:702/1/1,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 1,Norway,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis (RA) Remission,Active (RA) Rheumatoid Arthritis,Individuals with active rheumatoid arthritis (RA),28,60,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 3, text",2 November 2022,Tislam,"Tislam,Peace Sandy","(B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:702/1/2,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 1,Norway,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis (RA) Remission,Active (RA) Rheumatoid Arthritis,Individuals with active rheumatoid arthritis (RA),28,60,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 2, text",2 November 2022,Tislam,Tislam,"(B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|201174|84998|84999|1643824|1380;2|1239|186801|186802|1898207;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|976|200643|171549|171550;2|1239|909932|909929|1843491|970,Complete,Peace Sandy
bsdb:702/2/1,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,No prednisolone,Prednisolone,Individuals who received prednisolone,57,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4F Table,20 January 2024,Peace Sandy,Peace Sandy,"Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1224|28216|206351|481|32257;2|976|117743|200644|49546|1016;2|1239|91061|186826|1300|1301;2|1224|1236|135615|868|2717;2|1239|909932|909929|1843491|970,Complete,Peace Sandy
bsdb:702/2/2,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,No prednisolone,Prednisolone,Individuals who received prednisolone,57,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4F Table,20 January 2024,Peace Sandy,Peace Sandy,"Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|201174|84998|84999|1643824|1380;2|1239|186801|186802|543314|2137877;2|201174|84998|84999|84107;2|1239|186801|3085636|1185407;2|1239|909932|1843489|31977|39948;2|508458|649775|649776|3029087|1434006;2|32066|203490|203491|203492|848;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,Peace Sandy
bsdb:702/3/1,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 3,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Former Smokers,Former Smokers,29,35,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4A,20 January 2024,Peace Sandy,Peace Sandy,"S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|416916;2|976|117743|200644|2762318|59735;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|201174|1760|85007|1653|1716;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482,Complete,Peace Sandy
bsdb:702/3/2,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 3,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Former Smokers,Former Smokers,29,35,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4A Table,20 January 2024,Peace Sandy,Peace Sandy,"S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|201174|1760|2037|2049|76833;2|1224|1236|135615|868|2717;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482,Complete,Peace Sandy
bsdb:702/4/1,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 4,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Current Smokers,Current Smokers,29,14,3 Months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4A Table,20 January 2024,Peace Sandy,Peace Sandy,"S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|32066|203490|203491|203492|848;2|508458|649775|649776|649777;2|508458|649775|649776|3029087|1434006;2|976|200643|171549|2005523|346096;2|201174|1760|2037|2049|1654;2|203691|203692|136|2845253|157;2|976|200643|171549|2005525|195950;2|1239|909932|909929|1843491|970;2|544448|31969|2085|2092|2093;2|1239|186801|3085636|1185407;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:702/4/2,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 4,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Current Smokers,Current Smokers,29,14,3 Months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4A Table,20 January 2024,Peace Sandy,Peace Sandy,"S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|32066|203490|203491|1129771|32067;2|201174|1760|2037|2049|76833;2|1224|28216|206351|481|482;2|1224|1236|135615|868|2717,Complete,Peace Sandy
bsdb:702/5/1,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 5,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Former Smokers,Current Smokers,Current Smokers,35,14,3 Months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4A Table,20 January 2024,Peace Sandy,Peace Sandy,"S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|32066|203490|203491|203492|848;2|508458|649775|649776|649777;2|508458|649775|649776|3029087|1434006;2|976|200643|171549|2005523|346096;2|201174|1760|2037|2049|1654;2|203691|203692|136|2845253|157;2|976|200643|171549|2005525|195950;2|1239|909932|909929|1843491|970;2|544448|31969|2085|2092|2093;2|1239|186801|3085636|1185407;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:702/5/2,Study 702,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W , Bolstad AI",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 5,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Former Smokers,Current Smokers,Current Smokers,35,14,3 Months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4A Table,20 January 2024,Peace Sandy,Peace Sandy,"S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella",2|1224|28216|206351|481|482;2|201174|1760|85007|1653|1716;2|1224|1236|135625|712|724;2|976|117743|200644|49546|1016;2|1224|1236|135625|712|416916;2|1224|28216|80840|119060|47670;2|1224|1236|135615|868|2717;2|1239|91061|1385|539738|1378;2|201174|1760|2037|2049|1654;2|976|117743|200644|2762318|59735,Complete,Peace Sandy
bsdb:703/1/1,Study 703,case-control,36077282,10.3390/ijms23179883,NA,"Chen YJ, Hung WC, Chou YH, Lai CH, Peng P, Jhou PS, Tsai MR, Sheu JJ , Yen JH",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 1,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All Matched (AM) Rheumatoid Arthritis,All Matched (AM) Rheumatoid Arthritis Patients,21,21,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Text , Supplementary Figure S1A",2 November 2022,Tislam,"Tislam,Peace Sandy","he composition of subgingival microbiota between the RA 
patients and controls in groups AM and PD were estimated by LEfSe with the parameter 
of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found 
(Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, 
Streptococcus",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1239|91061|186826|1300|1301|1328;2|203691|203692|136|2845253|157|158;2|32066|203490|203491|203492|848,Complete,Peace Sandy
bsdb:703/1/2,Study 703,case-control,36077282,10.3390/ijms23179883,NA,"Chen YJ, Hung WC, Chou YH, Lai CH, Peng P, Jhou PS, Tsai MR, Sheu JJ , Yen JH",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 1,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All Matched (AM) Rheumatoid Arthritis,All Matched (AM) Rheumatoid Arthritis Patients,21,21,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Text , Supplementary Figure S1A",2 November 2022,Tislam,"Tislam,Peace Sandy","he composition of subgingival microbiota between the RA 
patients and controls in groups AM and PD were estimated by LEfSe with the parameter 
of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found 
(Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, 
Streptococcus",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",2|1224|1236|135625|712|724|729;2|1239|91061|186826|1300|1301|1305,Complete,Peace Sandy
bsdb:703/2/1,Study 703,case-control,36077282,10.3390/ijms23179883,NA,"Chen YJ, Hung WC, Chou YH, Lai CH, Peng P, Jhou PS, Tsai MR, Sheu JJ , Yen JH",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 2,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Periodontally diseased (PD) Rheumatoid Arthritis,"Patients with periodontally
diseased) Rheumatoid Arthritis",12,12,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Text , Supplementary Figure S1B",28 December 2023,Peace Sandy,Peace Sandy,"In group PD, a total of 129 taxa showed differential abundances between the
RA patients and controls (Supplementary Figure S1B). Of the species level with the loga�rithmic LDA score > 4, S. anginosus and three unidentified species of genera Actinomyces,
Fusobacterium, and Parvimonas demonstrated a significant increase in the RA patients, while
Pseudomonas batumici (P. batumici) was the only enriched species found in the controls (the
logarithmic LDA score = 5.42).",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|1239|91061|186826|1300|1301|1328;2|201174|1760|2037|2049|1654;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311,Complete,Peace Sandy
bsdb:703/2/2,Study 703,case-control,36077282,10.3390/ijms23179883,NA,"Chen YJ, Hung WC, Chou YH, Lai CH, Peng P, Jhou PS, Tsai MR, Sheu JJ , Yen JH",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 2,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Periodontally diseased (PD) Rheumatoid Arthritis,"Patients with periodontally
diseased) Rheumatoid Arthritis",12,12,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Text , Supplementary Figure S1B",28 December 2023,Peace Sandy,Peace Sandy,"In group PD, a total of 129 taxa showed differential abundances between the
RA patients and controls (Supplementary Figure S1B). Of the species level with the loga�rithmic LDA score > 4, S. anginosus and three unidentified species of genera Actinomyces,
Fusobacterium, and Parvimonas demonstrated a significant increase in the RA patients, while
Pseudomonas batumici (P. batumici) was the only enriched species found in the controls (the
logarithmic LDA score = 5.42)",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas batumici,2|1224|1236|72274|135621|286|226910,Complete,Peace Sandy
bsdb:704/1/1,Study 704,case-control,33964928,10.1186/s12903-021-01597-x,NA,"Lehenaff R, Tamashiro R, Nascimento MM, Lee K, Jenkins R, Whitlock J, Li EC, Sidhu G, Anderson S, Progulske-Fox A, Bubb MR, Chan EKL , Wang GP",Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study,BMC oral health,2021,"16S rRNA sequencing, Microbial dysbiosis, Periodontal disease, Rheumatoid arthritis, Subgingival microbiome",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,Healthy Non-RA Controls,Rheumatoid Arthritis,Biologic Naive Rheumatoid Arthritis patient,10,8,3 months,16S,123,Illumina,LEfSe,NA,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 6,2 November 2022,Tislam,"Tislam,Aiyshaaaa,Peace Sandy","Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|201174|1760|2037|2049|2529408|52773;2|1239|91061|186826|1300|1301|1318,Complete,Peace Sandy
bsdb:704/1/2,Study 704,case-control,33964928,10.1186/s12903-021-01597-x,NA,"Lehenaff R, Tamashiro R, Nascimento MM, Lee K, Jenkins R, Whitlock J, Li EC, Sidhu G, Anderson S, Progulske-Fox A, Bubb MR, Chan EKL , Wang GP",Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study,BMC oral health,2021,"16S rRNA sequencing, Microbial dysbiosis, Periodontal disease, Rheumatoid arthritis, Subgingival microbiome",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,Healthy Non-RA Controls,Rheumatoid Arthritis,Biologic Naive Rheumatoid Arthritis patient,10,8,3 months,16S,123,Illumina,LEfSe,NA,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 6,2 November 2022,Tislam,"Tislam,Aiyshaaaa,Peace Sandy","Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",2|1239|91061|1385|539738|1378|29391;2|1224|28216|206351|481|32257|502;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|838|28132,Complete,Peace Sandy
bsdb:705/1/1,Study 705,case-control,29562298,10.1093/rheumatology/key052,NA,"Mikuls TR, Walker C, Qiu F, Yu F, Thiele GM, Alfant B, Li EC, Zhao LY, Wang GP, Datta S , Payne JB",The subgingival microbiome in patients with established rheumatoid arthritis,"Rheumatology (Oxford, England)",2018,"osteoarthritis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 1,NA,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,Osteoarthritis (OA),Rheumatoid Arthritis (RA),Patients with Rheumatoid Arthritis,296,260,NA,16S,123,Illumina,Linear Regression,0.05,TRUE,NA,NA,"comorbidity,marital status,race,smoking status",NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,text,2 November 2022,Tislam,"Tislam,Peace Sandy","Differential expression of OTUs between RA and OA patients based on periodontitis status 

Differential expression analysis conducted using two separate linear models: the first fitted with RA vs OA status, periodontitis status and the interaction between these factors (base model); and the second fitted with the same factors as the base model in addition to race, marital status and smoking (fully adjusted model). OTU: operational taxonomic unit; FDR: false discovery rate.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multiformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.",2|1239|186801|3085636|186803|43996;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|282402;2|976|200643|171549|171552|838|59823;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157|166,Complete,Peace Sandy
bsdb:706/1/1,Study 706,"cross-sectional observational, not case-control",24273047,10.1093/rheumatology/ket362,NA,"Wolff B, Berger T, Frese C, Max R, Blank N, Lorenz HM , Wolff D","Oral status in patients with early rheumatoid arthritis: a prospective, case-control study","Rheumatology (Oxford, England)",2014,"case–control studies, oral hygiene, periodontal attachment loss, periodontal index, plaque index, rheumatoid arthritis",Experiment 1,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,22,22,Intake of antibiotics during the past 6 months,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 3, Table 4,  Text",2 November 2022,Tislam,"Tislam,Atrayees,Peace Sandy","Microbiological data and quantitative real-time PCR measurements of abundance of subgingival microbiota in ERA patients and controls. 

Microbiological data and quantitative real-time PCR measurements of abundance of supragingival microbiota in ERA patients and controls",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|976|200643|171549|2005525|195950|28112;2|1239|91061|186826|1300|1301|1328,Complete,Peace Sandy
bsdb:706/1/2,Study 706,"cross-sectional observational, not case-control",24273047,10.1093/rheumatology/ket362,NA,"Wolff B, Berger T, Frese C, Max R, Blank N, Lorenz HM , Wolff D","Oral status in patients with early rheumatoid arthritis: a prospective, case-control study","Rheumatology (Oxford, England)",2014,"case–control studies, oral hygiene, periodontal attachment loss, periodontal index, plaque index, rheumatoid arthritis",Experiment 1,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,22,22,Intake of antibiotics during the past 6 months,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 3, Table 4,  Text",2 November 2022,Tislam,"Tislam,Peace Sandy","Microbiological data and quantitative real-time PCR measurements of abundance of subgingival microbiota in ERA patients and controls

Microbiological data and quantitative real-time PCR measurements of abundance of supragingival microbiota in ERA patients and controls",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|2037|2049|1654|29317;2|201174|1760|85007|1653|1716|61592;2|32066;2|1239|91061|186826|33958|1578|1596;2|32066|203490|203491|1129771|32067|104608;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:707/1/1,Study 707,case-control,22576262,10.1002/art.34539,NA,"Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA , Abramson SB",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy controls,NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],18,31,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 1,Table 2,2 November 2022,Tislam,"Tislam,Peace Sandy","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|1239|909932|1843489|31977|156454;2|976|200643|171549|171552;2|976|200643|171549|815|909656;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|970;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836,Complete,Peace Sandy
bsdb:707/1/2,Study 707,case-control,22576262,10.1002/art.34539,NA,"Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA , Abramson SB",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy controls,NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],18,31,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 2,Table 2,2 November 2022,Tislam,"Tislam,Peace Sandy","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|201174|1760|85007|1653|1716;2|1239|909932|909929|1843491|52225;2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|32067,Complete,Peace Sandy
bsdb:707/2/1,Study 707,case-control,22576262,10.1002/art.34539,NA,"Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA , Abramson SB",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 2,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,CRA - [Chronic Established  Rheumatoid Arthritis],NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],34,31,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 1,Table 2,1 February 2024,Peace Sandy,Peace Sandy,"Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171551|836;2|1239|909932|909929|1843491|970;2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|976|200643|171549|2005525|195950,Complete,Peace Sandy
bsdb:707/2/2,Study 707,case-control,22576262,10.1002/art.34539,NA,"Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA , Abramson SB",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 2,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,CRA - [Chronic Established  Rheumatoid Arthritis],NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],34,31,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 2,Table 2,1 February 2024,Peace Sandy,Peace Sandy,"Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977;2|1239|909932|909929|1843491|52225;2|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:707/3/1,Study 707,case-control,22576262,10.1002/art.34539,NA,"Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA , Abramson SB",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 3,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All [RA] - Rheumatoid Arthritis Patients,"All [RA] - Rheumatoid Arthritis Patients, which includes NORA [new-onset RA] and CRA [Chronic-established RA]",18,65,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 1,Table 2,1 February 2024,Peace Sandy,Peace Sandy,"Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1239|909932|1843489|31977|156454;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|970,Complete,Peace Sandy
bsdb:707/3/2,Study 707,case-control,22576262,10.1002/art.34539,NA,"Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA , Abramson SB",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 3,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All [RA] - Rheumatoid Arthritis Patients,"All [RA] - Rheumatoid Arthritis Patients, which includes NORA [new-onset RA] and CRA [Chronic-established RA]",18,65,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 2,Table 2,1 February 2024,Peace Sandy,Peace Sandy,"Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|201174|1760|85007|1653|1716;2|32066|203490|203491|1129771|32067;2|976|117743|200644|49546|1016,Complete,Peace Sandy
bsdb:708/1/1,Study 708,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X, Tian K, Ma X, Wang S, Luo C , Du Q",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 1,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients RA,44,54,Three months,16S,4,Illumina,NA,0.05,NA,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 5, 6, 7",14 March 2023,Sophy,"Sophy,Atrayees","Different relative abundance of bacterial taxonomy profiles of RA, PD and control group",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643;2|203691|203692|136|137;2|203691|203692|136;2|203691|203692;2|203691|203692|136|2845253|157;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:708/1/2,Study 708,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X, Tian K, Ma X, Wang S, Luo C , Du Q",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 1,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients RA,44,54,Three months,16S,4,Illumina,NA,0.05,NA,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 6, 7",14 March 2023,Sophy,"Sophy,Atrayees",The profile of periodontal pathogens in RA and PE groups compared with controls (*P < 0.05).,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950,Complete,Atrayees
bsdb:708/2/1,Study 708,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X, Tian K, Ma X, Wang S, Luo C , Du Q",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,rheumatoid arthritis patients,periodontal disease patients,periodontal disease patients PA,54,45,Three months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 7,29 May 2023,Atrayees,Atrayees,Profile of periodontal pathogens in RA and PE groups compared with controls,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:708/2/2,Study 708,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X, Tian K, Ma X, Wang S, Luo C , Du Q",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,rheumatoid arthritis patients,periodontal disease patients,periodontal disease patients PA,54,45,Three months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 6, 7",29 May 2023,Atrayees,Atrayees,Profile of periodontal pathogens in RA and PE groups compared with controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|976|200643|171549|2005525|195950;2|976|200643|171549|171551|836,Complete,Atrayees
bsdb:709/1/1,Study 709,case-control,34442739,10.3390/microorganisms9081657,NA,"Esberg A, Johansson L, Johansson I , Dahlqvist SR",Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis,Microorganisms,2021,"16S rDNA sequencing, oral microbiota, periodontitis, rheumatoid arthritis",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,59,61,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 3 (B),2 November 2022,Tislam,"Tislam,Peace Sandy",(b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 314,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 349,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacteroidota",2|976|200643|171549|171552|1283313|76122;2|32066|203490|203491|203492|848|76857;2|976|117743|200644|49546|1016|327575;2|976|200643|171549|171552|838|712464;2|976|200643|171549|171551|836|28124;2|32066|203490|203491|203492|848|155615;2|1224|28216|206351|481|482|495;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|2974257|407975;2|976|200643|171549|171552|838|28137;2|1224|1236|135625|712|416916|1872413;2|203691|203692|136|2845253|157|158;2|29547|3031852|213849|72294|194|824;2|1239|186801|3082720|3118655|44259|143361;2|1239|1737404|1737405|1570339|543311|33033;2|95818|713051;2|976|200643|171549|171552|2974257|633701;2|203691|203692|136|2845253|157|166;2|976|200643|171549|171552|2974251|439703;2|976|200643|171549|171552|838|52227;2|1239|526524|526525|128827|118747|118748;2|508458|649775|649776|3029087|1434006|2699746;2|976|117743|200644|49546|1016;2|203691|203692|136|2845253|157;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|39948;2|1239|186801|3082720|3118655|44259;2|508458|649775|649776|3029087|1434006;2|1239|526524|526525|128827|118747;2|976,Complete,Peace Sandy
bsdb:709/1/2,Study 709,case-control,34442739,10.3390/microorganisms9081657,NA,"Esberg A, Johansson L, Johansson I , Dahlqvist SR",Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis,Microorganisms,2021,"16S rDNA sequencing, oral microbiota, periodontitis, rheumatoid arthritis",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,59,61,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 3 (B),2 November 2022,Tislam,"Tislam,Peace Sandy",(b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__uncultured Stomatobaculum sp.",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|29317;2|29547|3031852|213849|72294|194|199;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|43996|43997;2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060|47670|47671;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|265975|237576;2|1239|186801|3085636|186803|1213720;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|423477;2|1239|186801|3085636|186803|1213720|1662277,Complete,Peace Sandy
bsdb:710/1/1,Study 710,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D, Eiberg JM, Enevold C, Grande MA, Jensen CAJ, Skov L , Hansen PR",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 1,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,orally healthy individuals,Psoriasis patient,NA,52,27,3 months,16S,123,Illumina,LEfSe,1e-4,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2(b),30 March 2023,Ellajessica,"Ellajessica,Aiyshaaaa",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls and Psoriasis.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",2|1224|1236|135625|712|416916|1872413;2|976|117743|200644|49546|1016|44737;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482|33053;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207|43675,Complete,Atrayees
bsdb:710/1/2,Study 710,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D, Eiberg JM, Enevold C, Grande MA, Jensen CAJ, Skov L , Hansen PR",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 1,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,orally healthy individuals,Psoriasis patient,NA,52,27,3 months,16S,123,Illumina,LEfSe,1e-4,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 2(b),30 March 2023,Ellajessica,"Ellajessica,Aiyshaaaa",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls and Psoriasis.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",2|201174|1760|2037|2049|1654|29317;2|201174|1760|85009|31957|2801844|1750;2|976|117743|200644|49546|1016|44737;2|1239|91061|186826|33958|1578|1596;2|1224|28216|206351|481|482|496;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|1300|1301|1310;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|1926307,Complete,Atrayees
bsdb:710/2/1,Study 710,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D, Eiberg JM, Enevold C, Grande MA, Jensen CAJ, Skov L , Hansen PR",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 2,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,periodntitis,Psoriasis,Individuals who have been diagnosed with Psoriasis.,27,58,3 months,16S,123,Illumina,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2(a),24 April 2023,Aiyshaaaa,Aiyshaaaa,Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between Periodontitis (P) versus Psoriasis (PS).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp.,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium neglectum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",2|1224|1236|135625|712|416916|1872413;2|1239|186801|3085636|186803|830|28121;2|29547|3031852|213849|72294|194|199;2|976|117743|200644|49546|1016|44737;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|539738|1378|29391;2|1224|28216|206351|481|32257|502;2|32066|203490|203491|1129771|32067|157691;2|32066|203490|203491|1129771|32067|104608;2|1239|186801|3082720|3030910|86331|114528;2|1224|28216|206351|481|482|33053;2|1224|28216|206351|481|482|28449;2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301|1306,Complete,Atrayees
bsdb:710/2/2,Study 710,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D, Eiberg JM, Enevold C, Grande MA, Jensen CAJ, Skov L , Hansen PR",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 2,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,periodntitis,Psoriasis,Individuals who have been diagnosed with Psoriasis.,27,58,3 months,16S,123,Illumina,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 2(a),24 April 2023,Aiyshaaaa,Aiyshaaaa,Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between Periodontitis (P) versus Psoriasis (PS).,decreased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",2|508458|649775|649776|3029087|1434006|2699746;2|203691|203692|136|2845253|157|158;2|32066|203490|203491|203492|848|77917;2|203691|203692|136|2845253|157|166;2|508458|649775|649776|3029087|1434006|651822;2|1239|91061|186826|1300|1301|76860;2|976|200643|171549|171551|836|837;2|201174|1760|85006|1268|32207|2047;2|200940|3031451|3024411|213121|893|895;2|976|200643|171549|2005525|195950|28112;2|1239|186801|3082720|3030910|86331|35519;2|544448|2790996|2895623|2895509|56142;2|976|200643|171549|171552|2974257|407975;2|203691|203692|136|2845253|157|53419;2|32066|203490|203491|203492|848;2|1239|91061|186826|1300|1301|1309;2|1239|186801|3082720|3118655|44259|143361;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171551|836|28124;2|201174|1760|2037|2049|2529408|1660;2|201174|1760|85006|1268|32207|43675,Complete,Atrayees
bsdb:710/3/1,Study 710,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D, Eiberg JM, Enevold C, Grande MA, Jensen CAJ, Skov L , Hansen PR",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 3,Denmark,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,orally healthy individuals,Periodontitis patients,Patients who have been diagnosed with periodontitis,52,27,3 months,16S,123,Illumina,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2(c),31 May 2023,Atrayees,Atrayees,Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls versus Periodontitis (P).,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus ultunensis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.",2|201174|1760|2037|2049|1654|544580;2|976|200643|171549|171552|1283313|76122;2|1239|526524|526525|128827|118747|118748;2|29547|3031852|213849|72294|194|205;2|1239|186801|186802|1898207;2|200940|3031451|3024411|213121|893|895;2|1239|186801|3082720|3118655|44259|143361;2|508458|649775|649776|3029087|1434006|651822;2|508458|649775|649776|3029087|1434006|2699746;2|32066|203490|203491|203492|848|851;2|32066|203490|203491|203492|848|68766;2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|2974257|407975;2|1239|91061|186826|33958|1578|227945;2|544448|2790996|2895623|2895509|56142;2|1239|186801|3082720|3030910|86331|35519;2|1239|186801|3082720|186804|1904861;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|59823;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|76860;2|976|200643|171549|2005525|195950|28112;2|203691|203692|136|2845253|157|59892;2|203691|203692|136|2845253|157|158;2|203691|203692|136|2845253|157|53418;2|203691|203692|136|2845253|157|53419;2|203691|203692|136|2845253|157|166,Complete,Atrayees
bsdb:710/3/2,Study 710,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D, Eiberg JM, Enevold C, Grande MA, Jensen CAJ, Skov L , Hansen PR",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 3,Denmark,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,orally healthy individuals,Periodontitis patients,Patients who have been diagnosed with periodontitis,52,27,3 months,16S,123,Illumina,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 2(c),31 May 2023,Atrayees,Atrayees,Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls versus Periodontitis (P).,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella sp. (in: b-proteobacteria),k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium neglectum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium vescum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",2|976|117743|200644|49546|1016|1017;2|1239|91061|186826|186828|117563|137732;2|1239|909932|1843489|31977|29465|419208;2|1224|28216|206351|481|482|192066;2|1239|186801|3085636|186803|1898203;2|32066|203490|203491|1129771|32067|104608;2|976|200643|171549|171552|2974257|633701;2|1239|909932|909929|1843491|52225|2049034;2|1224|28216|206351|481|32257|2020713;2|1224|28216|80840|80864|219181|1898956;2|1239|186801|3082720|3030910|86331|114528;2|32066|203490|203491|1129771|32067|40542;2|201174|1760|85009|31957|2801844|1750;2|1224|1236|135625|712|416916|1872413;2|1239|91061|186826|81852|1350|53345;2|1239|186801|186802|216572|2485925;2|1224|28216|206351|481|482|1107316;2|1239|186801|3082720|3030910|86331|86333;2|1239|526524|526525|128827|123375|102148;2|1224|28216|206351|481|482|496;2|976|200643|171549|171552|838|470565,Complete,Atrayees
bsdb:711/1/1,Study 711,"cross-sectional observational, not case-control",34341764,https://doi.org/10.1155%2F2021%2F5579608,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325587/,"Wen M, Liu T, Zhao M, Dang X, Feng S, Ding X, Xu Z, Huang X, Lin Q, Xiang W, Li X, He X , He Q",Correlation Analysis between Gut Microbiota and Metabolites in Children with Systemic Lupus Erythematosus,Journal of immunology research,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Systemic lupus erythematosus,MONDO:0007915,HC,SLE,Individuals who have been diagnosed with systemic lupus erythematosus (SLE). Systemic lupus erythematosus (SLE) is an autoimmune-mediated diffuse connective tissue disease characterized by immune inflammation with an unclear aetiology and pathogenesis.,28,33,3 months,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 2,20 March 2023,Aiyshaaaa,Aiyshaaaa,"The differently abundant species at genus, class, phylum, order and family level in both the groups are listed.",increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rudaea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1224|28211;2|1239|91061;2|1224|28211|204458|76892;2|1224|28211|204458;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1224|1236;2|1239|186801|3085636|186803|1649459;2|1224|1236|91347|543|570;2|1224|1236|91347|543|579;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826;2|1224;2|1224|1236|135614|1775411;2|1224|1236|135614|1775411|886360;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810280|3025755;2|1224|1236|135614;2|1239|526524|526525|128827|1522;2|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:711/1/2,Study 711,"cross-sectional observational, not case-control",34341764,https://doi.org/10.1155%2F2021%2F5579608,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325587/,"Wen M, Liu T, Zhao M, Dang X, Feng S, Ding X, Xu Z, Huang X, Lin Q, Xiang W, Li X, He X , He Q",Correlation Analysis between Gut Microbiota and Metabolites in Children with Systemic Lupus Erythematosus,Journal of immunology research,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Systemic lupus erythematosus,MONDO:0007915,HC,SLE,Individuals who have been diagnosed with systemic lupus erythematosus (SLE). Systemic lupus erythematosus (SLE) is an autoimmune-mediated diffuse connective tissue disease characterized by immune inflammation with an unclear aetiology and pathogenesis.,28,33,3 months,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 2,20 March 2023,Aiyshaaaa,Aiyshaaaa,"The differently abundant species at genus, class, phylum, order and family level in both the groups are listed in this table.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|1239|186801|3085636|186803|1766253;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|1239|186801|3082768|990719;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|1410626;2|1239|186801|3085636|186803|877420;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|28050|39485,Complete,Claregrieve1
bsdb:712/1/1,Study 712,"cross-sectional observational, not case-control",29513935,10.1002/art.40485,NA,"Lopez-Oliva I, Paropkari AD, Saraswat S, Serban S, Yonel Z, Sharma P, de Pablo P, Raza K, Filer A, Chapple I, Dietrich T, Grant MM , Kumar PS",Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis,"Arthritis & rheumatology (Hoboken, N.J.)",2018,NA,Experiment 1,United Kingdom,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,healthy controls,Rheumatoid Arthritis,periodontally healthy patients with Rheumatoid Arthritis,19,22,12 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 November 2022,Tislam,"Tislam,Aiyshaaaa,Claregrieve1",Differential microbial abundance between RA patients and controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces radicidentis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium|s__Cryptobacterium curtum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma orale,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma salivarium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia|s__Parascardovia denticolens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium acidifaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 136,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 140,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 143,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus downei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. oral taxon 808,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 346,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema parvum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 132,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 145,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 148,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 150,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 155,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 483",2|201174|1760|2037|2049|2529408|181487;2|201174|1760|2037|2049|1654|272548;2|201174|1760|2037|2049|1654|1659;2|201174|1760|2037|2049|1654|544581;2|201174|1760|2037|2049|1654|1655;2|201174|1760|2037|2049|1654|544580;2|201174|1760|2037|2049|1654|111015;2|1239|909932|1843489|31977|156454|156456;2|201174|84998|84999|1643824|2767353|1382;2|201174|84998|84999|1643824|2767353|1383;2|976|200643|171549|815;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|1689;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|158787;2|200795|32061;2|201174|84998|1643822|1643826|84162|84163;2|200940|3031451|3024411|213121|893;2|200940|3031449|213115|194924|872;2|1239|909932|1843489|31977|39948|218538;2|1239|909932|1843489|31977|39948|1955814;2|1239|526524|526525|128827;2|508458|649775|649776|3029087|1434006|651822;2|508458|649775|649776|3029087|1434006|2699746;2|1239|186801|3085636|186803|43994;2|1239|186801|3085636|186803|1164882|979627;2|1239|186801|3085636|186803|1164882|467210;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|1598;2|32066|203490|203491|1129771|32067|554406;2|32066|203490|203491|1129771|32067|157691;2|32066|203490|203491|1129771|32067|157687;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906|187326;2|1239|909932|909929|1843491|52225;2|1239|186801|3085636|186803|437755;2|544448|2790996|2895623|2895509|56142;2|544448|2790996|2895623|2895509|2121;2|544448|2790996|2895623|2895509|2124;2|201174|84998|84999|1643824|133925;2|201174|84998|84999|1643824|133925|133926;2|1239|186801|3085636|186803|265975|652706;2|201174|1760|85004|31953|196082|78258;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|2974251|439703;2|976|200643|171549|171552|2974251|28136;2|976|200643|171549|171552|2974257|28134;2|976|200643|171549|171552|2974251|228604;2|201174|1760|85009|31957|1743|556499;2|201174|1760|85004|31953|196081|230143;2|1239|909932|909929|1843491|970|135080;2|1239|909932|909929|1843491|970|713030;2|1239|909932|909929|1843491|970|671225;2|1239|909932|909929|1843491|970|712533;2|1239|909932|909929|1843491|970|135083;2|1239|909932|909929|1843491|970|69823;2|201174|84998|1643822|1643826|84108|84109;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|1317;2|976|200643|171549|2005525|195950|712711;2|95818|713049;2|203691|203692|136|2845253|157|138851;2|203691|203692|136|2845253|157|53419;2|203691|203692|136|2845253|157|69710;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|671229;2|1239|909932|1843489|31977|713066;2|1239|909932|1843489|31977|713068;2|1239|909932|1843489|31977|713069;2|1239|909932|1843489|31977|671234;2|1239|909932|1843489|31977|671235;2|1239|909932|1843489|31977|713070,Complete,Claregrieve1
bsdb:712/1/2,Study 712,"cross-sectional observational, not case-control",29513935,10.1002/art.40485,NA,"Lopez-Oliva I, Paropkari AD, Saraswat S, Serban S, Yonel Z, Sharma P, de Pablo P, Raza K, Filer A, Chapple I, Dietrich T, Grant MM , Kumar PS",Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis,"Arthritis & rheumatology (Hoboken, N.J.)",2018,NA,Experiment 1,United Kingdom,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,healthy controls,Rheumatoid Arthritis,periodontally healthy patients with Rheumatoid Arthritis,19,22,12 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 1,10 November 2022,Tislam,"Tislam,Claregrieve1",Differential microbial abundance between RA patients and healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. oral taxon 408,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 458,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 513,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 308,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella sp. oral taxon 164,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella sp. oral taxon 451,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium orale,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus italicus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus saccharolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. oral taxon 035,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. oral taxon 036,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella sp. oral taxon 012,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella sp. oral taxon 459,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix|s__Leptothrix sp. oral taxon 025,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus fusiformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria polysaccharea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp. oral taxon 393,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp. oral taxon 167,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 106,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. oral taxon 279,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. oral taxon 284,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oleovorans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pyogenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus|s__Terrahaemophilus aromaticivorans,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 250,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",2|1224|1236|2887326|468|469|470;2|1224|1236|2887326|468|469|712104;2|1224|1236|135625|712|416916|712148;2|1224|1236|135625|712|416916|712150;2|1224|1236|135625|712|416916|739;2|976|200643|171549|171552|1283313|671218;2|976|200643|171549|171552|1283313|712462;2|1239|91061|1385|186817|2893057|79880;2|976|117743|200644|2762318|59735|712187;2|29547|3031852|213849|72294|194|204;2|976|117743|200644|49546|1016|45243;2|976|117743|200644|49546|1016|1019;2|1239|186801|3085636|186803|43996|712233;2|1239|186801|3085636|186803|43996|712234;2|1239|186801|3085636|186803|43996|43997;2|1224|28216|80840|80864|283|285;2|200940|3031449|213115|213116|898|132132;2|1224|28216|206351|481|538|539;2|1239|91061|186826|81852|1350|246144;2|1239|91061|186826|81852|1350|41997;2|1239|91061|1385|539738|1378|1379;2|1239|91061|1385|539738|1378|29391;2|1239|91061|1385|539738|1378|84135;2|1239|91061|186826|186828|117563|46124;2|1224|1236|135625|712|724|726;2|1224|1236|135625|712|724|712309;2|1224|1236|135625|712|724|712310;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|43994|43995;2|1224|28216|206351|481|32257|505;2|1224|28216|206351|481|32257|502;2|1224|28216|206351|481|32257|712319;2|1224|28216|206351|481|32257|712320;2|1224|28216|206351|481|32257|504;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|1224|28216|80840|2975441|88|712353;2|32066|203490|203491|1129771|32067|712357;2|1239|91061|1385|186817|400634|28031;2|1224|28216|206351|481|482|267212;2|1224|28216|206351|481|482|34026;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|487;2|1224|28216|206351|481|482|489;2|1224|28216|80840|80864|219181|1658672;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|1737404|1737405|1570339|543311|713008;2|1239|186801|186802|186807|2740|671215;2|1239|186801|3082720|186804|713019;2|976|200643|171549|171551|836|41976;2|976|200643|171549|171551|836|712438;2|976|200643|171549|171551|836|712439;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|2974257|228603;2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1224|1236|72274|135621|286|294;2|1224|1236|72274|135621|2901164|316;2|1224|1236|72274|135621|286|330;2|1239|91061|1385|90964|1279|29380;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1292;2|1224|1236|135614|32033|40323|40324;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1338;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1314;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1343;2|1224|1236|135625|712|217201|217202;2|203691|203692|136|2845253|157|712731;2|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:713/1/1,Study 713,case-control,31842923,10.1186/s12969-019-0387-5,NA,"Grevich S, Lee P, Leroux B, Ringold S, Darveau R, Henstorf G, Berg J, Kim A, Velan E, Kelly J, Baltuck C, Reeves A, Leahey H, Hager K, Brittnacher M, Hayden H, Miller S, McLean J , Stevens A",Oral health and plaque microbial profile in juvenile idiopathic arthritis,Pediatric rheumatology online journal,2019,"Gingivitis, Juvenile idiopathic arthritis, Microbiota, Oral health",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,healthy controls,Juvenile Idiopathic Arthritis,Juvenile Idiopathic Arthritis,11,85,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,Signature 1,"Figure 2, text",10 November 2022,Tislam,Tislam,c Linear discriminant analysis (LDA) through the LefSe tool. Enriched microbial communities between the two groups with a two log-fold difference or greater are shown in the LEfSe plot. d Bacteria genera found to be significantly different between the polyarticular JIA and healthy control groups.*p-value < 0.05,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae",2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|32066|203490|203491|1129771|32067;2|201174|1760|2037|2049,Complete,Atrayees
bsdb:713/1/2,Study 713,case-control,31842923,10.1186/s12969-019-0387-5,NA,"Grevich S, Lee P, Leroux B, Ringold S, Darveau R, Henstorf G, Berg J, Kim A, Velan E, Kelly J, Baltuck C, Reeves A, Leahey H, Hager K, Brittnacher M, Hayden H, Miller S, McLean J , Stevens A",Oral health and plaque microbial profile in juvenile idiopathic arthritis,Pediatric rheumatology online journal,2019,"Gingivitis, Juvenile idiopathic arthritis, Microbiota, Oral health",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,healthy controls,Juvenile Idiopathic Arthritis,Juvenile Idiopathic Arthritis,11,85,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,Signature 2,"Figure 2, text",10 November 2022,Tislam,"Tislam,Atrayees",c Linear discriminant analysis (LDA) through the LefSe tool. Enriched microbial communities between the two groups with a two log-fold difference or greater are shown in the LEfSe plot. d Bacteria genera found to be significantly different between the polyarticular JIA and healthy control groups.*p-value < 0.05,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella",2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|724|729;2|32066|203490|203491|1129771|32067;2|1224|1236|135625|712|724;2|1224|28216|206351|481|32257,Complete,Atrayees
bsdb:714/1/1,Study 714,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD , Turnbaugh PJ",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Overweight/Obese Men on Baseline Diet (BD),Overweight/Obese Men on Ketogenic Diet (KD),Overweight or class I Obese non-diabetic men who consumed an isocaloric ketogenic diet for 4weeks,17,17,No,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1E,21 November 2022,Fatima,"Fatima,Lwaldron,Joan Chuks","Bacterial taxa identified by DESeq2 as differentially abundant in Overweight/class I Obese non-diabetic Men, who consumed an isocaloric ketogenic diet for 4weeks Versus the same Overweight/class I Obese non-diabetic Men on Baseline Diet for 4weeks.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 1-8,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|1224|1236|91347|543|1940338;2|1239|526524|526525|128827|1573534;2|1239|186801|186802|216572|946234;2|32066|203490|203491|203492|848;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|1392389;2|1239|909932|909929|1843491|158846;2|1239|1980693;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552|838|1486937;2|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:714/1/2,Study 714,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD , Turnbaugh PJ",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Overweight/Obese Men on Baseline Diet (BD),Overweight/Obese Men on Ketogenic Diet (KD),Overweight or class I Obese non-diabetic men who consumed an isocaloric ketogenic diet for 4weeks,17,17,No,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1E,14 March 2024,Joan Chuks,Joan Chuks,"Bacterial taxa identified by DESeq2 as differentially abundant in Overweight/class I Obese non-diabetic Men, who consumed an isocaloric ketogenic diet for 4weeks Versus the same Overweight/class I Obese non-diabetic Men on Baseline Diet for 4weeks.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|1263|41978,Complete,NA
bsdb:714/2/1,Study 714,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD , Turnbaugh PJ",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD),Mice fed on Ketogenic Diet (KD),"Wild-type C57BL/6J mice of both sexes, between age 5 - 10 weeks, fed on ketogenic diet for 3 weeks.",6,6,No,16S,4,Illumina,DESeq2,0.1,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3G + Figure S4F + Figure 5I,17 March 2024,Joan Chuks,Joan Chuks,Bacterial taxa identified by DESeq2 as differentially abundant in Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on Ketogenic Diet(KD) Versus the Mice fed on High-Fat Diet (HFD).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus",2|1239|186801|3085636|186803|1427378;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485|1506;2|201174|84998|1643822|1643826|580024;2|1239|186801|186802;2|1239|186801|186802|1392389;2|200930|68337|191393|2945020|248038;2|1239|526524|526525|128827|1470349,Complete,NA
bsdb:714/2/2,Study 714,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD , Turnbaugh PJ",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD),Mice fed on Ketogenic Diet (KD),"Wild-type C57BL/6J mice of both sexes, between age 5 - 10 weeks, fed on ketogenic diet for 3 weeks.",6,6,No,16S,4,Illumina,DESeq2,0.1,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3G + Figure S4F,17 March 2024,Joan Chuks,Joan Chuks,Bacterial taxa identified by DESeq2 as differentially abundant in Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on Ketogenic Diet(KD) Versus Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on High-Fat Diet (HFD).,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|1937008;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|248744;2|976|200643|171549|2005473;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|877420,Complete,NA
bsdb:714/3/1,Study 714,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD , Turnbaugh PJ",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD-control),Mice fed High-fat Diet + Ketone Ester (HFD-KE),"C57BL/6J mice fed on High-fat diet that was supplemented with a synthetic Ketone ester(KE), beta-hydroxybutyrate(bHB).",NA,NA,No,16S,4,Illumina,DESeq2,0.05,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5I + Figure 5M,19 March 2024,Joan Chuks,Joan Chuks,"Bacterial taxa identified by DESeq2 as differentially abundant in C57BL/6J mice fed on High-fat diet supplemented with Ketone ester(KE), beta-hydroxybutyrate(bHB) Versus Mice fed on only High-Fat Diet (HFD).",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803|1427378;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:714/3/2,Study 714,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD , Turnbaugh PJ",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD-control),Mice fed High-fat Diet + Ketone Ester (HFD-KE),"C57BL/6J mice fed on High-fat diet that was supplemented with a synthetic Ketone ester(KE), beta-hydroxybutyrate(bHB).",NA,NA,No,16S,4,Illumina,DESeq2,0.05,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5M,19 March 2024,Joan Chuks,Joan Chuks,"Bacterial taxa identified by DESeq2 as differentially abundant in C57BL/6J mice fed on High-fat diet supplemented with Ketone ester(KE), beta-hydroxybutyrate(bHB) Versus Mice fed on only High-Fat Diet (HFD).",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303,Complete,NA
bsdb:715/1/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 1,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory distress syndrome,EFO:1000637,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,"patients stratified on the basis of 30-day mortality [survivors vs. non-survivors], for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,2 March 2024,Folakunmi,Folakunmi,Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:715/2/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 2,United States of America,Homo sapiens,Epithelium of oropharynx,UBERON:0001952,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),"Clinical outcome stratification by numbers of ventilator-free days (VFDs) at 30 days in patients for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,20 June 2023,Atrayees,"Atrayees,Folakunmi",Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174|1760|85006|1268|32207;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712,Complete,Folakunmi
bsdb:715/2/2,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 2,United States of America,Homo sapiens,Epithelium of oropharynx,UBERON:0001952,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),"Clinical outcome stratification by numbers of ventilator-free days (VFDs) at 30 days in patients for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary figure E8,20 June 2023,Atrayees,"Atrayees,Folakunmi",Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:715/3/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 3,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,participants  were classified into a hyperinflammatory subphenotype of host responses associated with worse outcomes in the pathogen-enriched cluster,112,51,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,Folakunmi,The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|32066|203490|203491|203492|848;2|1224|1236|91347|543;2|1224|1236|72274|135621;2|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:715/4/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 4,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,participants  were classified into a hyperinflammatory subphenotype of host responses associated with worse outcomes in the pathogen-enriched cluster,96,51,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,Folakunmi,The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:715/5/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 5,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,patients stratified on the basis of 30-day mortality [survivors vs. non-survivors],92,55,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,Folakunmi,The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482,Complete,Folakunmi
bsdb:715/6/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 6,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,patients stratified on the basis of 30-day mortality [survivors vs. non-survivors],111,52,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",2|201174|1760|85007|1653|1716;2|1239|186801|186802|186806,Complete,Folakunmi
bsdb:715/6/2,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 6,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,patients stratified on the basis of 30-day mortality [survivors vs. non-survivors],111,52,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|976|200643|171549|171552|838;2|1224|1236|135625|712|724,Complete,Folakunmi
bsdb:715/7/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 7,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),clinical outcome stratifications by the number of days patients were ventilator-free,103,60,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:715/7/2,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 7,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),clinical outcome stratifications by the number of days patients were ventilator-free,103,60,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|135625|712|724;2|201174|1760|85006|1268|32207;2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:715/8/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 8,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),clinical outcome stratifications by the number of days patients were ventilator-free,106,41,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,Folakunmi,The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes in oral swab samples genera,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712,Complete,Folakunmi
bsdb:715/9/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 9,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,"patients stratified on the basis of 30-day mortality [survivors vs. non-survivors] , for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,30 days,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,2 March 2024,Folakunmi,Folakunmi,"Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive
respiratory cultures.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:715/10/1,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 10,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),"clinical outcome stratifications by the number of days patients were ventilator-free for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,2 March 2024,Folakunmi,Folakunmi,Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|135625|712|724;2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:715/11/NA,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 11,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,"participants who were classified into a hyperinflammatory subphenotype of host responses, for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:715/12/NA,Study 715,prospective cohort,32717152,10.1164/rccm.201912-2441OC,https://pubmed.ncbi.nlm.nih.gov/32717152/,"Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A , McVerry BJ",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 12,United States of America,Homo sapiens,Epithelium of oropharynx,UBERON:0001952,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,"participants who were classified into a hyperinflammatory subphenotype of host responses, for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,none,16S,34,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:716/1/1,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's disease,"Patient diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",45,75,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,1 February 2023,Jacquelynshevin,Jacquelynshevin,Specific microbial differences in taxa between PD and control in LEFSe and its adjusted P values.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",2|1239|91061|186826|186827;2|201174|1760|85004|31953;2|200940|3031449|213115|194924;2|1239|186801|186802|186806,Complete,Fatima
bsdb:716/1/2,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's disease,"Patient diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",45,75,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,1 February 2023,Jacquelynshevin,"Jacquelynshevin,Aleru002",Specific microbial differences in taxa between PD and control in LEFSe and its adjusted P values.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|201174|1760|2037|2049;2|1239;2|201174|1760|85006|85019;2|1224|28211|356|118882;2|1224|28216|80840|80864;2157|28890;2|1239|91061|1385|539738;2|1224|1236|135619|28256;2|1224|28211|2800060|69657;2|1224|1236|135622|267893;2|201174|1760|85006|85021;2|1239|186801|3085636|186803;2157|28890|183925|2158|2159;2|1224|28211|356|119045;2|201174|1760|85006|1268;2|544448;2|1224|1236|135625|712;2|1224|28211|204457|41297;2|1239|91061|186826|1300;2|1224|1236|135614|32033,Complete,Fatima
bsdb:716/2/1,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD duration less than 5 years,PD duration more than 5 years,"Patients with PD were classified into two groups according to disease duration: at least five years and less than five years.. Patients with PD were diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",44,30,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,9 February 2023,Jacquelynshevin,Jacquelynshevin,Taxa identified as significant difference between clinical phenotypes.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1224|1236|135625|712|416916;2|200930|68337|191393|191394;2|200930|68337|191393|2945020|248038;2|976|200643|171549|171550,Complete,Fatima
bsdb:716/2/2,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD duration less than 5 years,PD duration more than 5 years,"Patients with PD were classified into two groups according to disease duration: at least five years and less than five years.. Patients with PD were diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",44,30,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,9 February 2023,Jacquelynshevin,Jacquelynshevin,Taxa identified as significant difference between clinical phenotypes.,decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,2|1224|28211|356|69277|28100,Complete,Fatima
bsdb:716/3/1,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Late-onset PD,Early-onset PD,Parkinson's disease patient with age of onset less than 50.,51,23,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,9 February 2023,Jacquelynshevin,Jacquelynshevin,Taxa identified as significant difference between clinical phenotypes.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|28216|80840|506;2|1239|91061|186826|186827|66831;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1357;2|1224|28216|80840|995019|40544;2|1224|1236|135625|712;2|1239|186801|186802|31979|1485,Complete,Fatima
bsdb:716/3/2,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Late-onset PD,Early-onset PD,Parkinson's disease patient with age of onset less than 50.,51,23,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,9 February 2023,Jacquelynshevin,Jacquelynshevin,Taxa identified as significant difference between clinical phenotypes.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",2|1239|186801|186802|216572|244127;2|1224|28216|80840|80864|283,Complete,Fatima
bsdb:716/4/1,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Non-tremor dominant PD,Tremor dominant PD,Parkinson's disease patient with tremor dominant motor symptoms.,56,18,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,9 February 2023,Jacquelynshevin,Jacquelynshevin,Taxa identified as significant difference between clinical phenotypes.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|1239|186801|186802|216572|244127;2|32066|203490|203491|1129771,Complete,Fatima
bsdb:716/4/2,Study 716,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H , Xie H",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Non-tremor dominant PD,Tremor dominant PD,Parkinson's disease patient with tremor dominant motor symptoms.,56,18,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,9 February 2023,Jacquelynshevin,Jacquelynshevin,Taxa identified as significant difference between clinical phenotypes.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,2|1239|186801|3085636|186803|841,Complete,Fatima
bsdb:717/1/1,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at baseline,Participants with Parkinson's Disease at baseline,Patients with Parkinson's disease at baseline.,64,64,None.,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Baseline",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",2|976|200643|171549|171550|239759;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3082720|186804|1501226,Complete,ChiomaBlessing
bsdb:717/1/2,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at baseline,Participants with Parkinson's Disease at baseline,Patients with Parkinson's disease at baseline.,64,64,None.,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Baseline",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1239|186801|3085636|186803|572511;2|976|200643|171549|1853231|574697;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|39948,Complete,ChiomaBlessing
bsdb:717/2/1,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at follow up,Progressed PD patients at follow up,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,None,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 9: Follow up.,2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing",Summary of differential abundance results contrasting follow-up progressed and stable PD patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|201174|1760|85004|31953|1678;2|544448|31969|186332|186333;2|544448|31969|186332|186333|2152;2|1239|186801|3085636|186803;2|1239|186801|186802,Complete,ChiomaBlessing
bsdb:717/2/2,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at follow up,Progressed PD patients at follow up,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,None,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 9: Follow-up,10 January 2024,ChiomaBlessing,ChiomaBlessing,Summary of differential abundance results contrasting follow-up progressed and stable PD patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|33042;2|200940|3031449|213115|194924|872,Complete,ChiomaBlessing
bsdb:717/3/1,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at time of follow-up,Participants with Parkinson's Disease at time of follow-up,Participants with Parkinson's Disease at time of follow-up,64,64,None.,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3082720|186804|1501226,Complete,ChiomaBlessing
bsdb:717/3/2,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at time of follow-up,Participants with Parkinson's Disease at time of follow-up,Participants with Parkinson's Disease at time of follow-up,64,64,None.,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|74201|414999|415001|415002;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|976|200643|171549|171551;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977,Complete,ChiomaBlessing
bsdb:717/4/1,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at baseline,Postural instability and gait difficulty (PIGD) phenotype at baseline,Parkinson's disease patients with PIGD phenotype at baseline.,21,28,none,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,MyleeeA",Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at baseline.,decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|544448|31969|186332|186333;2|544448|31969|186332|186333|2152;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|1432051;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|91061|186826|1300|1357;2|976|200643|171549|171552|838;2|28221;2|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:717/4/2,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at baseline,Postural instability and gait difficulty (PIGD) phenotype at baseline,Parkinson's disease patients with PIGD phenotype at baseline.,21,28,none,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at baseline.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|830;2|1239|186801|186802|204475;2|1239|909932|1843488|909930;2|1239|186801|3085636|186803;2|1239|186801|186802;2,Complete,ChiomaBlessing
bsdb:717/5/1,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at follow-up,Postural instability and gait difficulty (PIGD) phenotype at follow-up,Parkinson's disease patients with PIGD phenotype at follow-up,20,35,none,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,"Folakunmi,Peace Sandy,Hodan Issah,ChiomaBlessing",Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at follow-up,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia",2|976|200643|171549|2005519|397864;2|1239|91061|186826|1300|1357;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|976|200643|171549|171551;2|544448|31969|186332|186333;2|544448|31969|186332|186333|2152;2|1239|186801|186802;2|1239|186801,Complete,ChiomaBlessing
bsdb:717/5/2,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at follow-up,Postural instability and gait difficulty (PIGD) phenotype at follow-up,Parkinson's disease patients with PIGD phenotype at follow-up,20,35,none,16S,34,Illumina,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,Folakunmi,Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group),increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:717/6/1,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at baseline,Progressed PD patients at baseline,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,None,16S,34,Illumina,DESeq2,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 9: Baseline,11 January 2024,ChiomaBlessing,ChiomaBlessing,Summary of differential abundance results contrasting follow-up progressed and stable PD patients,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:717/6/2,Study 717,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho VTE, Pereira PAB, Voutilainen S, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at baseline,Progressed PD patients at baseline,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,None,16S,34,Illumina,DESeq2,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 9: Baseline,11 January 2024,ChiomaBlessing,ChiomaBlessing,Summary of differential abundance results contrasting follow-up progressed and stable PD patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|33042;2|200940|3031449|213115|194924|872,Complete,ChiomaBlessing
bsdb:718/1/1,Study 718,"laboratory experiment,time series / longitudinal observational",26731268,https://doi.org/10.1371/journal.pone.0146509,https://pubmed.ncbi.nlm.nih.gov/26731268/,"Kelley ST, Skarra DV, Rivera AJ , Thackray VG",The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome,PloS one,2016,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Placebo-treated,Letrozole-treated,"At 4 weeks of age, the mice were implanted subcutaneously with a 3 mg letrozole pellet (Innovative Research of America, Sarasota, FL) that provided a constant, slow release of letrozole (50 μg/day) (n = 10/group).",10,10,N/A,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,S2 Fig,5 December 2022,Testuser,"Testuser,Tolulopeo,Peace Sandy",Letrozole treatment results in significant changes in 48 bacterial OTUs as assessed by Kruskal-Wallis test.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|526524|526525|128827|174708;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:718/1/2,Study 718,"laboratory experiment,time series / longitudinal observational",26731268,https://doi.org/10.1371/journal.pone.0146509,https://pubmed.ncbi.nlm.nih.gov/26731268/,"Kelley ST, Skarra DV, Rivera AJ , Thackray VG",The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome,PloS one,2016,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Placebo-treated,Letrozole-treated,"At 4 weeks of age, the mice were implanted subcutaneously with a 3 mg letrozole pellet (Innovative Research of America, Sarasota, FL) that provided a constant, slow release of letrozole (50 μg/day) (n = 10/group).",10,10,N/A,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,S2 Fig,5 December 2022,Testuser,"Testuser,Peace Sandy",Letrozole treatment results in significant changes in 48 bacterial OTUs as assessed by Kruskal-Wallis test.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",2|976|200643|171549|2005473;2|976|200643|171549|171550|239759;2|1239|186801|186802|186807|51514;2|976|200643|171549|2005525|375288|823,Complete,NA
bsdb:719/1/1,Study 719,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B , Wilmes P",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 1,Germany,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results of the differential analysis of the nasal microbiota,11 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae",2|1239|91061|186826|186828;2|1224|2008785|119069|206349;2|1224|28211|356|45401,Complete,Fatima
bsdb:719/1/2,Study 719,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B , Wilmes P",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 1,Germany,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Results of the differential analysis of the nasal microbiota,11 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae",2|1239|91061|1385|186817;2|1239|91061|1385;2|200940|3031449|213115|194924;2|1239|91061|1385|186820;2|201174|1760|85006|1268;2|1239|186801|186802|216572;2|1224|28216|80840|75682,Complete,Fatima
bsdb:719/2/1,Study 719,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B , Wilmes P",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 2,Germany,Homo sapiens,Nasal cavity,UBERON:0001707,REM sleep behavior disorder,EFO:0007462,Healthy Controls,idiopathic rapid eye movement sleep behavior disorder,Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).,78,21,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results of the differential analysis of the nasal microbiota,11 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae",2|1239|91061|1385;2|200940|3031449|213115|194924;2|1224|28216|80840|75682,Complete,Fatima
bsdb:719/3/1,Study 719,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B , Wilmes P",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 1,Summarized results of the differential and regression analyses of the gut microbiota,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572|244127;2;2|976|200643;2|201174|1760|85004|31953;2|1239|526524|526525|128827;2|1239|186801|186802;2|1239|186801|186802|216572|946234;2|32066|203490|203491|203492;2|1239|186801|3085636|186803;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1535;2|1239|186801|3085636|186803|572511|1532,Complete,Fatima
bsdb:719/3/2,Study 719,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B , Wilmes P",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 2,Summarized results of the differential and regression analyses of the gut microbiota,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacteria|p__Bacillota,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239;2;2|976|200643|171549|815|816;2|976|200643|171549|1853231|574697;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|1578;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572;2|976|200643|171549|171552;2|1224;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544,Complete,Fatima
bsdb:719/4/1,Study 719,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B , Wilmes P",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,Healthy Controls,idiopathic rapid eye movement sleep behavior disorder,Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).,78,21,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 1,Summarized results of the differential and regression analyses of the gut microbiota:,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides",2|1239|186801|186802|216572|244127;2|1239|526524|526525|128827;2|1239|186801|186802|216572|946234;2|201174|84998|1643822|1643826|644652;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511|1532,Complete,Fatima
bsdb:719/4/2,Study 719,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B , Wilmes P",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,Healthy Controls,idiopathic rapid eye movement sleep behavior disorder,Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).,78,21,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 2,Summarized results of the differential and regression analyses of the gut microbiota,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera",2|1239|909932|1843488|909930;2|1239;2;2|976|200643|171549|815|816;2|976|200643;2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572;2|1224|1236|135625|712;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1224|28216|80840|995019|40544;2157|28890|183925|2158|2159|2316,Complete,NA
bsdb:720/1/1,Study 720,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C, Foschi C, Parolin C, D'Antuono A, Gaspari V, Consolandi C, Laghi L, Camboni T, Vitali B, Severgnini M , Marangoni A",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 1,Italy,Homo sapiens,Vagina,UBERON:0000996,Chlamydia trachomatis infectious disease,EFO:0007205,Healthy Controls,Chlamydia trachomatis,‘Chlamydia’ (CT) (detection of C. trachomatis DNA by Versant CT/GC DNA 1.0 Assay),21,20,n/a,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1",Differential microbial abundance between controls and chlamydia subjects,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|201174|1760|85004|31953|419014;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572;2|1239|186801|3085636|186803|841;2|32066|203490|203491|1129771|168808;2|1239|91061|186826|1300|1301;2|544448|2790996|2790998|2129;2|1239|909932|1843489|31977;2|201174|84998|84999|84107;2|1239|186801|3085636|186803;2|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:720/2/1,Study 720,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C, Foschi C, Parolin C, D'Antuono A, Gaspari V, Consolandi C, Laghi L, Camboni T, Vitali B, Severgnini M , Marangoni A",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 2,Italy,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis,vulvovaginal candidiasis (VVC),21,18,n/a,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1",Differential microbial abundance between controls and vulvovaginal candidiasis subjects,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:720/2/2,Study 720,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C, Foschi C, Parolin C, D'Antuono A, Gaspari V, Consolandi C, Laghi L, Camboni T, Vitali B, Severgnini M , Marangoni A",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 2,Italy,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis,vulvovaginal candidiasis (VVC),21,18,n/a,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1",Differential microbial abundance between controls and vulvovaginal candidiasis subjects,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|201174|1760|2037|2049;2|201174;2|201174|1760|85004|31953|419014;2|201174|84998|84999|1643824|1380;2|976|200643;2|201174|1760|85004|31953;2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|216851;2|1239|1737404|1737405|1570339|150022;2|201174|1760|85004|31953|2701;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1737406;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1224|1236|135614|32033|338;2|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:720/3/1,Study 720,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C, Foschi C, Parolin C, D'Antuono A, Gaspari V, Consolandi C, Laghi L, Camboni T, Vitali B, Severgnini M , Marangoni A",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 3,Italy,Homo sapiens,Vagina,UBERON:0000996,Bacterial vaginosis,EFO:0003932,Healthy Controls,bacterial vaginosis,bacterial vaginosis (BV),21,20,n/a,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,unchanged,Signature 1,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1",Differential microbial abundance between controls and bacterial vaginosis subjects,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:720/3/2,Study 720,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C, Foschi C, Parolin C, D'Antuono A, Gaspari V, Consolandi C, Laghi L, Camboni T, Vitali B, Severgnini M , Marangoni A",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 3,Italy,Homo sapiens,Vagina,UBERON:0000996,Bacterial vaginosis,EFO:0003932,Healthy Controls,bacterial vaginosis,bacterial vaginosis (BV),21,20,n/a,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,unchanged,Signature 2,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1",Differential microbial abundance between controls and bacterial vaginosis subjects,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Caryophyllales|f__Cactaceae|s__Cactoideae|g__Rebutia|s__Rebutia arenacea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Eukaryota|k__Metazoa|p__Platyhelminthes|c__Rhabditophora|o__Rhabdocoela|f__Typhloplanidae,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|201174|1760|2037|2049;2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107;2|1239|909932|1843489|31977|39948;2|201174|1760|85004|31953|2701;2|1239|91061|1385|539738|1378;2|1239|186801|3085636|186803;2|32066|203490|203491|1129771;2|1239|909932|1843489|31977|906;2|201174|1760|2037|2049|2050;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2759|33090|35493|3398|3524|3593|186265|432459|1001126;2|1239|186801|3085636|186803|841;2|32066|203490|203491|1129771|168808;2|1239|1737404|1737405|1737406;2759|33208|6157|147100|27901|27902;2|544448|2790996|2790998|2129;2|1239|909932|1843489|31977;2|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:721/1/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 6 weeks,HIV-exposed uninfected infants (HEU) at 6 weeks,In utero-HIV exposed uninfected infants (HEU) at 6 weeks,78,76,"Infants that did not pass the sequence quality control, those on antibiotics, and HEU infants on Bactrim after 6 weeks of birth.",16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2d,9 March 2023,BLESSING123,BLESSING123,Genera with significantly different relative abundances between HEU and HUU at 6-weeks.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|2005519|397864;2|1239|186801|3085636|186803|572511;2|201174|84998|1643822|1643826|84111;2|976|200643|171549|1853231|283168;2|32066|203490|203491|1129771|168808;2|1239;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:721/1/2,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 6 weeks,HIV-exposed uninfected infants (HEU) at 6 weeks,In utero-HIV exposed uninfected infants (HEU) at 6 weeks,78,76,"Infants that did not pass the sequence quality control, those on antibiotics, and HEU infants on Bactrim after 6 weeks of birth.",16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2d,9 March 2023,BLESSING123,BLESSING123,Genera with significantly different relative abundances between HEU and HUU at 6-weeks.,decreased,"k__Bacteria|p__Candidatus Saccharibacteria|s__Candidatus Saccharibacteria genomosp. TM7-H1,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota",2|95818|2080739;2|1239|526524|526525|2810280|135858;2|1224|1236|91347|543|547;2|1239|909932|909929|1843491|158846;2|976,Complete,Atrayees
bsdb:721/2/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 28 weeks,HIV-exposed uninfected infants (HEU) at 28 weeks,In utero-HIV exposed uninfected infants (HEU),74,71,Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2d,9 March 2023,BLESSING123,BLESSING123,Genera with significantly different relative abundances between HEU and HUU at 28-weeks.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium|s__Candidatus Epulonipiscium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3085636|186803|2383|2384;2|1224|1236|91347|543|570;2|1239|91061|186826|1300|1357;2|1239|909932|909929|1843491|158846;2|1224|28216|80840|995019|577310;2|1239|186801|186802,Complete,Atrayees
bsdb:721/2/2,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 28 weeks,HIV-exposed uninfected infants (HEU) at 28 weeks,In utero-HIV exposed uninfected infants (HEU),74,71,Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2d,9 March 2023,BLESSING123,BLESSING123,Genera with significantly different relative abundances between HEU and HUU at 28-weeks.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|2701;2|1239|91061|1385|539738|1378;2|201174|1760|2037|2049|2050;2|1239|1737404|1737405|1570339|543311;2|32066|203490|203491|1129771|168808,Complete,Atrayees
bsdb:721/3/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 62 weeks,HIV-exposed uninfected infants (HEU) at 62 weeks,In utero-HIV exposed uninfected infants (HEU) at 62 weeks,70,61,Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 62 weeks of birth were excluded,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2d,9 March 2023,BLESSING123,BLESSING123,Genera with significantly different relative abundances between HEU and HUU at the indicated time points (FDR P < 0.05). 62 weeks,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1224|1236|91347|1903414|583;2|201174|84998|84999|84107,Complete,Atrayees
bsdb:721/4/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at delivery,HIV-infected mothers at delivery,Mothers infected with HIV at delivery time point,110,119,Mothers on antibiotics as at the time of delivery,16S,34,Illumina,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3F,10 March 2023,BLESSING123,"BLESSING123,Folakunmi",Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). Delivery,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|909932|1843488|909930|904;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|815|816;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|201174|1760|85007|1653|1716;2|1239|186801|186802|216572|946234;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1224|1236|91347|543|570;2|544448|31969|2085|2092|2093;2|1239|91061|1385|90964|1279;2|1224|28216|80840|995019|40544;2|1239|91061;2|1224|28216|80840;2|201174|1760|85007|1653;2|1239|526524|526525|128827;2|32066|203490|203491;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804,Complete,Atrayees
bsdb:721/4/2,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at delivery,HIV-infected mothers at delivery,Mothers infected with HIV at delivery time point,110,119,Mothers on antibiotics as at the time of delivery,16S,34,Illumina,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3F,13 March 2023,BLESSING123,BLESSING123,Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). Delivery,decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis",2|544448|31969|186332|186333|2152;2|74152|641853|641854|641876|423604;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|186801|186802|539000,Complete,Atrayees
bsdb:721/5/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 5,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at 62 weeks,HIV-infected  mothers at 62 weeks,Mothers infected with HIV at 62 weeks time point,65,71,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3F,13 March 2023,BLESSING123,"BLESSING123,Folakunmi",Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). 62 weeks,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",2|1239|909932|1843488|909930|904;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|909932|909929|1843491|158846;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|292632;2|1224|28211|204441|2844866|168934;2|508458|649775|649776|649777;2|1239|526524|526525|128827|61170,Complete,Folakunmi
bsdb:721/5/2,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 5,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at 62 weeks,HIV-infected  mothers at 62 weeks,Mothers infected with HIV at 62 weeks time point,65,71,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3F,13 March 2023,BLESSING123,BLESSING123,Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). 62 weeks,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|1236|2887326|468|469;2|74152|641853|641854|641876|423604;2|1239|91061|1385|539738|1378;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279;2|1239|909932|1843489|31977|29465;2|201174|1760|85007|1653;2|1239|909932|1843489|31977,Complete,Folakunmi
bsdb:721/6/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 6,South Africa,Homo sapiens,Milk,UBERON:0001913,HIV mother to child transmission,EFO:0004595,Healthy controls,HIV-infected mothers,Mothers infected with HIV,76,88,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4F,13 March 2023,BLESSING123,BLESSING123,Genera with significantly different abundances in mothers with and without HIV (FDR P < 0.05).,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,2|1239|186801|3082720|186804,Complete,Folakunmi
bsdb:721/6/2,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 6,South Africa,Homo sapiens,Milk,UBERON:0001913,HIV mother to child transmission,EFO:0004595,Healthy controls,HIV-infected mothers,Mothers infected with HIV,76,88,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4F,13 March 2023,BLESSING123,BLESSING123,Genera with significantly different abundances in mothers with and without HIV (FDR P < 0.05).,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1239|1737404|1737405|1570339|165779;2|201174|1760|85006|1268|1663;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|186817|1386;2|201174|1760|1643682|85030|38501;2|201174|1760|85006|85019|1696;2|976|117743|200644|2762318|59732;2|201174|1760|85007|1653|1716;2|1239|91061|186826|81852|1350;2|1239|91061|1385|33986;2|1239|186801|186802|216572|216851;2|1239|1737404|1737405|1570339|150022;2|201174|1760|85004|31953|2701;2|1224|28216|80840|75682|963;2|976|768503|768507|1853232|89966;2|1239|91061|186826|1300|1357;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045|407;2|201174|1760|85006|1268|1269;2|1224|28211|356|119045|186650;2|1224|1236|2887326|468|475;2|1224|28216|206351|481|482;2|201174|1760|85009|85015|1839;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171552|838;2|201174|1760|85009|31957|1743;2|1239|186801|3085636|186803|46205;2|201174|1760|85010|2070|1847;2|1224|28211|204455|2854170|295418;2|201174|84995|84996|84997|42255;2|1239|91061|1385|90964|1279;2|201174|84992|84993;2|1239|91061|1385;2|1239|91061|186826|186828;2|976|1853228|1853229|563835;2|201174|1760|85007;2|1224|1236|91347|543;2|201174|1760|1643682|85030;2|1239|186801|3085636|186803;2|1239|91061|186826;2|201174|1760|85006|85023;2|201174|1760|85008|28056;2|1224|28216|206351|481;2|201174|1760|85007|85025;2|1239|186801|186802|216572;2|1224|28216|80840|75682;2|1224|28211|204457;2|1224|1236|135614|32033,Complete,Folakunmi
bsdb:721/7/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 7,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Exclusively breastfed In utero-HIV exposed uninfected infants (HEU) at 28 weeks,40,52,Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2e,9 February 2024,Folakunmi,Folakunmi,Genera with significantly different relative abundances between HEU and HUU exclusively (Excl.) breastfed at 28 weeks of life,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,2|1239|186801|3085636|186803|2383,Complete,Folakunmi
bsdb:721/7/2,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 7,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Exclusively breastfed In utero-HIV exposed uninfected infants (HEU) at 28 weeks,40,52,Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2e,9 February 2024,Folakunmi,Folakunmi,Genera with significantly different relative abundances between HEU and HUU exclusively (Excl.) breastfed at 28 weeks of life,decreased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,2|32066|203490|203491|1129771|168808,Complete,Folakunmi
bsdb:721/8/1,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 8,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Not exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Not exclusively breastfed (formula feeding) In utero-HIV exposed uninfected infants (HEU) at 28 weeks,9,19,Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2e,9 February 2024,Folakunmi,Folakunmi,Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of lif,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella",2|1239|186801|3085636|186803|2383;2|1224|1236|91347|543|570;2|1224|1236|135625|712|745,Complete,Folakunmi
bsdb:721/8/2,Study 721,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D , Weinberg A",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 8,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Not exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Not exclusively breastfed (formula feeding) In utero-HIV exposed uninfected infants (HEU) at 28 weeks,9,19,Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 2e,9 February 2024,Folakunmi,Folakunmi,Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of life,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|201174|1760|85004|31953|2701;2|201174|1760|2037|2049|2050;2|976|200643|171549|171550|239759;2|1239|526524|526525|2810280|135858;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|1239|526524|526525|128827|123375;2|32066|203490|203491|1129771|168808,Complete,Folakunmi
bsdb:722/1/1,Study 722,case-control,31200089,10.1016/j.neulet.2019.134297,https://pubmed.ncbi.nlm.nih.gov/31200089/,"Li F, Wang P, Chen Z, Sui X, Xie X , Zhang J",Alteration of the fecal microbiota in North-Eastern Han Chinese population with sporadic Parkinson's disease,Neuroscience letters,2019,"16S rRNA gene, Gut microbiome, Microbiota–gut–brain axis, Parkinson’s disease, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with sporadic PD and over 65 age.,10,10,One month.,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2023,Jacquelynshevin,"Jacquelynshevin,Chloe","The histogram of the LDA scores presents species whose abundance
showed significant differences between the heathy controls and PD patients in
the fecal samples. The length of each bin, namely, the LDA score. A p-value
of < 0.05 and a score ≥ 2.0 were considered significant in KW rank sum test
and Wilcox tests, respectively. The horizontal straight line in the panel indicated the group means, and the dotted line indicated the group medians.",increased,"k__Bacteria,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota",2;2|74201|203494|48461|1647988|239934;2|976|200643|171549|1853231|574697;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802|186806|1730|39496;2|1239|526524|526525|128827|61170;2|1239|186801|186802|216572|596767;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572;2|1224|28216|80840|995019|577310;2|976|200643|171549|171551;2|1239|186801|186802|216572|292632;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201,Complete,Atrayees
bsdb:722/1/2,Study 722,case-control,31200089,10.1016/j.neulet.2019.134297,https://pubmed.ncbi.nlm.nih.gov/31200089/,"Li F, Wang P, Chen Z, Sui X, Xie X , Zhang J",Alteration of the fecal microbiota in North-Eastern Han Chinese population with sporadic Parkinson's disease,Neuroscience letters,2019,"16S rRNA gene, Gut microbiome, Microbiota–gut–brain axis, Parkinson’s disease, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with sporadic PD and over 65 age.,10,10,One month.,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,4 May 2023,Jacquelynshevin,"Jacquelynshevin,Chloe,WikiWorks","The histogram of the LDA scores presents species whose abundance showed significant differences between the heathy controls and PD patients in the fecal samples. The length of each bin, namely, the LDA score. A p-value of < 0.05 and a score ≥ 2.0 were considered significant in KW rank sum test and Wilcox tests, respectively. The horizontal straight line in the panel indicated the group means, and the dotted line indicated the group medians.",decreased,"k__Bacteria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2;2|1239|909932|1843489|31977|209879;2|976|200643|171549;2|976|200643|171549|815|816;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|526524|526525|128827|1573535;2|1239|91061|186826|33958;2|976|200643|171549|171552;2|1239|186801|3085636|186803|1506577,Complete,Atrayees
bsdb:723/1/1,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that either referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group) or reported stability of body weight from the diagnosis to the time of evaluation (NWL group).",8,20,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1,9 May 2023,Jacquelynshevin,Jacquelynshevin,"The most differentially enriched taxa in Parkinson’s disease patients (PARK) and CTRL groups. Computed Linear discriminant analysis (LDA) scores of the taxa relative
abundance difference between the PARK and CTRL groups at phylum (A)
and genus (B) levels. Positive LDA scores (green) are enriched in PARK
group, while negative LDA scores (red) are enriched in CTRL.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota",2|1224|28216|80840|75682;2|1224,Complete,Folakunmi
bsdb:723/1/2,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that either referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group) or reported stability of body weight from the diagnosis to the time of evaluation (NWL group).",8,20,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1,9 May 2023,Jacquelynshevin,"Jacquelynshevin,Folakunmi","Figure 1. The most differentially enriched taxa in Parkinson’s disease
patients (PARK) and CTRL groups. Computed Linear discriminant analysis
(LDA) scores of the taxa relative abundance difference between the
PARK and CTRL groups at phylum (A) and genus (B) levels. Positive LDA
scores (green) are enriched in PARK group, while negative LDA scores (red)
are enriched in CTRL.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678|1694;2|1239|186801|186802|31979;2|1239|186801|186802|2937910|1562;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803;2|1239|91061|1385|186818;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|91061|1385|90964;2|1239|1737404|1737405|1737406;2|976|200643|171549|171552|577309,Complete,Folakunmi
bsdb:723/2/1,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls and Idiopathic Parkinson's Disease Patients with Weight Loss,Idiopathic Parkinson's Disease Patients without Weight Loss,Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).,18,10,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,9 May 2023,Jacquelynshevin,Jacquelynshevin,"The most differentially enriched taxa in non weight loss, weight loss and CTRL groups. Computed LDA scores of the relative abundance difference between the three groups. Positive LDA scores (red) are enriched in NWL group.",increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Folakunmi
bsdb:723/3/1,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",8,10,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4A,9 May 2023,Jacquelynshevin,"Jacquelynshevin,Folakunmi",The most differentially enriched taxa in the CTRL versus weight loss comparison.,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|200940|3031449|213115|194924|35832;2|200940|3031449|213115|194924;2|976|200643|171549|1853231|283168;2|1224|28216|80840|75682;2|976|200643|171549|171552|577309,Complete,Folakunmi
bsdb:723/3/2,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",8,10,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4A,9 May 2023,Jacquelynshevin,Jacquelynshevin,The most differentially enriched taxa in the CTRL versus weight loss comparison.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae",2|1239|186801|3082720|3030910|109326;2|201174|1760|85004|31953|1678|1694;2|1239|91061|186826|186828|117563;2|201174|1760|2037|2049|1654;2|976|200643|171549|171552;2|201174|84998|84999|1643824|1380;2|1239|1737404|1737405|1570339|165779;2|1239|91061|1385|186818,Complete,Folakunmi
bsdb:723/4/1,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients without Weight Loss,Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).,8,10,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4B,9 May 2023,Jacquelynshevin,Jacquelynshevin,The most differentially enriched taxa in the CTRL versus NWL comparison.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium",2|1224|1236|91347|543;2|201174|84998|1643822|1643826|84111|84112;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803|2383,Complete,Folakunmi
bsdb:723/4/2,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients without Weight Loss,Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).,8,10,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4B,9 May 2023,Jacquelynshevin,"Jacquelynshevin,Folakunmi",The most differentially enriched taxa in the CTRL versus NWL comparison.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186807|51514;2|1239|186801|3082720|186804|2743582|89152;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|301302;2|1239|186801|186802|216572|1263|1265;2|1239|91061|1385|90964|1279|1280;2|1239|186801|3085636|186803;2|976|200643|171549|171552|577309,Complete,Folakunmi
bsdb:723/5/1,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Idiopathic Parkinson's Disease Patients without Weight Loss,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",10,10,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex,time from diagnosis",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4C,9 May 2023,Jacquelynshevin,Jacquelynshevin,The most differentially enriched taxa in the NWL versus weight loss comparison.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3082768|990719;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|31979;2|1239|186801|186802|186807;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|216572;2|201174|84998|84999|84107|102106;2|200940|3031449|213115|194924;2|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:723/5/2,Study 723,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F, Grassini P, Quagliariello A, Torti M, Russo A, Reddel S , Stocchi F",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Idiopathic Parkinson's Disease Patients without Weight Loss,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",10,10,2 months.,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex,time from diagnosis",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4C,9 May 2023,Jacquelynshevin,Jacquelynshevin,The most differentially enriched taxa in the NWL versus weight loss comparison.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|91061|186826|1300;2|1224|1236|91347|543|561|562;2|1239|91061|186826|81852|1350;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|216572|216851|853;2|1239|91061|186826|81852|1350|44008;2|1224|1236|91347|543,Complete,Folakunmi
bsdb:724/1/1,Study 724,case-control,32161568,10.3389/fneur.2020.00137,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052381/,"Ren T, Gao Y, Qiu Y, Jiang S, Zhang Q, Zhang J, Wang L, Zhang Y, Wang L , Nie K",Gut Microbiota Altered in Mild Cognitive Impairment Compared With Normal Cognition in Sporadic Parkinson's Disease,Frontiers in neurology,2020,"Parkinson's disease, cognition impairment, gut micro biome, high throughput sequencing, short fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses and Parkinson's disease patients with mild cognitive impairment,Parkinson's disease patients with normal cognition,"All patients eligible for this study were diagnosed for PD according to the UK Brain Bank criteria. Cognition abilities were estimated using the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA), and the scores were obtained from two other neuropsychological tests in each of the five cognitive domains.",26,14,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,"age,body mass index,constipation,education level,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S3,20 May 2023,Jacquelynshevin,Jacquelynshevin,"Alteration in the taxa between PD-MCI, PD-NC and healthy groups(LDA)",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",2|1239|186801|186802;2|1239|186801;2|1239|186801|186802|216572;2|976|200643|171549|171551;2|1239|186801|186802|216572|707003;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|572511;2|201174;2|1239|186801|3082768|990719;2|976|200643|171549|2005525|375288|328812;2|1239|186801|186802|216572|1263|40519;2|1239|186801|3085636|186803|572511|33035;2|201174|84998|84999|84107;2|201174|84998;2|201174|84998|84999,Complete,Atrayees
bsdb:724/2/1,Study 724,case-control,32161568,10.3389/fneur.2020.00137,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052381/,"Ren T, Gao Y, Qiu Y, Jiang S, Zhang Q, Zhang J, Wang L, Zhang Y, Wang L , Nie K",Gut Microbiota Altered in Mild Cognitive Impairment Compared With Normal Cognition in Sporadic Parkinson's Disease,Frontiers in neurology,2020,"Parkinson's disease, cognition impairment, gut micro biome, high throughput sequencing, short fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses and Parkinson's disease patients with normal cognition,Parkinson's disease patients with mild cognitive impairment,"All patients eligible for this study were diagnosed for PD according to the UK Brain Bank criteria. Cognition abilities were estimated using the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA), and the scores were obtained from two other neuropsychological tests in each of the five cognitive domains.",27,13,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,"age,body mass index,constipation,education level,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S3,20 May 2023,Jacquelynshevin,Jacquelynshevin,"Alteration in the taxa between PD-MCI, PD-NC and healthy groups(LDA)",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. N15.MGS-57,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus",2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|1263|1637508;2|1224|1236|91347|543|570;2|1224|1236|91347|543|570|573;2|976|200643|171549|2005519|397864;2|976|200643|171549|1853231|574697;2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|2316020|33039;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231|283168|28118,Complete,Atrayees
bsdb:724/3/1,Study 724,case-control,32161568,10.3389/fneur.2020.00137,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052381/,"Ren T, Gao Y, Qiu Y, Jiang S, Zhang Q, Zhang J, Wang L, Zhang Y, Wang L , Nie K",Gut Microbiota Altered in Mild Cognitive Impairment Compared With Normal Cognition in Sporadic Parkinson's Disease,Frontiers in neurology,2020,"Parkinson's disease, cognition impairment, gut micro biome, high throughput sequencing, short fatty acids",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses,Parkinson's disease patients with mild cognitive impairment and Parkinson's disease patients with normal cognition,"All patients eligible for this study were diagnosed for PD according to the UK Brain Bank criteria. Cognition abilities were estimated using the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA), and the scores were obtained from two other neuropsychological tests in each of the five cognitive domains.",13,27,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,"age,body mass index,constipation,education level,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure S3,20 May 2023,Jacquelynshevin,Jacquelynshevin,"Alteration in the taxa between PD-MCI, PD-NC and healthy groups(LDA)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota",2|976|200643|171549;2|976|200643;2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|29465;2|976,Complete,Atrayees
bsdb:725/1/1,Study 725,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE , Nagarajan N",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 1,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Healthy controls,Atopic dermatitis case group,Atopic dermatitis case group with volunteers reporting past atopic dermatitis episodes,15,19,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 5,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Lwaldron
bsdb:725/1/2,Study 725,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE , Nagarajan N",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 1,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Healthy controls,Atopic dermatitis case group,Atopic dermatitis case group with volunteers reporting past atopic dermatitis episodes,15,19,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 5,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus",2|201174|1760|85006|145357|57495;2|1224|28211|356|119045|407;2|1297|188787|118964|183710|1298,Complete,Lwaldron
bsdb:725/2/1,Study 725,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE , Nagarajan N",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 2,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Females (controls),Females (cases),Atopic dermatitis (AD) case females,7,11,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 6B,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between female controls and female AD case group,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",2|201174|1760|85006|145357|57495;2|1224|28211|356|119045|407,Complete,Lwaldron
bsdb:725/3/1,Study 725,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE , Nagarajan N",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 3,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Males (control),Males (case),Atopic dermatitis (AD) case males,8,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 6B,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between male controls and male AD case group,decreased,"k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus",2|1297|188787|118964|183710|1298;2|201174|1760|85006|145357|57495,Complete,Lwaldron
bsdb:725/3/2,Study 725,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE , Nagarajan N",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 3,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Males (control),Males (case),Atopic dermatitis (AD) case males,8,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 6B,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between male controls and male AD case group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1239|91061|1385|539738|1378;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712|724,Complete,Lwaldron
bsdb:725/4/1,Study 725,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE , Nagarajan N",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 4,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Normal control,AD cases with no reported cream usage,AD cases with no reported cream usage (no emollient creams or topical corticosteroids),15,11,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 6C,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group with no cream usage,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",2|201174|1760|85006|145357|57495;2|1224|28211|356|119045|407,Complete,Lwaldron
bsdb:725/4/2,Study 725,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE , Nagarajan N",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 4,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Normal control,AD cases with no reported cream usage,AD cases with no reported cream usage (no emollient creams or topical corticosteroids),15,11,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 6C,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group with no cream usage,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1239|91061|1385|539738|1378;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712|724,Complete,Lwaldron
bsdb:726/1/1,Study 726,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A , Mathur R",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 1,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 2,36-50 years old,32,41,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1224|1236|135625|712|713;2|976|200643|171549|815|816;2|1224|1236|91347|543|561;2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:726/1/2,Study 726,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A , Mathur R",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 1,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 2,36-50 years old,32,41,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2,2 January 2024,Folakunmi,Folakunmi,"Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,2|1224|1236|135614|32033,Complete,Folakunmi
bsdb:726/2/1,Study 726,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A , Mathur R",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 2,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 3,participants aged 51 to 65 years old,32,96,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1224|1236|135625|712|713;2|1239|91061|186826|33958|1578;2|976|200643|171549|815|816;2|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:726/2/2,Study 726,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A , Mathur R",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 2,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 3,participants aged 51 to 65 years old,32,96,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,2|1224|1236|135614|32033,Complete,Folakunmi
bsdb:726/3/1,Study 726,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A , Mathur R",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 3,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 4,66 to 80 years old,32,82,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1224|1236|135625|712|713;2|976|200643|171549|815|816;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:726/3/2,Study 726,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A , Mathur R",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 3,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 4,66 to 80 years old,32,82,NA,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,2|1224|1236|135614|32033,Complete,Folakunmi
bsdb:727/1/1,Study 727,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE , Waldron L",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never smokers,Current cigarette smokers,"Participants who reported smoking more than 100 cigarettes in their lifetime, smoking a cigarette in the last 5 days, and not using any alternative tobacco product in the last 5 days (the 90 with highest measured serum cotinine were selected)",43,86,NA,16S,4,Illumina,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Supplementary Fig. 4 , Supplementary Fig. 5",28 March 2023,Atrayees,"Atrayees,Peace Sandy","Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers. 

Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota",2|1224|1236|135625|712|713;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1224|1236|135615|868|2717;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1239|91061|186826|1300|1357;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|1239|91061|186826|1300|1301;2|1224,Complete,Peace Sandy
bsdb:727/1/2,Study 727,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE , Waldron L",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never smokers,Current cigarette smokers,"Participants who reported smoking more than 100 cigarettes in their lifetime, smoking a cigarette in the last 5 days, and not using any alternative tobacco product in the last 5 days (the 90 with highest measured serum cotinine were selected)",43,86,NA,16S,4,Illumina,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Supplementary Fig. 4 , Supplementary Fig. 5",28 March 2023,Atrayees,"Atrayees,Peace Sandy","Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers. 

Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Synergistota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Spirochaetota",2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|156454;2|29547|3031852|213849|72294|194;2|508458|649775|649776|3029087|1434006;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|976|200643|171549|2005473;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|201174|1760|85006|1268|32207;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|508458;2|201174;2|95818;2|203691,Complete,Peace Sandy
bsdb:727/2/1,Study 727,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE , Waldron L",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never Smokers,Alternative Tobacco Smokers,"Participants who used e-cigarettes, hookah, and/or 
cigar or cigarillo but not cigarettes",43,49,NA,16S,4,Illumina,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text,4 January 2024,Peace Sandy,Peace Sandy,"Differential abundance of OTUs from participants who used e-cigarettes, hookah, and/or 
cigar or cigarillo but not cigarettes",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|201174;2|1239;2|1224,Complete,Lwaldron
bsdb:727/2/2,Study 727,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE , Waldron L",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never Smokers,Alternative Tobacco Smokers,"Participants who used e-cigarettes, hookah, and/or 
cigar or cigarillo but not cigarettes",43,49,NA,16S,4,Illumina,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Text,4 January 2024,Peace Sandy,Peace Sandy,"Differential abundance of OTUs from participants who used e-cigarettes, hookah, and/or 
cigar/cigarillo but not cigarettes",decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|s__uncultured bacterium",2|976;2|77133,Complete,Lwaldron
bsdb:727/3/1,Study 727,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE , Waldron L",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never Smokers,participants who only smoked hookah,participants who only smoked hookah,43,28,NA,16S,4,Illumina,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text,5 January 2024,Peace Sandy,Peace Sandy,"In those who only smoked hookah (n = 28), genera Porphyromonas, Leptotrichia, 
Streptobacillus, Fusobacterium, and an uncultured bacterium from Saccharibacteria were 
depleted.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|s__uncultured bacterium",2|976|200643|171549|171551|836;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771|34104;2|32066|203490|203491|203492|848;2|77133,Complete,Lwaldron
bsdb:728/1/1,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Controls (No Diarrhea Group),Diarrhea Group,Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,18,"Applicable, but exact duration not specified",16S,45,Illumina,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 2, Table 2",29 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between Controls and Diarrhea group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|216572|459786;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|33042,Complete,Atrayees
bsdb:728/1/2,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Controls (No Diarrhea Group),Diarrhea Group,Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,18,"Applicable, but exact duration not specified",16S,45,Illumina,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2,29 March 2023,Ufuoma Ejite,Ufuoma Ejite,Differential microbial abundance between Controls and Diarrhea group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803|1506553,Complete,Atrayees
bsdb:728/2/1,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Antibiotic-excluded Controls (No Diarrhea Group),Antibiotic-excluded Diarrhea Group,Antibiotic-excluded diarrheal group; Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,13,Applicable; but exact duration not specified,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,antibiotic exposure,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,18 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|207244;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|1407607;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1508657;2|976|200643|171549|815|816;2|1239|186801|186802|204475;2|1239|526524|526525|2810280|100883,Complete,Atrayees
bsdb:728/2/2,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Antibiotic-excluded Controls (No Diarrhea Group),Antibiotic-excluded Diarrhea Group,Antibiotic-excluded diarrheal group; Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,13,Applicable; but exact duration not specified,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,antibiotic exposure,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,18 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803|1506553;2|1224|1236|91347|543|561;2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|572511;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:728/3/1,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage administered to the No Diarrhea Group,21,25,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S4,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage No Diarrhea Group,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|1239|526524|526525|128827;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|189330;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|186806|1730;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|207244,Complete,Atrayees
bsdb:728/3/2,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage administered to the No Diarrhea Group,21,25,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S4,6 June 2023,Atrayees,Atrayees,Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage No Diarrhea Group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger",2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|572511;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1506553;2|1239|186801|186802|204475,Complete,Atrayees
bsdb:728/4/1,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,1000 mg/day MMF Dosage Diarrhea Group,1000 mg/day MMF Dosage administered to the Diarrhea Group,21,4,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",2|976|200643|171549|815|816;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|33042;2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|572511;2|1239|186801|3082720|186804|1505657,Complete,Atrayees
bsdb:728/4/2,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,1000 mg/day MMF Dosage Diarrhea Group,1000 mg/day MMF Dosage administered to the Diarrhea Group,21,4,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1506553;2|1239|526524|526525|2810280|100883,Complete,Atrayees
bsdb:728/5/1,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage Diarrhea Group,2000 mg/day MMF Dosage administered to the Diarrhea Group,25,13,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S6,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1508657;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|459786;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|572511;2|976|200643|171549|815|816;2|1239|186801|186802|204475;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|2810280|3025755,Complete,Atrayees
bsdb:728/5/2,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage Diarrhea Group,2000 mg/day MMF Dosage administered to the Diarrhea Group,25,13,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S6,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees",Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|1300|1301;2|1239|186801|3082720|186804|1505657,Complete,Atrayees
bsdb:728/6/1,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Pre-Diarrheal specimens,Diarrheal specimens,Diarrheal specimens,14,14,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,7 June 2023,Atrayees,Atrayees,Relative abundance of taxa in Diarrheal specimens,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|1239|186801|186802|204475;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|207244;2|1239|526524|526525|2810280|3025755;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1508657;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|33042;2|1224|1236|91347|543|561;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:728/6/2,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Pre-Diarrheal specimens,Diarrheal specimens,Diarrheal specimens,14,14,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,7 June 2023,Atrayees,Atrayees,Relative abundance of taxa in Diarrheal specimens,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1506553,Complete,Atrayees
bsdb:728/7/1,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,First Diarrheal Specimens Time-Matched Fecal Specimens from the No Diarrhea Group,First Diarrheal Specimens in the Diarrhea group,First Diarrheal Specimens in the Diarrhea group,46,18,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,7 June 2023,Atrayees,Atrayees,Relative abundance of taxa in the Diarrhea Group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|207244;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1508657;2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|204475;2|1239|526524|526525|2810280|3025755;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:728/7/2,Study 728,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E , Suthanthiran M",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,First Diarrheal Specimens Time-Matched Fecal Specimens from the No Diarrhea Group,First Diarrheal Specimens in the Diarrhea group,First Diarrheal Specimens in the Diarrhea group,46,18,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,7 June 2023,Atrayees,Atrayees,Relative abundance of taxa in the Diarrhea Group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803|1506553;2|1239|186801|3082720|186804|1505657,Complete,Atrayees
bsdb:729/1/1,Study 729,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z, Jin G, Yan X, Cheng Y, Shao L, Song Q, Liu X , Zhao L",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Elderly Schizophrenia Patients,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2A,10 March 2023,Dupe,"Dupe,Aiyshaaaa,Atrayees",Differential LEfSe- associated bacterial taxa between the elderly SZ patients and the healthy controls,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Synergistota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|201174;2|1224|1236|135624;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171552|1283313;2|976|200643;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|526524|526525|128827;2|1239|526524|526525;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1239|526524|526525|128827|1573535;2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|186804;2|976|200643|171549|171552;2|1239|186801|3082720|186804|1501226;2|201174|84998|84999|84107|1473205;2|201174|84998|1643822|1643826|84108;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|135624|83763|83770;2|1224|28216|80840|995019|40544;2|508458;2|74201;2|976|200643|171549;2|201174|84998|84999|84107;2|976|200643|171549|171551,Complete,Atrayees
bsdb:729/1/2,Study 729,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z, Jin G, Yan X, Cheng Y, Shao L, Song Q, Liu X , Zhao L",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Elderly Schizophrenia Patients,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2A,10 March 2023,Dupe,"Dupe,Atrayees",Differential LEfSe- associated bacterial taxa between the elderly SZ patients and the healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|207244;2|1239|91061;2|1239;2|1239|186801|186802|3085642|580596;2|1224|1236|91347|543|544;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|204475;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803;2|1239|91061|186826;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:729/2/1,Study 729,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z, Jin G, Yan X, Cheng Y, Shao L, Song Q, Liu X , Zhao L",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Schizophrenia,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,3,"age,sex",NA,NA,decreased,increased,decreased,NA,NA,Signature 1,Figure 2B,11 March 2023,Dupe,Dupe,the mean relative abundances of bacterial taxa in SZ patients and healthy control from phylum to genus level,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|904;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|976|200643;2|200940|3031449|213115|194924|35832;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|32066|203490;2|1224|1236|135625|712|724;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|1239|526524|526525|128827|1573535;2|1224|28211|356|45401;2|1224|28211|2800060|69657;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|201174|1760|85006|1268;2|201174|84998|84999|1643824|133925;2|1224|28211|204455|31989;2|1239|1737404|1737405|1570339|543311;2|1224|1236|135625|712;2|1224|28211|356|2831106|1082930;2|1239|186801|3082720|186804;2|1239|909932|1843488|909930|33024;2|1224|28211|356|69277;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3082720|186804|1501226;2|201174|84998|84999|84107|1473205;2|1239|91061|1385|90964;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|1224|28216|80840|995019|40544;2|508458|649775|649776|649777;2|508458;2|74201|203494|48461|203557;2|74201;2|1224|1236|135614|32033,Complete,Atrayees
bsdb:729/2/2,Study 729,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z, Jin G, Yan X, Cheng Y, Shao L, Song Q, Liu X , Zhao L",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Schizophrenia,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,3,"age,sex",NA,NA,decreased,increased,decreased,NA,NA,Signature 2,Figure 2B,11 March 2023,Dupe,"Dupe,Atrayees",the mean relative abundances of bacterial taxa in SZ patients and healthy control from phylum to genus level,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|3085636|186803;2|1224;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:730/1/1,Study 730,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G, Zhang W, Zhang S, Chen J, He K, Zhang C, Yuan X , Xie B",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,11,Patients taking antibiotics or probiotics one month prior to the study were excluded from the SCI group for this experiment.,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2e,26 March 2023,Kahvecirem,"Kahvecirem,Atrayees,Boadiwaa","The species with different abundances are listed in the genus, class, phylum, order, and family levels for each group.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3085636|186803|1766253;2|976|200643|171549|2005519|397864;2|976|200643|171549|2005519;2|1239|186801|3085636|186803|572511;2|1224|28216|80840;2|1239|186801|186802|3085642|580596;2|1239|186801;2|1239|186801|186802|1898207;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|1224|1236|91347|543|1940338;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|216851;2|1239|186801|186802|1686313;2|1239|186801|3085636|186803|1407607;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|1898203;2|1239|186801|3085636|186803|248744;2|1224|28216|80840|995019|577310;2|1224|1236|135625;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|201174|84998|1643822|1643826|84108;2|1224|28216|80840|995019|40544;2|1224|28216|80840|995019;2|1239|186801|186802|216572|39492;2|1239|186801;2|1239|186801|3085636|186803;2|1239|186801|186802,Complete,Atrayees
bsdb:730/1/2,Study 730,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G, Zhang W, Zhang S, Chen J, He K, Zhang C, Yuan X , Xie B",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,11,Patients taking antibiotics or probiotics one month prior to the study were excluded from the SCI group for this experiment.,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2e,26 March 2023,Kahvecirem,"Kahvecirem,Atrayees","The species with different abundances are listed in the genus, class, phylum, order, and family levels for each group.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|1239|186801|186802|216572|52784;2|1239|186801|3085636|186803|2383;2|1239|186801|3082768|990719|990721;2|976|200643|171549|2005520;2|976|200643|171549|2005520|156973;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|946234;2|1239|186801|3082720|186804|1505657;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|1769710;2|1239|526524|526525|2810280|3025755,Complete,Atrayees
bsdb:730/2/1,Study 730,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G, Zhang W, Zhang S, Chen J, He K, Zhang C, Yuan X , Xie B",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 2,United States of America,Homo sapiens,Venous blood,UBERON:0013756,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,10,Patients taking antibiotics or probiotics one month prior to the study were excluded from the SCI group for this experiment.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Figure 2b, 2c",2 June 2023,Atrayees,Atrayees,Differential abundance of taxa at phylum and genus level,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803|1766253;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1407607;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|216572|1263;2|1239|186801;2|1239|186801|3085636|186803,Complete,Atrayees
bsdb:730/2/2,Study 730,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G, Zhang W, Zhang S, Chen J, He K, Zhang C, Yuan X , Xie B",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 2,United States of America,Homo sapiens,Venous blood,UBERON:0013756,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,10,Patients taking antibiotics or probiotics one month prior to the study were excluded from the SCI group for this experiment.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Figure 2b, 2c",2 June 2023,Atrayees,Atrayees,Differential abundance of taxa at phylum and genus level,increased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,2|201174|84998|1643822|1643826|84111,Complete,NA
bsdb:731/1/1,Study 731,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F , van Laar T",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Dutch(NL) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the Movement Disorders Society (MDS) clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by FDOPA-PET or one-year follow-up if no FDOPA-PET was performed.",85,136,1 month,16S,4,Illumina,ANCOM,0.1,NA,NA,NA,"age,body mass index",NA,NA,increased,NA,NA,increased,Signature 1,Table 3. Differentially abundant taxa between PD and HC in NL cohort..,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees","Differentially abundant taxa between PD and HC detected using ANCOM.



*(A negative change indicates lower abundance in PD compared to HC)",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,2|976|200643|171549|171550,Complete,Atrayees
bsdb:731/1/2,Study 731,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F , van Laar T",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Dutch(NL) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the Movement Disorders Society (MDS) clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by FDOPA-PET or one-year follow-up if no FDOPA-PET was performed.",85,136,1 month,16S,4,Illumina,ANCOM,0.1,NA,NA,NA,"age,body mass index",NA,NA,increased,NA,NA,increased,Signature 2,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees",Differentially abundant taxa between PD and HC detected using ANCOM.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977,Complete,Atrayees
bsdb:731/2/1,Study 731,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F , van Laar T",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,Recent antibiotics usage in the previous month.,16S,4,Illumina,ANCOM,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 1,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees",Differentially abundant taxa between PD and HC detected using ANCOM,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,2|1239|186801|3082768|990719,Complete,Atrayees
bsdb:731/2/2,Study 731,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F , van Laar T",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,Recent antibiotics usage in the previous month.,16S,4,Illumina,ANCOM,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 2,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees",Differentially abundant taxa between PD and HC detected using ANCOM,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|1506553|1926283;2|1239|186801|3085636|186803;2|1239|186801|186802|1980681;2|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:731/3/1,Study 731,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F , van Laar T",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Dutch(NL) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the Movement Disorders Society (MDS) clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by FDOPA-PET or one-year follow-up if no FDOPA-PET was performed.",85,136,Recent antibiotics usage in the previous month.,16S,4,Illumina,DESeq2,0.1,NA,NA,NA,"age,body mass index",NA,NA,increased,NA,NA,increased,Signature 1,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees",Differentially abundant taxa between PD and HC detected using DESeq2.,decreased,k__Bacteria|p__Bacillota|c__Clostridia,2|1239|186801,Complete,Atrayees
bsdb:731/4/1,Study 731,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F , van Laar T",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,Recent antibiotics usage in the previous month.,16S,4,Illumina,DESeq2,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 1,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees",Differentially abundant taxa between PD and HC detected using DESeq2.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae",2|74201|203494|48461|1647988;2|201174|84998|1643822|1643826,Complete,Atrayees
bsdb:731/4/2,Study 731,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F , van Laar T",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,Recent antibiotics usage in the previous month.,16S,4,Illumina,DESeq2,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 2,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees",Differentially abundant taxa between PD and HC detected using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae",2|1239|186801|3085636|186803;2|1239|186801|186802|3085642|580596;2|544448|31969|186329|2146,Complete,Atrayees
bsdb:732/1/1,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Individuals with a healthy body mass index,Obese individuals,Individuals who had a class II or class III obesity,293,294,6 months,16S,4,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S4,17 March 2023,Ombati,"Ombati,Chloe,Atrayees","Association of genus level 16S data with obesity, adjusted for age, sex, field
center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.",decreased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|508458|649775|649776|649777|508459;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572;2|1239|186801|186802;2|201174|84998|84999|84107;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|119852;2|201174|84998|1643822|1643826|84111;2|976|200643|171549|171550;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|572511;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934,Complete,Atrayees
bsdb:732/1/2,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Individuals with a healthy body mass index,Obese individuals,Individuals who had a class II or class III obesity,293,294,6 months,16S,4,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S4,8 June 2023,Atrayees,Atrayees,"Association of genus level 16S data with obesity, adjusted for age, sex, field center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|909932|1843488|909930|904;2|1239|909932|1843489|31977|906;2|1239|526524|526525|2810280|135858;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:732/2/1,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Early age,Later age,NA,1674,1674,6 months,16S,4,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,race,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S5,28 March 2023,Ombati,"Ombati,Atrayees","Association of genus level 16S data with age at relocation among Latin American born individuals, adjusted for age, sex, field center and Hispanic background.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|186801|186802;2|976|200643|171549|1853231|574697;2|1224|1236|135625|712|724;2|1239|909932|1843488|909930|33024;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|570;2|976|200643|171549|171552|838;2|976|200643|171549|171552|577309;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|140625;2|200940|3031449|213115|194924|872;2|976|200643|171549|2005519;2|1239|91061|186826|33958;2|544448|31969|186332|186333;2|1239|186801|186802|216572;2|201174|84998|84999|84107;2|1239|186801|3082768|990719;2|1224|1236|91347|543,Complete,Atrayees
bsdb:732/2/2,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Early age,Later age,NA,1674,1674,6 months,16S,4,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,race,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S5,12 June 2023,Atrayees,Atrayees,"Association of genus level 16S data with age at relocation among Latin American born individuals, adjusted for age, sex, field center and Hispanic background.",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|1239|526524|526525|2810280|100883;2|976|200643|171549|815|816;2|1239|909932|1843488|909930|904;2|1224|28216|80840|995019|40544;2|1239|526524|526525|128827|61170;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|1239|186801|186802|216572|119852;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|572511;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|244127;2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|186806|1730,Complete,Atrayees
bsdb:732/4/1,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USB (US born),LAB,Latin American Born,225,1532,6 months,16S,4,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 1,Table S7,28 March 2023,Ombati,"Ombati,Atrayees",Fungal taxa that differ after comparing those born in the mainland USA versus those born in Latin America.,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera|s__Cyberlindnera jadinii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium roqueforti,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Mycenaceae|g__Panellus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria rosae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|f__Xenasmatellaceae|g__Xenasmatella|s__Xenasmatella ardosiaca,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium salinae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Corticiales|f__Corticiaceae|g__Erythricium|s__Erythricium laetum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Corticiales|f__Corticiaceae|g__Erythricium",2759|4751|4890|4891|3243778|115784|604195|4903;2759|4751|4890|4891|3243778|115784|604195;2759|4751|5204|155619;2759|4751|4890|147545|5042|1131492|5073|5082;2759|4751|5204|155619|5338|2024004|5635;2759|4751|4890|4891|4892|4893|4910|4911;2759|4751|4890|147541|92860|28556|5598|1187941;2759|4751|5204|155619|3118719|301415|467934;2759|4751|4890|147541|2726946|452563|5498|1052097;2759|4751|5204|155619|452338|5304|264095|264096;2759|4751|5204|155619|452338|5304|264095,Complete,Atrayees
bsdb:732/4/2,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USB (US born),LAB,Latin American Born,225,1532,6 months,16S,4,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 2,Table S7,13 June 2023,Atrayees,Atrayees,Fungal taxa that differ after comparing those born in the mainland USA versus those born in Latin America.,increased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Cystofilobasidiaceae|g__Cystofilobasidium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Kurtzmaniella|s__[Candida] railenensis",2759|4751|5204|155616|90883|165808|5410;2759|4751|4890|3239874|2916678|766764|549703|45579,Complete,Atrayees
bsdb:732/5/1,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Individuals with a healthy body mass index,Individuals who were obese,Individuals with class II or class III obesity,293,294,6 months,16S,4,Illumina,Linear Regression,NA,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S8,28 March 2023,Ombati,"Ombati,Atrayees","Association of genus level ITS1 data with obesity, adjusted for age, sex, field
center, and Hispanic background. Only one met Pvalue < 0.05.",decreased,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces sp.,2759|4751|4890|3239874|2916678|766764|4958|1853546,Complete,Atrayees
bsdb:732/6/2,Study 732,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R , Burk RD","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Early age,Later age,Individuals who had relocated to the USA at a younger age( 18 and below),1674,1674,6 months,16S,4,Illumina,Linear Regression,NA,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S9,8 June 2023,Atrayees,Atrayees,"Association of genus level ITS1 data with age at relocation among Latin
American-born individuals, adjusted for age, sex, field center, and Hispanic background",increased,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,2759|4751|4890|3239874|2916678|766764|5475,Complete,Atrayees
bsdb:733/1/1,Study 733,"cross-sectional observational, not case-control",33996618,https://doi.org/10.3389/fcimb.2021.625589,NA,"Han J, Wu S, Fan Y, Tian Y , Kong J",Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota,Frontiers in cellular and infection microbiology,2021,"antimicrobial resistance, biliary microbiota, choledocholithiasis, duodenal microbiota, duodenal–biliary reflux",Experiment 1,China,Homo sapiens,"Duodenum,Bile duct","UBERON:0002114,UBERON:0002394",Sampling site,EFO:0000688,biliary microbiota,duodenal microbiota,duodenal juice samples from patients with choledocholithiasis,10,10,4 weeks,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 2D,14 December 2023,Folakunmi,Folakunmi,microbial taxa characterizing duodenal juice from bile in patients with choledocholithiasis as determined by LEfSe,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota",2|201174;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|201174,Complete,ChiomaBlessing
bsdb:734/1/1,Study 734,case-control,36894986,https://doi.org/10.1186/s40168-023-01472-7,NA,"de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O'Sullivan MP, Ghosh S, Satagopam V, Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P , Wilmes P",Altered infective competence of the human gut microbiome in COVID-19,Microbiome,2023,"COVID-19, Gut microbiome, Metagenomics, Metatranscriptomics, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Control group,COVID-19 infection cases.,"These individuals had confirmed SARS-CoV-2 infection by a positive RT-PCR test result and presented with COVID-19 symptoms such as fever, cough, and difficulty breathing.",57,61,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),NA,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2B,11 March 2023,Busayo,"Busayo,Fatima","Relative abundance of bacterial species
significantly enriched in COVID-19 patients compared to the control group",increased,"k__Bacteria|p__Bacillota|s__Firmicutes bacterium AM10-47,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea",2|1239|2292890;2|976|200643|171549|171552|838|1262929;2|1239|186801|3085636|186803|841|1262948;2|976|200643|171549|171552|2974265|363265,Complete,Fatima
bsdb:734/1/2,Study 734,case-control,36894986,https://doi.org/10.1186/s40168-023-01472-7,NA,"de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O'Sullivan MP, Ghosh S, Satagopam V, Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P , Wilmes P",Altered infective competence of the human gut microbiome in COVID-19,Microbiome,2023,"COVID-19, Gut microbiome, Metagenomics, Metatranscriptomics, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Control group,COVID-19 infection cases.,"These individuals had confirmed SARS-CoV-2 infection by a positive RT-PCR test result and presented with COVID-19 symptoms such as fever, cough, and difficulty breathing.",57,61,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),NA,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2C,11 March 2023,Busayo,Busayo,Relative abundance of bacterial species significantly decreased in COVID-19 patients compared to the control group,decreased,"k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",2|1239|1263005;2|1239|186801|3085636|186803|841|301302;2|1239|526524|526525|2810281|191303|154288,Complete,Fatima
bsdb:735/1/1,Study 735,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R , Xavier RJ",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 1,China,Homo sapiens,"Ileum,Rectum","UBERON:0002116,UBERON:0001052",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Table S2A,13 March 2023,Khadeeejah,"Khadeeejah,Atrayees,Chloe,Aiyshaaaa","Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|201174|1760|85006|1268;2|29547|3031852|213849;2|1224|28216|206351|481|482;2|1239|909932|1843489|31977|29465|29466;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|739;2|1224|28216|206351|481;2|1239|909932|1843489|31977|29465|39778;2|32066|203490|203491;2|32066|203490|203491|203492;2|1224|28216|80840|119060;2|1239|909932|1843489|31977;2|1224|28216;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|1236|135625|712;2|1224|1236|91347|543,Complete,Atrayees
bsdb:735/1/2,Study 735,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R , Xavier RJ",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 1,China,Homo sapiens,"Ileum,Rectum","UBERON:0002116,UBERON:0001052",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,decreased,Signature 2,Table S2A,13 March 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Chloe,Atrayees","Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|526524|526525|128827;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|186802|216572|1263;2|976|200643|171549|815|816|820;2|1239|186801|186802|186806|1730;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|2749846|31971;2|201174|1760|85004|31953;2|201174;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|1678|1680;2|1239|186801|3085636|186803|33042|116085;2|74201|203494|48461|203557;2|1239|186801|3085636|186803|841|301302;2|1239|186801|3082768|990719;2|1239|186801|186802|216572|1263|40518;2|74201|203494|48461|1647988|239934|239935,Complete,Atrayees
bsdb:735/2/1,Study 735,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R , Xavier RJ",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S2B,4 April 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Atrayees",Taxa in stool samples significantly associated with disease.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|3085636|186803;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|572511|33035;2|1239|186801|3085636|186803|2316020|33039,Complete,Atrayees
bsdb:735/3/1,Study 735,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R , Xavier RJ",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 3,China,Homo sapiens,"Ileum,Rectum,Feces","UBERON:0002116,UBERON:0001052,UBERON:0001988",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S2C,4 April 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Atrayees",precise differences between the mucosal tissue and stool samples within patients with new-onset CD,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|91061|186826|33958;2|1239|186801|186802|186806;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|572511|33035;2|1239|526524|526525|128827|2749846|31971;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|31979|1485;2|1239|91061;2|201174|84998|1643822|1643826|84111;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|31979;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572;2|1239|91061|186826;2|1239|91061|186826|1300;2|201174|84998|84999|84107;2|201174;2|1239|526524|526525|128827;2|1239|186801|3085636|186803|33042;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803;2|1239;2|1239|186801|186802,Complete,Atrayees
bsdb:735/3/2,Study 735,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R , Xavier RJ",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 3,China,Homo sapiens,"Ileum,Rectum,Feces","UBERON:0002116,UBERON:0001052,UBERON:0001988",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,NA,Signature 2,Tabls S2C,4 April 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Atrayees",precise differences between the mucosal tissue and stool samples within patients with new-onset CD,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|815|816;2|1224;2|976|200643|171549;2|976|200643;2|1224|1236;2|1224|28216;2|976|200643|171549|815|816|817;2|1224|28216|80840;2|200940|3031449|213115|194924;2|1224|28216|206389|75787;2|1224|28211|204457;2|1224|1236|135625|712|416916;2|1224|1236|72274;2|1224|1236|2887326|468;2|1224|1236|2887326|468|469;2|32066|203490|203491;2|32066|203490|203491|203492;2|1239|91061|1385|90964|1279;2|1224|28216|206351|481;2|1239|91061|1385;2|1239|1737404|1737405|1737406;2|1224|28216|206351|481|482;2|976|117743|200644|2762318;2|201174|1760|85006|1268;2759|33090|35493|3398|72025|3803|3814|508215;2|29547|3031852|213849;2|201174|1760|85006|1268|32207|43675;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836,Complete,Atrayees
bsdb:736/1/1,Study 736,case-control,33614635,https://doi.org/10.3389/fcell.2020.634069,https://www.frontiersin.org/articles/10.3389/fcell.2020.634069,"Ling Z, Zhu M, Yan X, Cheng Y, Shao L, Liu X, Jiang R , Wu S",Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer's Disease,Frontiers in cell and developmental biology,2020,"Alzheimer's disease, Bifidobacterium, Faecalibacterium, gut-brain axis, sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease patients,patients with Alzheimer’s disease,71,100,"1 month including prebiotic, probiotic or synbiotic use.",16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2,11 March 2023,Sophy,"Sophy,Mcarlson,Atrayees,Peace Sandy",Differential bacterial taxa between the Chinese AD patients and the healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MCF-1,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus|s__Alkaliphilus crotonatoxidans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. DL-VIII",2|201174|1760|2037;2|201174;2|74201|203494|48461|1647988|239934;2|1239|91061;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|84998|84999;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|526524;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|292632;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201|203494|48461|203557|2735;2|1239|186801|186802|31979|1485|48257;2|1239|186801|3082720|3118656|114627|185693;2|1239|186801|186802|31979|1485|641107,Complete,Atrayees
bsdb:736/1/2,Study 736,case-control,33614635,https://doi.org/10.3389/fcell.2020.634069,https://www.frontiersin.org/articles/10.3389/fcell.2020.634069,"Ling Z, Zhu M, Yan X, Cheng Y, Shao L, Liu X, Jiang R , Wu S",Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer's Disease,Frontiers in cell and developmental biology,2020,"Alzheimer's disease, Bifidobacterium, Faecalibacterium, gut-brain axis, sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease patients,patients with Alzheimer’s disease,71,100,"1 month including prebiotic, probiotic or synbiotic use.",16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2,11 March 2023,Sophy,"Sophy,Mcarlson,Atrayees,Peace Sandy",Differential bacterial taxa between the Chinese AD patients and the healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|186801|3085636|186803|207244;2|1239;2|1239|186801|186802|3085642|580596;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|3085636|186803;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:737/1/1,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,123,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 1,"Figure 3A, 4A",5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V1-V3 regions,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|32066|203490|203491|203492|848,Complete,Atrayees
bsdb:737/1/2,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,123,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 2,"Figure 3A, 4A",5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V1-V3 regions,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|201174|1760|2037|2049|1654;2|32066|203490|203491|203492|848;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:737/2/1,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 2,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,123,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,increased,increased,Signature 1,Figure 3A,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:737/2/2,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 2,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,123,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,increased,increased,Signature 2,Figure 3A,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Eukaryota|c__Raphidophyceae|o__Chattonellales|f__Chattonellaceae|g__Heterosigma|s__Heterosigma akashiwo,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2759|38410|658125|658124|2828|28465;2|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:737/3/1,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,345,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 1,Figure 3B and Figure 4B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium",2|976|200643|171549;2|1239|91061|186826;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|976|200643|171549|2030927,Complete,ChiomaBlessing
bsdb:737/3/2,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,345,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 2,Figure 3B and Figure 4B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|265975;2|1224|1236|135625|712;2|976|200643|171549|171552|838;2|201174|1760|85006|2805591|2038;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:737/4/1,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 4,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,345,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,decreased,decreased,Signature 1,Figure 3B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at V3-V5 regions.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|976|200643|171549;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|186826;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:737/4/2,Study 737,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM , Weinstock GM",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 4,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,No use of antibiotics in the past 3 months.,16S,345,Roche454,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,decreased,decreased,Signature 2,Figure 3B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at V3-V5 regions.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803|265975;2|1224|1236|135625|712;2|201174|1760|85006|2805591|2038;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838,Complete,ChiomaBlessing
bsdb:738/1/1,Study 738,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,https://www.nature.com/articles/s41467-020-17916-9,"Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A , Figeys D",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 1,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0001988,UBERON:0004992",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,4 weeks including probiotics use,NA,NA,Mass spectrometry,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5a,11 March 2023,Sophy,"Sophy,Chloe",Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of lysine acetylome-based taxonomic compositions.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491|158846|437897;2|1239|186801|3085636|186803|841|360807;2|1239|909932|909929|1843491;2|1239|909932|909929;2|1239|186801|3085636|186803|28050|39485,Complete,Claregrieve1
bsdb:738/1/2,Study 738,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,https://www.nature.com/articles/s41467-020-17916-9,"Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A , Figeys D",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 1,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0001988,UBERON:0004992",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,4 weeks including probiotics use,NA,NA,Mass spectrometry,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5a,11 March 2023,Sophy,Sophy,Taxonomic alterations of protein acetylation in the pediatric CD microbiome. acetylome-based. LEfSe analysis of lysine acetylome-based taxonomic compositions.,increased,k__Bacteria|p__Bacillota|c__Bacilli,2|1239|91061,Complete,Chloe
bsdb:738/2/1,Study 738,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,https://www.nature.com/articles/s41467-020-17916-9,"Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A , Figeys D",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 2,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0001988,UBERON:0004992",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,4 weeks including probiotics use,NA,NA,Mass spectrometry,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 5b,23 November 2023,Folakunmi,Folakunmi,Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of metaproteome-based taxonomic compositions.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Eukaryota|k__Fungi,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Viruses,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Eukaryota|k__Fungi|p__Ascomycota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes",2|1224|1236;2759|4751;2|203691|203692;2759|4751|4890|4891;2759|4751|4890|4891|4892;10239;2|203691|203692|136|137|146;2759|4751|4890;2|1239|186801|186802|216572|244127;10239|2731360|2731618|2731619,Complete,Folakunmi
bsdb:738/2/2,Study 738,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,https://www.nature.com/articles/s41467-020-17916-9,"Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A , Figeys D",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 2,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0001988,UBERON:0004992",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,4 weeks including probiotics use,NA,NA,Mass spectrometry,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 5b,23 November 2023,Folakunmi,Folakunmi,Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of metaproteome-based taxonomic compositions.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|189330;2|976|200643|171549|171552|838|189723;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810280|3025755|29348;2|1239|186801|3085636|186803|572511|1322;2|1239|91061|186826|1300;2|1239|91061;2|1239|186801|3085636|186803|841|301302;2|1239|91061|186826;2|1239|186801|3085636|186803|841|166486;2|1239|526524|526525|2810280|3025755,Complete,Folakunmi
bsdb:738/3/1,Study 738,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,https://www.nature.com/articles/s41467-020-17916-9,"Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A , Figeys D",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 3,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0001988,UBERON:0004992",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,4 weeks including probiotics use,NA,NA,Mass spectrometry,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 5e,23 November 2023,Folakunmi,Folakunmi,Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of the acetylome-to-metaproteome ratios of all quantified taxa in the lysine acetylome data set.,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|91061;2|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:738/4/1,Study 738,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,https://www.nature.com/articles/s41467-020-17916-9,"Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A , Figeys D",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Metaproteome aliquot of human gut,Lysine acetylome aliquot of human gut,relative abundance of kac levels (for each taxon listed in supplementary data 3) in human fecal microbiome samples lysine acetylome aliquot,209,209,4 weeks including probiotics use,NA,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 2b,24 November 2023,Folakunmi,Folakunmi,"Lysine acetylome-to-metaproteome ratios of quantified phyla and genera in
human gut microbiome. Comparisons of the percentage of acetylation in lysine acetylomic aliquot with that in metaproteomic aliquot.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota",2|1239|186801|3085636|186803|1407607;2|976|200643|171549|1853231|283168;2|1239|186801|3085636|186803|1506553;2|1239|186801|186802|3085642|580596;2|1239,Complete,Folakunmi
bsdb:738/4/2,Study 738,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,https://www.nature.com/articles/s41467-020-17916-9,"Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A , Figeys D",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Metaproteome aliquot of human gut,Lysine acetylome aliquot of human gut,relative abundance of kac levels (for each taxon listed in supplementary data 3) in human fecal microbiome samples lysine acetylome aliquot,209,209,4 weeks including probiotics use,NA,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 2b,24 November 2023,Folakunmi,Folakunmi,Lysine acetylome-to-metaproteome ratios of quantified phyla and genera in human gut microbiome. Comparisons of the percentage of acetylation in lysine acetylomic aliquot with that in metaproteomic aliquot.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Eukaryota|k__Metazoa|p__Chordata,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|s__Homininae|g__Homo",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|830;2|201174;2|1224;2|1224|28216|80840|995019|577310;2|201174|84998|84999|84107|102106;2759|33208|7711;2|1239|186801|186802|204475;2759|33208|7711|40674|9443|9604|207598|9605,Complete,Folakunmi
bsdb:739/1/1,Study 739,randomized controlled trial,36198385,10.1016/j.anaerobe.2022.102652,NA,"Bamola VD, Dubey D, Samanta P, Kedia S, Ahuja V, Madempudi RS, Neelamraju J , Chaudhry R",Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease,Anaerobe,2022,"Bacillus clausii UBBC-07, Cytokines, Gut microbiome, IBD, Probiotic",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo group before intervention/treatment,Bacillus clausii UBBC-07 group after intervention/treatment,"Patients who were treated with Bacillus clausii UBBC-07 and evaluated after treatment/intervention for the effect of the probiotic on gut microbiota. Patients were of either sex, clinically diagnosed with Ulcerative Colitis or Crohn's Disease, and between 18 and 60 years.",54,54,NA,16S,34,Illumina,Kruskall-Wallis,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text: Page 4, under subheading ""Metagenomic analysis""",17 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa in the UC patients of the Bacillus clausii UBBC-07 group post intervention/ treatment compared to placebo groups post intervention/ treatment,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|91061;2|1239;2|1239|526524|526525;2|1239|186801|186802|216572|216851;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:739/1/2,Study 739,randomized controlled trial,36198385,10.1016/j.anaerobe.2022.102652,NA,"Bamola VD, Dubey D, Samanta P, Kedia S, Ahuja V, Madempudi RS, Neelamraju J , Chaudhry R",Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease,Anaerobe,2022,"Bacillus clausii UBBC-07, Cytokines, Gut microbiome, IBD, Probiotic",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo group before intervention/treatment,Bacillus clausii UBBC-07 group after intervention/treatment,"Patients who were treated with Bacillus clausii UBBC-07 and evaluated after treatment/intervention for the effect of the probiotic on gut microbiota. Patients were of either sex, clinically diagnosed with Ulcerative Colitis or Crohn's Disease, and between 18 and 60 years.",54,54,NA,16S,34,Illumina,Kruskall-Wallis,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text: Page 4, under subheading ""Metagenomic analysis.""",18 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa in the UC patients of the Bacillus clausii UBBC-07 group post intervention/ treatment compared to placebo groups post intervention/ treatment,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales",2|976|200643;2|1239|909932|909929,Complete,ChiomaBlessing
bsdb:740/1/1,Study 740,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P, Wu L, Peng G, Han Y, Tang R, Ge J, Zhang L, Jia L, Yue S, Zhou K, Li L, Luo B , Wang B",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease,Patients with dementia stage of alzheimer's disease.,32,33,Two months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 2,12 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1",Differential microbial abundance between Alzheimers patients and healthy controls,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239;2|976|200643;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|186801|186802|216572|1263;2|1239|186801|186802|1898207;2|976|200643|171549;2|1239|91061|1385|186817|1386|1409;2|1239|186801;2|1224|1236|91347|543,Complete,Claregrieve1
bsdb:740/1/2,Study 740,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P, Wu L, Peng G, Han Y, Tang R, Ge J, Zhang L, Jia L, Yue S, Zhou K, Li L, Luo B , Wang B",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease,Patients with dementia stage of alzheimer's disease.,32,33,Two months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 2,12 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1",Differential microbial abundance between Alzheimers patients and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236;2|1224;2|1224|1236|91347;2|1224|1236|91347|543,Complete,Claregrieve1
bsdb:740/2/1,Study 740,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P, Wu L, Peng G, Han Y, Tang R, Ge J, Zhang L, Jia L, Yue S, Zhou K, Li L, Luo B , Wang B",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,32,32,Two months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2,25 March 2023,Sophy,"Sophy,Claregrieve1",Differential microbial abundance between aMCI patients and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511,Complete,Claregrieve1
bsdb:740/2/2,Study 740,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P, Wu L, Peng G, Han Y, Tang R, Ge J, Zhang L, Jia L, Yue S, Zhou K, Li L, Luo B , Wang B",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,32,32,Two months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2,25 March 2023,Sophy,"Sophy,Claregrieve1",Differential microbial abundance between aMCI patients and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|909932|1843489|31977;2|976|200643;2|976|200643|171549;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:740/3/1,Study 740,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P, Wu L, Peng G, Han Y, Tang R, Ge J, Zhang L, Jia L, Yue S, Zhou K, Li L, Luo B , Wang B",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Alzheimers patients in dementia stage,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,33,32,Two months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2,25 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1",Differential microbial abundance between Alzheimers patients with dementia and aMCI patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota",2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|1224,Complete,Claregrieve1
bsdb:740/3/2,Study 740,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P, Wu L, Peng G, Han Y, Tang R, Ge J, Zhang L, Jia L, Yue S, Zhou K, Li L, Luo B , Wang B",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Alzheimers patients in dementia stage,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,33,32,Two months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2,25 March 2023,Sophy,"Sophy,Claregrieve1",Differential microbial abundance between Alzheimers patients with dementia and aMCI patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|31979;2|1239|186801|186802|216572|1263;2|1239|186801;2|976|200643;2|1239|186801|186802|1898207;2|976|200643|171549;2|1239|186801|186802|216572;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:741/1/1,Study 741,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W, Bi Z, Zhu Q, Gao H, Fan Y, Zhang C, Liu X , Ye M",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls and Parkinson's Disease patients with constipation,Parkinson's Disease patients without constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,30,14,3 months.,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1G,21 May 2023,Jacquelynshevin,Jacquelynshevin,Difference contribution analysis chart,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Kopriimonadales|f__Kopriimonadaceae|g__Kopriimonas|s__uncultured Kopriimonas sp.",2|1224|28216|80840|995019|40544|437898;2|1224|28211|343329|343330|343331|1221381,Complete,Atrayees
bsdb:741/2/1,Study 741,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W, Bi Z, Zhu Q, Gao H, Fan Y, Zhang C, Liu X , Ye M",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease patients without constipation and Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,15,29,3 months.,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1G,21 May 2023,Jacquelynshevin,Jacquelynshevin,Difference contribution analysis chart,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",2|976|200643|171549|815|909656|204516;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|1407607,Complete,Atrayees
bsdb:741/3/1,Study 741,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W, Bi Z, Zhu Q, Gao H, Fan Y, Zhang C, Liu X , Ye M",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls and Parkinson's Disease patients without constipation,Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,29,15,3 months.,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1G,21 May 2023,Jacquelynshevin,Jacquelynshevin,Difference contribution analysis chart,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|201174;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572|292632|665956;2|201174|84998;2|201174|84998|84999;2|201174|84998|84999|84107;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|1649459;2|1239|91061|186826;2|1239|91061;2|1239|91061|186826|1300,Complete,Atrayees
bsdb:741/4/1,Study 741,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W, Bi Z, Zhu Q, Gao H, Fan Y, Zhang C, Liu X , Ye M",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's Disease patients without constipation,Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,14,15,3 months.,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2H,21 May 2023,Jacquelynshevin,Jacquelynshevin,Difference contribution analysis chart.,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",2|1239|526524|526525|128827|1573535;2|1239|909932|909929|1843491|158846;2|976|200643|171549|171552|2974265|363265;2|1224|28211|204441|41295;2|1224|28211|204441,Complete,Atrayees
bsdb:741/4/2,Study 741,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W, Bi Z, Zhu Q, Gao H, Fan Y, Zhang C, Liu X , Ye M",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's Disease patients without constipation,Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,14,15,3 months.,16S,45,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2H,21 May 2023,Jacquelynshevin,Jacquelynshevin,Difference contribution analysis chart.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",2|1239|186801|186802|216572|244127;2|1239|91061;2|1239|186801|3085636|186803|1649459;2|1239|91061|186826;2|1239|186801|186802|216572|2485925;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632|665956;2|1239|91061|186826|1300|1301|1304,Complete,Atrayees
bsdb:742/1/1,Study 742,"cross-sectional observational, not case-control",34650532,10.3389/fmicb.2021.728479,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8506127/,"Mao L, Zhang Y, Tian J, Sang M, Zhang G, Zhou Y , Wang P",Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China,Frontiers in microbiology,2021,"Parkinson’s disease, gastrointestinal dysbiosis, gut-brain-axis, short-chain fatty acids, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses,Parkinson's Disease Patients,Partcipants with Parkinson's Disease,39,39,3 months.,WMS,NA,BGISEQ-500 Sequencing,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2A and 2B,31 May 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy",The stool microbiota profile in PD and SP groups. Differential abundance of genera (A) and species (B) between PD and SP groups identified by LEfSe,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas synergistica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc pseudomesenteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1728,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|1470347;2|976|200643|171549|171550|239759|626932;2|976|200643|171549|171550|239759|28117;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|244127|169435;2|201174|1760|85004|31953|1678|1689;2|200940|3031449|213115|194924|35832;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|572511|53443;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|574697|544644;2|1239|186801|3085636|186803|830;2|1239|186801|186802|457421;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|2719313|333367;2|1239|186801|3085636|186803|2719313|358743;2|1239|526524|526525|128827|658657;2|1239|526524|526525|128827|457422;2|1239|186801|186802;2|1239|186801|3085636|186803|1649459|154046;2|1239|186801|3085636|186803|658086;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1243|33968;2|1239|91061|186826|33958|2767887|1624;2|1239|186801|186802|216572|459786|1226322;2|1224|28216|80840|75682|846;2|1224|28216|80840|75682|846|847;2|976|200643|171549|2005525|375288|328812;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85004|31953|196081;2|201174|1760|85004|31953|196081|78259;2|201174|1760|85004|31953|196081|230143;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|292632|665956;2|1239|186801|186802|216572|292632|214851;2|1239|186801|3085636|186803|1506553|89153;2|200940|3031449|213115|194924|35832;2|201174|84998|84999|1643824|133925;2|201174|1760|85004|31953|196081;2|1239|186801|186802|216572|292632,Complete,Peace Sandy
bsdb:742/1/2,Study 742,"cross-sectional observational, not case-control",34650532,10.3389/fmicb.2021.728479,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8506127/,"Mao L, Zhang Y, Tian J, Sang M, Zhang G, Zhou Y , Wang P",Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China,Frontiers in microbiology,2021,"Parkinson’s disease, gastrointestinal dysbiosis, gut-brain-axis, short-chain fatty acids, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses,Parkinson's Disease Patients,Partcipants with Parkinson's Disease,39,39,3 months.,WMS,NA,BGISEQ-500 Sequencing,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2A and 2B,31 May 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy",The stool microbiota profile in PD and SP groups. Differential abundance of genera (A) and species (B) between PD and SP groups identified by LEfSe,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_19,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 9_1_43BFAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Candidatus Saccharibacteria|s__candidate division TM7 single-cell isolate TM7b,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",2|976|200643|171549|815|816;2|976|200643|171549|815|816|469592;2|1239|186801|186802|31979|1485|411489;2|1239|526524|526525|2810280|1279384;2|1239|526524|526525|2810280|1279384|31973;2|32066|203490|203491|203492|848|856;2|1239|91061|1385|539738|1378|1379;2|1239|186801|3085636|186803|658088;2|1239|186801|186802|216572;2|976|200643|171549|815|909656|310298;2|1239|186801|186802|216572|552398;2|1239|91061|186826|1300|1301|197614;2|1239|186801|186802|216572|1535;2|1239|186801|3085636|186803|1506553|1512;2|95818|447455;2|1239|186801|3082720|186804;2|1224|28216|80840|995019,Complete,Peace Sandy
bsdb:743/1/1,Study 743,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A, Green SJ, Engen PA, Voigt RM, Naqib A, Forsyth CB, Mutlu E , Shannon KM",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,The use of probiotics or antibiotics within three months prior to sample collection.,16S,4,NA,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,TABLE 1. Relative increased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,Fcuevas3,Feces: Parkinson's disease vs. Healthy controls.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643;2|1239|186801|186802|31979;2|1239|186801|186802|216572|119852;2|1224;2|74201|203494|48461|203557;2|74201,Complete,Atrayees
bsdb:743/1/2,Study 743,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A, Green SJ, Engen PA, Voigt RM, Naqib A, Forsyth CB, Mutlu E , Shannon KM",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,The use of probiotics or antibiotics within three months prior to sample collection.,16S,4,NA,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,TABLE 1. Relative decreased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,Fcuevas3,Feces: Parkinson's Disease vs. Healthy Controls,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|2810280;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:743/2/1,Study 743,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A, Green SJ, Engen PA, Voigt RM, Naqib A, Forsyth CB, Mutlu E , Shannon KM",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 2,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,The use of probiotics or antibiotics within three months prior to sample collection.,16S,4,NA,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,TABLE 1. Relative increased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,Fcuevas3,Sigmoid Mucosa: Parkinson's Disease vs. Healthy Controls.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia",2|1224|28216|80840|75682;2|1224|28216|80840|119060|48736,Complete,Atrayees
bsdb:743/2/2,Study 743,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A, Green SJ, Engen PA, Voigt RM, Naqib A, Forsyth CB, Mutlu E , Shannon KM",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 2,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,The use of probiotics or antibiotics within three months prior to sample collection.,16S,4,NA,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,TABLE 1. Relative decreased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,Fcuevas3,Sigmoid Mucosa: Parkinson's Disease vs. Healthy Controls,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|526524|526525|2810280;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:744/1/1,Study 744,case-control,36442206,10.3233/JPD-223500,NA,"Zhang K, Paul KC, Jacobs JP, Chou HL, Duarte Folle A, Del Rosario I, Yu Y, Bronstein JM, Keener AM , Ritz B",Parkinson's Disease and the Gut Microbiome in Rural California,Journal of Parkinson's disease,2022,"Parkinson’s disease, Unified Parkinson’s Disease Rating Scale, brain-gut axis, gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Parkinson's Disease Patients,Participants newly diagnosed with Parkinson's Disease (within 3–5 years).,74,96,Participants were required to not have taken antibiotics within the past 3 months.,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,race,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table 2.,3 June 2023,Fcuevas3,"Fcuevas3,Peace Sandy",Differential taxa abundance associated with PD compared to controls (N=170).,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Verrucomicrobiota",2|201174;2|74201|203494|48461|1647988|239934;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803|1649459;2|1224;2|74201,Complete,Peace Sandy
bsdb:745/1/1,Study 745,time series / longitudinal observational,32073296,https://doi.org/10.3920/BM2019.0039,NA,"Ozkul C, Yalinay M , Karakan T",Structural changes in gut microbiome after Ramadan fasting: a pilot study,Beneficial microbes,2020,"Ramadan fasting, gut microbiota, intermittent fasting, microbiome",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Fasting,EFO:0002756,Adults before fasting,Adults after fasting,healthy adults who were on Ramadan fast with a fasting period of approximately 17H per day for 29 days.,9,9,8 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure S2,13 March 2023,Barakat Dindi,"Barakat Dindi,Chloe",LeFSe analysis and Linear discriminant effect size showing the differential abundance of discriminative taxa at the two-time points I.e before and after fasting.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",2|74201|203494|48461|1647988|239934;2|1239|526524|526525|128827|174708;2|976|200643|171549|815|816;2|1239|186801|186802|3085642|580596;2|1239|909932|1843489|31977|39948;2|1239|526524;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|841;2|74201|203494;2|1239|526524|526525,Complete,Atrayees
bsdb:745/1/2,Study 745,time series / longitudinal observational,32073296,https://doi.org/10.3920/BM2019.0039,NA,"Ozkul C, Yalinay M , Karakan T",Structural changes in gut microbiome after Ramadan fasting: a pilot study,Beneficial microbes,2020,"Ramadan fasting, gut microbiota, intermittent fasting, microbiome",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Fasting,EFO:0002756,Adults before fasting,Adults after fasting,healthy adults who were on Ramadan fast with a fasting period of approximately 17H per day for 29 days.,9,9,8 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure S2,13 March 2023,Barakat Dindi,"Barakat Dindi,Chloe",LeFSe analysis and Linear discriminant effect size showing the differential abundance of discriminative taxa at the two-time points I.e before and after fasting.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Pseudomonadota",2|1239;2|74152|641853;2|74152|641853|641854|641876;2|74152|641853|641854;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350;2|1239|526524;2|1224|1236|91347|543|561;2|1239|186801|186802;2|1239|91061|186826;2|544448|31969;2|1224,Complete,Atrayees
bsdb:746/1/1,Study 746,case-control,36376318,10.1038/s41467-022-34667-x,NA,"Wallen ZD, Demirkan A, Twa G, Cohen G, Dean MN, Standaert DG, Sampson TR , Payami H",Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms,Nature communications,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Parkinson's Disease subjects.,Potential PD cases for enrollment were identified via systematic pre-screening of electronic medical records (EMR) of patients with an upcoming appointment in the Movement Disorder Clinic at UAB. Subjects were invited to enroll in the study after their clinic visit if the attending specialist confirmed PD diagnosis and the patient was willing to hear about the study.,234,490,3 Months,WMS,NA,Illumina,"ANCOM,MaAsLin2",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3,3 June 2023,Fcuevas3,"Fcuevas3,Peace Sandy","Differential abundances and effect sizes of PD-associated species.
Analysis included N = 724 biologically independent samples from 490 PD and 234 neurologically healthy control (NHC) subjects. Forty-six species that had at least 75% (and up to 750%) change in abundance in PD are shown here; for all 84 PD-associated species see Supplementary Fig. 3. a Distribution of relative abundances. Log2 transformed relative abundance values, as used in MaAsLin2, were used to generate the boxplots. Untransformed relative abundances, shown in parenthesis, are provided on the X-axis for easier interpretation of data. Boxplots show distribution of the data for PD (blue green) and NHC (orange). Each sample was plotted according to its abundance of the species. The left, middle, and right vertical boundaries of each box represents the first, second (median), and third quartiles of the data; that is, 25% of samples have abundance lower than the left border of the box, 25% of samples have abundances that are higher than the right border of the box. Absence of a box indicates 75% of samples had zero abundance. The lines extending from the two ends of each box represent 1.5x outside the interquartile range (range = (abundance value at 75% minus abundance value at 25%) x 1.5). Points beyond the lines are outlier samples.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum",2|201174|1760|85004|31953|1678|1689;2|201174|1760|2037|2049|1654|544580;2|1239|91061|186826|1300|1301|1309;2|1239|186801|186802|216572|1535;2|1239|909932|1843488|909930|904|187327;2|1239|186801|3085636|186803|1432051|1432052;2157|28890|183925|2158|2159|2172|2173;2|976|200643|171549|171550|239759|626932;2|201174|1760|85004|31953|1678|1681;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|552398;2|201174|1760|85004|31953|1678|216816;2|1239|186801|3085636|186803|1649459|154046;2|1239|186801|186802|216572|1905344|1550024;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171550|239759|214856;2|1224|1236|91347|543|570|573;2|201174|1760|2037|2049|1654;2|1239|526524|526525|128827|1522,Complete,Peace Sandy
bsdb:746/1/2,Study 746,case-control,36376318,10.1038/s41467-022-34667-x,NA,"Wallen ZD, Demirkan A, Twa G, Cohen G, Dean MN, Standaert DG, Sampson TR , Payami H",Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms,Nature communications,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Parkinson's Disease subjects.,Potential PD cases for enrollment were identified via systematic pre-screening of electronic medical records (EMR) of patients with an upcoming appointment in the Movement Disorder Clinic at UAB. Subjects were invited to enroll in the study after their clinic visit if the attending specialist confirmed PD diagnosis and the patient was willing to hear about the study.,234,490,3 Months,WMS,NA,Illumina,"ANCOM,MaAsLin2",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3,3 June 2023,Fcuevas3,"Fcuevas3,Peace Sandy","Differential abundances and effect sizes of PD-associated species. Analysis included N = 724 biologically independent samples from 490 PD and 234 neurologically healthy control (NHC) subjects. Forty-six species that had at least 75% (and up to 750%) change in abundance in PD are shown here; for all 84 PD-associated species see Supplementary Fig. 3. a Distribution of relative abundances. Log2 transformed relative abundance values, as used in MaAsLin2, were used to generate the boxplots. Untransformed relative abundances, shown in parenthesis, are provided on the X-axis for easier interpretation of data. Boxplots show distribution of the data for PD (blue green) and NHC (orange). Each sample was plotted according to its abundance of the species. The left, middle, and right vertical boundaries of each box represents the first, second (median), and third quartiles of the data; that is, 25% of samples have abundance lower than the left border of the box, 25% of samples have abundances that are higher than the right border of the box. Absence of a box indicates 75% of samples had zero abundance. The lines extending from the two ends of each box represent 1.5x outside the interquartile range (range = (abundance value at 75% minus abundance value at 25%) x 1.5). Points beyond the lines are outlier samples.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|3085636|186803|841|301302;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263|1160721;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|841|360807;2|976|200643|171549|171552|838|28128;2|1239|186801|3085636|186803|572511|1322;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|31979|1485|1506;2|1239|186801|3085656|3085657|2039302|1981510;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|3085636|186803|28050|39485,Complete,Peace Sandy
bsdb:747/1/1,Study 747,"cross-sectional observational, not case-control",35615912,10.1002/acr2.11436,https://onlinelibrary.wiley.com/doi/pdf/10.1002/acr2.11436,"Bae SS, Dong TS, Wang J, Lagishetty V, Katzka W, Jacobs JP , Charles-Schoeman C",Altered Gut Microbiome in Patients With Dermatomyositis,ACR open rheumatology,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Dermatomyositis,EFO:0000398,healthy controls,dermatomyositis - ILD-MSA,Patients with dermatomyositis - ILD-associated myositis antibodies subgroup,26,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,12 March 2023,Merit,"Merit,Claregrieve1",Differential microbial abundance between healthy controls and ILD-MSA dermatomyositis patients,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,2|976|200643|171549|815,Complete,Claregrieve1
bsdb:747/2/1,Study 747,"cross-sectional observational, not case-control",35615912,10.1002/acr2.11436,https://onlinelibrary.wiley.com/doi/pdf/10.1002/acr2.11436,"Bae SS, Dong TS, Wang J, Lagishetty V, Katzka W, Jacobs JP , Charles-Schoeman C",Altered Gut Microbiome in Patients With Dermatomyositis,ACR open rheumatology,2022,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Dermatomyositis,EFO:0000398,healthy controls,dermatomyositis - Cancer-MSA,Patients with dermatomyositis - cancer-associated myositis antibodies subgroup,26,13,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,23 May 2023,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and cancer-MSA dermatomyositis patients,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:747/3/1,Study 747,"cross-sectional observational, not case-control",35615912,10.1002/acr2.11436,https://onlinelibrary.wiley.com/doi/pdf/10.1002/acr2.11436,"Bae SS, Dong TS, Wang J, Lagishetty V, Katzka W, Jacobs JP , Charles-Schoeman C",Altered Gut Microbiome in Patients With Dermatomyositis,ACR open rheumatology,2022,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Dermatomyositis,EFO:0000398,dermatomyositis - Cancer-MSA,dermatomyositis - ILD-MSA,Patients with dermatomyositis - ILD associated myositis antibodies,13,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Text , Figure 2F-H",15 December 2023,Peace Sandy,"Peace Sandy,Atrayees","Patients with DM with ILD�MSA also had significant depletion of the Christensenellaceae R-7
group (within the Christensenellaceae family), and multiple ASVs
within the Ruminococcaceae family (Ruminococcus 1, Ruminococ�caceae UCG-002, and Subdoligranulum) compared with controls
and the cancer-MSA group.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3082768|990719;2|1239|186801|186802|216572,Complete,Lwaldron
bsdb:748/1/1,Study 748,"cross-sectional observational, not case-control",26408641,https://doi.org/10.1136/gutjnl-2015-309800,https://gut.bmj.com/content/66/1/70,"Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, Tang L, Zhao H, Stenvang J, Li Y, Wang X, Xu X, Chen N, Wu WK, Al-Aama J, Nielsen HJ, Kiilerich P, Jensen BA, Yau TO, Lan Z, Jia H, Li J, Xiao L, Lam TY, Ng SC, Cheng AS, Wong VW, Chan FK, Xu X, Yang H, Madsen L, Datz C, Tilg H, Wang J, Brünner N, Kristiansen K, Arumugam M, Sung JJ , Wang J",Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer,Gut,2017,"BACTERIAL INTERACTIONS, COLONIC MICROFLORA, COLORECTAL CANCER",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,Colorectal cancer patients,Patients with colorectal cancer.,54,74,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Supplementary Table 8,12 March 2023,Sophy,"Sophy,Atrayees","Differential abundance of IMG, mOTU and MLG species associated with CRC patients and controls.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Beggiatoa|s__Beggiatoa sp. PS,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia mallei,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus evryensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. HGF2,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus sp. 3_3_56FAA,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Methylococcales|f__Crenotrichaceae|g__Crenothrix|s__Crenothrix polyspora,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. 6_1_46AFAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp. oral taxon 370,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_46FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_57FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus denitrificans,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp. oral taxon 110,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp. oral taxon 393,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus indolicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudoporcinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum|s__Sulfurovum sp. SCGC AAA036-O23,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__Synergistes sp. 3_1_syn1,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|976|200643|171549|171550|239759|626932;2|976|200643|171549|815|816|817;2|1224|1236|72273|135617|1021|422289;2|1224|28216|80840|119060|32008|13373;2|508458|649775|649776|649777|508459|508460;2|1239|186801|186802|457421;2|1239|186801|186802|31979|1485|908340;2|1239|526524|526525|2810280|100883|665941;2|1224|1236|135618|89377|200670|360316;2|200940|3031449|213115|194924|872|665942;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3082720|3118655|44259|143361;2|32066|203490|203491|203492|848|859;2|32066|203490|203491|203492|848|851;2|32066|203490|203491|203492|848|712288;2|32066|203490|203491|203492|848|856;2|1239|91061|1385|539738|1378|29391;2|1239|186801|3085636|186803|1649459|154046;2|1239|186801|3085636|186803|665950;2|1239|186801|3085636|186803|658086;2|1239|186801|3085636|186803|658085;2|1239|186801|3085636|186803|665951;2|32066|203490|203491|1129771|32067|40542;2759|4751|5204|1538075|162474|742845|55193|76773;2|1224|28211|204455|31989|265|266;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|671230;2|1239|1737404|1737405|1570339|543311|713008;2|1239|1737404|1737405|1570339|162289|33030;2|1239|186801|3082720|186804|1257|1261;2|1239|186801|3082720|186804|1257|341694;2|976|200643|171549|171552|838|28131;2|1239|526524|526525|128827|123375|102148;2|32066|203490|203491|1129771|34104|34105;2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|1300|1301|1334;2|1239|91061|186826|1300|1301|1336;2|1239|91061|186826|1300|1301|1335;2|1239|91061|186826|1300|1301|361101;2|1239|186801|186802|216572|292632|665956;2|29547|3031852|213849|2771472|265570|1001764;2|508458|649775|649776|649777|2753|457415;2|1239|186801|3085636|186803|1506553|1512,Complete,Atrayees
bsdb:748/1/2,Study 748,"cross-sectional observational, not case-control",26408641,https://doi.org/10.1136/gutjnl-2015-309800,https://gut.bmj.com/content/66/1/70,"Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, Tang L, Zhao H, Stenvang J, Li Y, Wang X, Xu X, Chen N, Wu WK, Al-Aama J, Nielsen HJ, Kiilerich P, Jensen BA, Yau TO, Lan Z, Jia H, Li J, Xiao L, Lam TY, Ng SC, Cheng AS, Wong VW, Chan FK, Xu X, Yang H, Madsen L, Datz C, Tilg H, Wang J, Brünner N, Kristiansen K, Arumugam M, Sung JJ , Wang J",Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer,Gut,2017,"BACTERIAL INTERACTIONS, COLONIC MICROFLORA, COLORECTAL CANCER",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,Colorectal cancer patients,Patients with colorectal cancer.,54,74,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Supplementary Table 8,12 March 2023,Sophy,"Sophy,Atrayees","Differential abundance of IMG, mOTU and MLG species associated with CRC patients and controls.",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Adhaeribacter|s__Adhaeribacter aquaticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SS3/4,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1224|28216|80840|469610;2|1239|186801|186802|186806|1730|39496;2|976|768503|768507|1853232|299566|299567;2|1239|186801|3085636|186803|33042|751585;2|1239|186801|186802|245014;2|1224|1236|135625|712|724|729;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|2316020|33039;2|1224|1236|91347|543|570|573;2|1239|186801|3085636|186803|28050|39485;2|976|200643|171549|815|816|626929;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|31979|1485|411489;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:749/1/1,Study 749,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S, Takeda K, Greenan S , Maki Y",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 1,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with primary dentition (PD),Down Syndrome children with primary dentition (PD),Children with Down Syndrome and in the primary dentition stage (from 0.5 years to around 6 years old),12,12,7 days,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,16 August 2023,Andre,Andre,Species-level of salivary microbiomes between children with DS and ND (PD stage),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca",2|1239|91061|1385|539738|1378|1379;2|1224|28216|206351|481|482|495;2|201174|1760|85006|1268|32207|172042;2|201174|1760|85006|1268|32207|2047;2|1224|28216|206351|481|482|490,Complete,Folakunmi
bsdb:749/1/2,Study 749,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S, Takeda K, Greenan S , Maki Y",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 1,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with primary dentition (PD),Down Syndrome children with primary dentition (PD),Children with Down Syndrome and in the primary dentition stage (from 0.5 years to around 6 years old),12,12,7 days,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,16 August 2023,Andre,Andre,Species-level of salivary microbiomes between children with DS and ND (PD stage),decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral strain T1-E5,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus genomosp. C5,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",2|1224|1236|135625|712|724|1078480;2|201174|1760|2037|2049|1654|29317;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|163599;2|1239|91061|186826|1300|1301|230122;2|32066|203490|203491|203492|848|860,Complete,Folakunmi
bsdb:749/2/1,Study 749,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S, Takeda K, Greenan S , Maki Y",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 2,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with mixed dentition (PD),Down Syndrome children with mixed dentition (PD),Children with Down Syndrome and in the mixed dentition stage (from 6 years to around 12 years old),15,15,7 days,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5,16 August 2023,Andre,Andre,Species level of salivary microbiomes between children with DS and ND (MD stage),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis",2|1239|91061|1385|539738|1378|1379;2|1239|91061|186826|186827|46123|46125;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|45634;2|201174|1760|85006|1268|32207|172042;2|1224|28216|80840|119060|47670|47671;2|201174|1760|85007|1653|1716|61592;2|201174|1760|85006|1268|32207|2047;2|201174|1760|2037|2049|1654|1655;2|1224|28216|206351|481|482|495;2|201174|1760|2037|2049|1654|544580;2|32066|203490|203491|1129771|32067|104608;2|201174|1760|2037|2049|1654|1656;2|1224|1236|135625|712|416916|739,Complete,Folakunmi
bsdb:749/2/2,Study 749,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S, Takeda K, Greenan S , Maki Y",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 2,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with mixed dentition (PD),Down Syndrome children with mixed dentition (PD),Children with Down Syndrome and in the mixed dentition stage (from 6 years to around 12 years old),15,15,7 days,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5,16 August 2023,Andre,Andre,Species-level of salivary microbiomes between children with DS and ND (MD stage),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral strain Hal-1065,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 352,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral clone IK062,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM39,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 158,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CD3:34,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",2|201174|1760|2037|2049|1654|163586;2|976|200643|171549|171552|838|712461;2|95818|713054;2|1239|526524|526525|128827|123375|102148;2|976|200643|171549|171552|838|242672;2|976|200643|171549|171552|838|60133;2|201174|1760|2037|2049|1654|936548;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|2974257|425941;2|201174|1760|2037|2049|1654|29317;2|201174|1760|2037|2049|2529408|52773;2|201174|1760|2037|2049|1654|1105029;2|201174|1760|2037|2049|1654|55565;2|1239|909932|1843489|31977|29465|671228;2|1239|91061|1385|539738|1378|84135;2|976|200643|171549|171552|838|1177577;2|1239|91061|186826|1300|1301|1304,Complete,Folakunmi
bsdb:750/1/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 1,Qatar,Homo sapiens,Saliva,UBERON:0001836,Sex design,EFO:0001752,Males,Females,NA,555,442,NA,16S,123,Illumina,LEfSe,2,NA,2,NA,"age,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,increased,Signature 1,Figure 1c,31 March 2023,Suwaiba,"Suwaiba,Atrayees",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red),decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota",2|976|117743|200644|2762318|59735;2|976|200643|171549|2005525|195950;2|976,Complete,Atrayees
bsdb:750/1/2,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 1,Qatar,Homo sapiens,Saliva,UBERON:0001836,Sex design,EFO:0001752,Males,Females,NA,555,442,NA,16S,123,Illumina,LEfSe,2,NA,2,NA,"age,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,increased,Signature 2,Figure 1c,31 March 2023,Suwaiba,"Suwaiba,Atrayees",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red),increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Spirochaetota",2|203691|203692|136|2845253|157;2|544448|31969|2085|2092|2093;2|201174|1760|85007|1653|1716;2|203691,Complete,Atrayees
bsdb:750/2/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 2,Qatar,Homo sapiens,Saliva,UBERON:0001836,Aging,GO:0007568,Adults,Elderly,People older than 65years of age,979,18,NA,16S,123,Illumina,LEfSe,0.007,NA,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,ChiomaBlessing",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Candidatus Saccharibacteria",2|976;2|976|200643|171549|171552|838;2|203691|203692|136|137|146;2|203691|203692|136|2845253|157;2|95818,Complete,Atrayees
bsdb:750/2/2,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 2,Qatar,Homo sapiens,Saliva,UBERON:0001836,Aging,GO:0007568,Adults,Elderly,People older than 65years of age,979,18,NA,16S,123,Illumina,LEfSe,0.007,NA,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,Peace Sandy",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter sp. TM7-053",2|1239|91061|186826|186827|46123;2|201174|1760|2037|2049|1654;2|201174;2|1224|1236|135625|712|416916;2|1239|909932|1843489|31977|156454;2|1239;2|29547|3031852|213849|72294|194;2|95818;2|1239|186801|3085636|186803|43996;2|1239|909932|1843489|31977|39948;2|1224|28216|206351|481|538;2|32066;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|28216|206351|481|32257;2|1239|186801|3085636|186803|1164882;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|186801|3082720|3030910|86331;2|1239|186801|3082720|186804;2|1224;2|201174|1760|85006|1268|32207;2|1239|909932|909929|1843491|970;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|95818|2093818|2093819|2093822|2093823|2902634,Complete,Atrayees
bsdb:750/3/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 3,Qatar,Homo sapiens,Saliva,UBERON:0001836,Gingival bleeding,HP:0000225,Participants without gingivitis bleeding,Participants with gingival bleeding,Participants reported suffering from a bleeding gum,913,84,NA,16S,123,Illumina,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3c,31 March 2023,Suwaiba,Suwaiba,Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red),increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976;2|976|117743|200644|49546|1016;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:750/3/2,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 3,Qatar,Homo sapiens,Saliva,UBERON:0001836,Gingival bleeding,HP:0000225,Participants without gingivitis bleeding,Participants with gingival bleeding,Participants reported suffering from a bleeding gum,913,84,NA,16S,123,Illumina,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,Peace Sandy",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red),decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter featherlites",2|201174;2|976|200643|171549|171552|1283313;2|1239;2|95818;2|32066;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|1224;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|95818|2093818|2093819|2093822|2093823|2572088,Complete,Atrayees
bsdb:750/4/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 4,Qatar,Homo sapiens,Saliva,UBERON:0001836,Oral ulcer,HP:0000155,Participants without oral ulcers,Participants with oral ulcers,Participants who reported suffering from oral ulcers,960,37,NA,16S,123,Illumina,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4c,31 March 2023,Suwaiba,Suwaiba,Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red),increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976;2|976|117743|200644|49546|1016;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:750/4/2,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 4,Qatar,Homo sapiens,Saliva,UBERON:0001836,Oral ulcer,HP:0000155,Participants without oral ulcers,Participants with oral ulcers,Participants who reported suffering from oral ulcers,960,37,NA,16S,123,Illumina,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4c,31 March 2023,Suwaiba,Suwaiba,Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red),decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota",2|1239;2|32066;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|1224;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174,Complete,Atrayees
bsdb:750/5/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 5,Qatar,Homo sapiens,Saliva,UBERON:0001836,Dentures,EFO:0010078,Participants without dentures,Participants with dentures,Participants who reported using dentures,861,136,NA,16S,123,Illumina,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 5c,31 March 2023,Suwaiba,"Suwaiba,Atrayees",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red),increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter",2|201174;2|1224;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186806|113286,Complete,Atrayees
bsdb:750/5/2,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 5,Qatar,Homo sapiens,Saliva,UBERON:0001836,Dentures,EFO:0010078,Participants without dentures,Participants with dentures,Participants who reported using dentures,861,136,NA,16S,123,Illumina,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 5c,31 March 2023,Suwaiba,"Suwaiba,Atrayees",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red),decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|29547|3031852|213849|72294|194;2|1239|186801|186802|216572,Complete,Atrayees
bsdb:750/6/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 6,Qatar,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Participants classified as smokers,733,264,NA,16S,123,Illumina,LEfSe,2,NA,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 6c,31 March 2023,Suwaiba,Suwaiba,Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red),increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:750/6/2,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 6,Qatar,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Participants classified as smokers,733,264,NA,16S,123,Illumina,LEfSe,2,NA,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 6c,31 March 2023,Suwaiba,Suwaiba,Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red),decreased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224;2|508458;2|1239|91061|186826|1300|1357;2|201174|1760|85007|1653|1716;2|1239|91061|1385|539738|1378;2|976|117743|200644|49546|1016;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:750/7/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 7,Qatar,Homo sapiens,Saliva,UBERON:0001836,Coffee consumption,EFO:0004330,Non-coffee drinkers,Coffee drinkers,Participants considered coffee drinkers,887,110,NA,16S,123,Illumina,LEfSe,2,NA,2,NA,"age,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 7c,31 March 2023,Suwaiba,"Suwaiba,Atrayees",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red),increased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|95818;2|201174;2|1224;2|1239;2|1224|28216|80840|119060|47670;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:750/7/2,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 7,Qatar,Homo sapiens,Saliva,UBERON:0001836,Coffee consumption,EFO:0004330,Non-coffee drinkers,Coffee drinkers,Participants considered coffee drinkers,887,110,NA,16S,123,Illumina,LEfSe,2,NA,2,NA,"age,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 7c,31 March 2023,Suwaiba,Suwaiba,Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red),decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976;2|32066;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:750/8/1,Study 750,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M , Al Khodor S",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 8,Qatar,Homo sapiens,Saliva,UBERON:0001836,Tea consumption measurement,EFO:0010091,Non tea drinkers,Tea drinkers,Participants considered tea drinkers,229,768,NA,16S,123,Illumina,LEfSe,2,NA,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 8c,31 March 2023,Suwaiba,Suwaiba,Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. Features with LDA scores ≥ 2 are presented,decreased,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,2|976|117743|200644|49546|1016,Complete,Atrayees
bsdb:751/1/1,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Moderate drinkers,"> 0 but ≤ 1 drinks per day, on average, for women, and > 0 but ≤ 2 drinks per day, on average, for men",270,614,NA,16S,34,Roche454,DESeq2,NA,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 1,Figure 3a,15 March 2023,Brian,"Brian,Suwaiba,Atrayees",Heatmap of fold changes and the correlations of the taxa related to alcohol drinking level,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|976|117743|200644|2762318|59735;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|32066|203490|203491|1129771|32067;2|1224|1236|135625|712;2|1224|1236|135625|712|416916;2|1224|1236|135615|868|2717;2|1224|28216|206351|481|538;2|1224|28216|206351|481|32257;2|1224|28216|206351|481|482;2|976|200643|171549,Complete,Atrayees
bsdb:751/1/2,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Moderate drinkers,"> 0 but ≤ 1 drinks per day, on average, for women, and > 0 but ≤ 2 drinks per day, on average, for men",270,614,NA,16S,34,Roche454,DESeq2,NA,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 2,Figure 3a,15 March 2023,Brian,"Brian,Suwaiba",Heat map fold changes and the correlations of the taxa related to alcohol drinking level,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans",2|1239|91061;2|1239|91061|186826|186828|117563|46124;2|1239|91061|186826|186828|117563|137732,Complete,Atrayees
bsdb:751/2/1,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Heavy drinkers,Women and men who had greater than one or two drinks per day respectively,270,160,NA,16S,34,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 1,Figure 3a,24 March 2023,Suwaiba,"Suwaiba,Atrayees",Heatmap fold changes and the correlations of the taxa related to alcohol drinking level,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|55565;2|1224|1236|135625|712|416916;2|976|117743|200644|2762318|59735;2|1239|186801|3085636|186803|1164882;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1224|1236|135625|712;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950;2|1239|91061|186826|186828|117563|137732;2|976|200643|171549,Complete,Atrayees
bsdb:751/2/2,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Heavy drinkers,Women and men who had greater than one or two drinks per day respectively,270,160,NA,16S,34,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 2,Figure 3a,24 March 2023,Suwaiba,Suwaiba,Heatmap of fold changes and the correlations of the taxa related to alcohol drinking level,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|186828|117563|46124;2|1239|91061|186826|186828|117563|137732,Complete,Atrayees
bsdb:751/3/1,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Wine drinkers,Alcohol drinkers who drank exclusively wine,270,101,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4a,24 March 2023,Suwaiba,Suwaiba,Heatmap of fold changes and the correlations of taxa related to alcohol drinking type,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella",2|1224|1236|135625|712|416916;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|538,Complete,Atrayees
bsdb:751/3/2,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Wine drinkers,Alcohol drinkers who drank exclusively wine,270,101,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4a,24 March 2023,Suwaiba,Suwaiba,Heatmap of fold changes and the correlations of taxa related to alcohol drinking type,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|1239;2|976;2|1239|186801|186802|186807;2|1239|186801|186802|186807|2740;2|976|200643|171549|171552|838;2|1239|186801|3082720|3030910|86331,Complete,Atrayees
bsdb:751/4/1,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Beer drinkers,Alcohol drinkers who drink beer exclusively,270,39,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4a,24 March 2023,Suwaiba,Suwaiba,Heatmap of fold changes of correlations of the taxa related to alcohol drinking type,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia",2|1224|1236|135625|712|416916;2|201174|1760|85004|31953|196082,Complete,Atrayees
bsdb:751/4/2,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Beer drinkers,Alcohol drinkers who drink beer exclusively,270,39,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4a,25 March 2023,Suwaiba,Suwaiba,Heatmap of fold changes and the correlations of the taxa related to alcohol drinking type,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239;2|976;2|1239|186801;2|1239|186801|186802;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:751/5/1,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 5,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Liquor drinkers,Alcohol drinkers who exclusively drank liquor,270,26,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4a,25 March 2023,Suwaiba,Suwaiba,Heatmap of fold changes and correlations of the taxa related to alcohol drinking type,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803;2|976|200643|171549|171552|838,Complete,Atrayees
bsdb:751/5/2,Study 751,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB , Ahn J",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 5,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Liquor drinkers,Alcohol drinkers who exclusively drank liquor,270,26,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4a,25 March 2023,Suwaiba,Suwaiba,Heatmap fold changes and correlations of taxa related to alcohol drinking type,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239;2|976;2|1239|186801;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|265975;2|201174|1760|85004|31953|196082;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:752/1/1,Study 752,case-control,30405010,https://doi.org/10.3390/ijerph15112479,https://www.mdpi.com/1660-4601/15/11/2479,"Rodríguez-Rabassa M, López P, Rodríguez-Santiago RE, Cases A, Felici M, Sánchez R, Yamamura Y , Rivera-Amill V",Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels,International journal of environmental research and public health,2018,"cytokines, microbiome, saliva, smoking, tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Current smokers.,16,18,None of the participants were taking antibiotics.,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,13 March 2023,Dupe,"Dupe,Mcarlson,Peace Sandy",Differential LEfSe-associated bacteria between the smoker and nonsmoker groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Leminorella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Necropsobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Archaea|p__Candidatus Bathyarchaeota",2|1224|1236|135625|712|713;2|1239|91061|186826|186828|1651;2|976|200643|171549|815;2|1239|526524|526525|128827|118747;2|976|117743|200644|2762318|59732;2|1239|526524|526525|128827|1647;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|91347|1903416|82980;2|1224|1236|135625|712|908284;2|1224|1236|91347|1903411|613;2|1224|28216|80840|995019|40544;2157|928852,Complete,Mcarlson
bsdb:752/1/2,Study 752,case-control,30405010,https://doi.org/10.3390/ijerph15112479,https://www.mdpi.com/1660-4601/15/11/2479,"Rodríguez-Rabassa M, López P, Rodríguez-Santiago RE, Cases A, Felici M, Sánchez R, Yamamura Y , Rivera-Amill V",Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels,International journal of environmental research and public health,2018,"cytokines, microbiome, saliva, smoking, tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Current smokers.,16,18,None of the participants were taking antibiotics.,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,13 March 2023,Dupe,"Dupe,Mcarlson,Peace Sandy",Differential LEfSe-associated bacteria between the smoker and nonsmoker groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Pilimelia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1239|91061|186826|186827|46123;2|201174|1760|2037|2049|1654;2|976|117743|200644|49546|1016;2|201174|1760|85007|1653|1716;2|1239|186801|3082720|3118655|44259;2|1239|91061|186826|186828|117563;2|32066|203490|203491|1129771|32067;2|1239|186801|3082720|3030910|86331;2|201174|1760|85008|28056|53370;2|1239|909932|909929|1843491|970;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950;2|1224|1236|2887326|468|469,Complete,Mcarlson
bsdb:753/1/1,Study 753,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,The both groups did not take any antibiotics 3 months prior to the study.,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3a,13 March 2023,Chioma,Chioma,Bacteria genera in saliva that differed significantly between smokers and nonsmokers.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157,Complete,Fatima
bsdb:753/1/2,Study 753,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,The both groups did not take any antibiotics 3 months prior to the study.,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3a,13 March 2023,Chioma,Chioma,Bacteria genera in saliva that differed significantly between smokers and nonsmokers.,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717,Complete,Fatima
bsdb:753/2/1,Study 753,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 2,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,The both groups did not take any antibiotics 3 months prior to the study.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3b,23 March 2023,Chioma,Chioma,Bacteria genera in tongue that differed significantly between smokers and nonsmokers,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|201174|84998|84999|1643824|1380;2|1239|909932|1843489|31977|39948,Complete,Fatima
bsdb:753/2/2,Study 753,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 2,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,The both groups did not take any antibiotics 3 months prior to the study.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3b,23 March 2023,Chioma,Chioma,Bacteria genera in tongue that differed significantly between smokers and nonsmokers,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|186801|3085636|186803|43996;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257,Complete,Fatima
bsdb:754/1/1,Study 754,case-control,25283067,https://doi.org/10.1111/omi.12086,https://pubmed.ncbi.nlm.nih.gov/25283067/,"Moon JH, Lee JH , Lee JY",Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients,Molecular oral microbiology,2015,"Korean, periodontitis, pyrosequencing, smoking, subgingival microflora",Experiment 1,Republic of Korea,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Non-smokers,Smokers,A patient was defined as a smoker if he was currently smoking and had been smoking five or more cigarettes a day for at least 10 years.,36,57,Patients were excluded if they had received antibiotic therapy within the past 3 months.,16S,123,Roche454,NA,NA,NA,NA,"age,sex",NA,NA,increased,NA,unchanged,NA,unchanged,Signature 1,"text, Figure 1, Figure 2, Figure 3",13 March 2023,Atrayees,"Atrayees,Lwaldron,Claregrieve1","Genera, phylum and species showing differences in relative abundance.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|815|816;2|29547|3031852|213849|72294|194|199;2|29547|3031852|213849|72294|194|204;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653|1716|43768;2|200940|3031451|3024411|213121|893;2|1239|186801|186802|186806|1730;2|1239|186801|3082720|3118655|44259;2|1239|186801|3082720|3118655|44259|143361;2|508458|649775|649776|3029087|1434006;2|32066|203490;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|851;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|976|200643|171549|171552|2974257|28134;2|1239|186801|3085636|186803|1164882|979627;2|1239|186801|3085636|186803|1164882|467210;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771;2|1239|186801|3082720|3030910|86331;2|1224|28216|206351|481|482|1107316;2|1224|28216|206351|481|482|490;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|2974251|305719;2|976|200643|171549|171552|2974251|28126;2|976|200643|171549|171552|2974251|439703;2|976|200643|171549|171552|2974251|228604;2|201174|1760|85006|1268|32207;2|203691|203692;2|1239|91061|186826|1300|1301;2|508458;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|3085636|186803|43996;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171551;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:754/1/2,Study 754,case-control,25283067,https://doi.org/10.1111/omi.12086,https://pubmed.ncbi.nlm.nih.gov/25283067/,"Moon JH, Lee JH , Lee JY",Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients,Molecular oral microbiology,2015,"Korean, periodontitis, pyrosequencing, smoking, subgingival microflora",Experiment 1,Republic of Korea,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Non-smokers,Smokers,A patient was defined as a smoker if he was currently smoking and had been smoking five or more cigarettes a day for at least 10 years.,36,57,Patients were excluded if they had received antibiotic therapy within the past 3 months.,16S,123,Roche454,NA,NA,NA,NA,"age,sex",NA,NA,increased,NA,unchanged,NA,unchanged,Signature 2,"text, Figure 1, Figure 2, Figure 3",13 March 2023,Atrayees,"Atrayees,Aiyshaaaa,Claregrieve1","Genera, phylum and species showing differences in relative abundance",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella seregens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rodentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] saphenum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|201174|1760|2037|2049|1654|544581;2|201174|1760|2037|2049|1654|1656;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|739;2|976|200643;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016|1018;2|976|117743|200644|49546|1016|1019;2|1224|1236|135615|868|2717;2|32066|203490|203491|203492|848|285729;2|1239|91061|186826|186828|117563|46124;2|1224|1236|135625|712|724;2|976|200643|171549|171552|52228|52229;2|1224|28216|80840|119060|47670|47671;2|32066|203490|203491|1129771|32067|40542;2|32066|203490|203491|1129771|32067|109328;2|1239|909932|1843489|31977|906|187326;2|1239|186801|3082720|3030910|86331|35519;2|1224|28216|206351|481|482|267212;2|1224|28216|206351|481|482|495;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|488;2|1224|28216|206351|481|482|33053;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|28133;2|976|200643|171549|171552|2974251|28136;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552;2|1224;2|201174|1760|85006|1268|32207|172042;2|201174|1760|85006|1268|32207|2047;2|201174|1760|2037|2049|2529408|1660;2|1239|909932|909929|1843491|970|135083;2|1239|91061|186826|1300|1301|45634;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|257758;2|1239|91061|186826|1300|1301|1305;2|203691|203692|136|2845253|157|59892;2|203691|203692|136|2845253|157|53418;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|248315;2|1239|186801|186802|543314|35517;2|1239|186801|186802|543314|35518;2|1239|186801|186802|543314|51123;2|1239|186801|3082720|3118655|1913599|39498;2|1224|1236|135625|712|416916;2|508458|649775|649776|3029087|1434006;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157,Complete,Claregrieve1
bsdb:755/1/NA,Study 755,case-control,33557896,https://doi.org/10.1186/s13024-021-00427-6,https://pubmed.ncbi.nlm.nih.gov/33557896/,"Aho VTE, Houser MC, Pereira PAB, Chang J, Rudi K, Paulin L, Hertzberg V, Auvinen P, Tansey MG , Scheperjans F","Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson's disease",Molecular neurodegeneration,2021,"Inflammation, Intestine, Microbiota, Parkinson’s disease, Short-chain fatty acids",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Parkinson's disease patients,Patients who have Parkinson's disease,56,55,NA,16S,34,Illumina,DESeq2,NA,TRUE,NA,"age,body mass index,sex",sex,NA,decreased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:756/1/1,Study 756,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas AM, Gleber-Netto FO, Fernandes GR, Amorim M, Barbosa LF, Francisco AL, de Andrade AG, Setubal JC, Kowalski LP, Nunes DN , Dias-Neto E",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 1,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,Smoking behavior,EFO:0004318,Controls (C),Smokers (S),All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years.,9,6,last 3 months,16S,1,Ion Torrent,Kruskall-Wallis,NA,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi",Relatively abundant phyla and genera found in the groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Oceanobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rhodanobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Thiomicrospira,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Saccharibacteria",2|1239|91061|186826|186827|46123;2|57723;2|1224|1236|135625|712|416916;2|67819;2|1239|91061|186826|186828|292480;2|1239;2|1239|91061|1385|186817|1386;2|976|117743|200644|2762318|59735;2|1224|28216|80840|80864|28219;2|1117;2|1239|186801|186802;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|32257;2|1239|186801|3085636|186803;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|437755;2|544448;2|1224|28216|206351|481|482;2|1224|1236|135619|135620|196079;2|1239|186801|3085636|186803|265975;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|1224;2|1224|1236|135622|267894|67572;2|1224|1236|135614|1775411|75309;2|201174|84995|84996|84997|42255;2|203691|203692;2|1239|91061|1385|90964|1279;2|29547|3031852|213849|2771472|265570;2|1224|1236|72273|135616|933;2|363464;2|95818,Complete,Folakunmi
bsdb:756/1/2,Study 756,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas AM, Gleber-Netto FO, Fernandes GR, Amorim M, Barbosa LF, Francisco AL, de Andrade AG, Setubal JC, Kowalski LP, Nunes DN , Dias-Neto E",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 1,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,Smoking behavior,EFO:0004318,Controls (C),Smokers (S),All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years.,9,6,last 3 months,16S,1,Ion Torrent,Kruskall-Wallis,NA,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi",Relatively abundant phyla and genera found in the groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halothermotrichaceae|g__Halothermothrix,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halocella",2|1224|28216|80840|506|222;2|201174;2|201174|1760|85006|85023|110934;2|1224|28216|80840|506|507;2|201174|1760|2037|2049|28263;2|201174|1760|85006|1268|1663;2|976|117743|200644|49546|1016;2|976|117743|200644|2762318|308865;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|186801|53433|3046412|32636;2|201174|1760|85006|85023|110932;2|201174|1760|85006|85023|33882;2|976|200643|171549|171552|838;2|1224|28216|80840|119060|48736;2|976|200643|171549|171550;2|1224|28211|204457|41297|13687;2|1224|1236|135614|32033|40323;2|976|200643|171549|2005525|195950;2|1224|28216|80840|80864|34072;2|976|117747|200666|84566|84567;2|1239|186801|53433|972|46466,Complete,Folakunmi
bsdb:756/2/1,Study 756,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas AM, Gleber-Netto FO, Fernandes GR, Amorim M, Barbosa LF, Francisco AL, de Andrade AG, Setubal JC, Kowalski LP, Nunes DN , Dias-Neto E",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 2,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,"Smoking behavior,Alcohol drinking","EFO:0004329,EFO:0004318",Controls (C),Smokers/Drinkers (SD),"All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years. These individuals also reported daily drinking habits (>1×/day, >3 drinks/occasion) and a regular drinking history of at least 10 years.",9,7,last 3 months,16S,1,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi",Relatively abundant phyla and genera found in the groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halocella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Oceanobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rhodanobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Thiomicrospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Saccharibacteria",2|1239|91061|186826|186827|46123;2|1224|1236|135625|712|416916;2|201174|1760|2037|2049|28263;2|67819;2|201174|1760|85006|1268|1663;2|1239;2|1239|91061|1385|186817|1386;2|976|200643;2|976|117743|200644|2762318|59735;2|1224|28216|80840|80864|28219;2|200795|32061;2|1117;2|1239|186801|186802;2|976|117743|200644|49546|237;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|186801|53433|972|46466;2|1224|28216|206351|481|32257;2|1239|186801|3085636|186803;2|201174|1760|85006|85023|110932;2|201174|1760|85006|85023|33882;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|437755;2|1224|28216|206351|481|482;2|1224|1236|135619|135620|196079;2|1239|186801|3085636|186803|265975;2|976|117747|200666|84566|84567;2|1239|186801|3082720|186804|1257;2|1224;2|1224|1236|135622|267894|67572;2|1224|28216|80840|119060|48736;2|1224|1236|135614|1775411|75309;2|201174|84995|84996|84997|42255;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279;2|29547|3031852|213849|2771472|265570;2|976|200643|171549|2005525|195950;2|1224|1236|72273|135616|933;2|1224|28216|80840|80864|34072;2|363464;2|95818,Complete,Folakunmi
bsdb:756/2/2,Study 756,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas AM, Gleber-Netto FO, Fernandes GR, Amorim M, Barbosa LF, Francisco AL, de Andrade AG, Setubal JC, Kowalski LP, Nunes DN , Dias-Neto E",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 2,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,"Smoking behavior,Alcohol drinking","EFO:0004329,EFO:0004318",Controls (C),Smokers/Drinkers (SD),"All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years. These individuals also reported daily drinking habits (>1×/day, >3 drinks/occasion) and a regular drinking history of at least 10 years.",9,7,last 3 months,16S,1,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi",Relatively abundant phyla and genera found in the groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halothermotrichaceae|g__Halothermothrix,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Oceanobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|28216|80840|506|222;2|57723;2|201174;2|201174|1760|85006|85023|110934;2|1224|28216|80840|506|507;2|976|117743|200644|49546|1016;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1239|186801|53433|3046412|32636;2|544448;2|1224|1236|135619|135620|196079;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171552|838;2|1224|1236|135614|32033|40323,Complete,Folakunmi
bsdb:757/1/1,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 1,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi","Bacteria identified at the eyelid margin which showed significant differences in mean
relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,2|1224|1236|72274|135621|286|303,Complete,Folakunmi
bsdb:757/1/2,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 1,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans",2|201174|1760|85007|1653|1716|38284;2|201174|1760|85007|1653|1716|38290;2|201174|1760|85007|1653|1716|146827,Complete,Folakunmi
bsdb:757/2/1,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 2,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Healthy Control,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean.  *P < 0.05,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,2|1224|1236|72274|135621|286|303,Complete,Folakunmi
bsdb:757/2/2,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 2,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Healthy Control,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean.  *P < 0.05,decreased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus nagyae,2|1239|1737404|1737405|1570339|165779|1755241,Complete,Folakunmi
bsdb:757/3/1,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 3,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Control,Meibomian Gland Dysfunction,Participants with MGD corresponding to  evaporative dry eye disease (moderate).,15,15,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans",2|201174|1760|85007|1653|1716|38284;2|201174|1760|85007|1653|1716|38290;2|201174|1760|85007|1653|1716|146827,Complete,Folakunmi
bsdb:757/3/2,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 3,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Control,Meibomian Gland Dysfunction,Participants with MGD corresponding to  evaporative dry eye disease (moderate).,15,15,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05,decreased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus nagyae,2|1239|1737404|1737405|1570339|165779|1755241,Complete,Folakunmi
bsdb:757/4/1,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 4,Australia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi","Bacteria identified from the conjunctiva which showed significant differences in
mean relative abundance between the groups - MGD   and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Caballeronia|s__Caballeronia zhejiangensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas azotoformans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oleovorans",2|1224|28216|80840|119060|1827195|871203;2|1224|1236|72274|135621|286|47878;2|1224|1236|72274|135621|286|301,Complete,Folakunmi
bsdb:757/4/2,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 4,Australia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi","Bacteria identified from the conjunctiva which showed significant differences in
mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi",2|201174|1760|85007|1653|1716|161879;2|201174|1760|85007|1653|1716|38290,Complete,Folakunmi
bsdb:757/5/1,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 5,Australia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,control,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi","Bacteria identified from the conjunctiva which showed significant differences in
mean relative abundance between the groups- MGD+LD and healthy controls. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Caballeronia|s__Caballeronia zhejiangensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas azotoformans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oleovorans",2|1224|28216|80840|119060|1827195|871203;2|1224|1236|72274|135621|286|47878;2|1224|1236|72274|135621|286|301,Complete,Folakunmi
bsdb:757/6/1,Study 757,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J, Majzoub ME, Coroneo M, Thomas T , Willcox M",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 6,Australia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,control,Meibomian Gland Dysfunction,Participants with MGD  to  evaporative dry eye disease (moderate DED).,15,15,No use of antibiotics in the prior 3 months.,16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi","Bacteria identified from the conjunctiva which showed significant differences in
mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi",2|201174|1760|85007|1653|1716|161879;2|201174|1760|85007|1653|1716|38290,Complete,Folakunmi
bsdb:758/1/1,Study 758,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y, Teng F, Huang S, Lin Z, Yuan X, Zeng X , Yang F",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,EFO:1000058,Healthy controls at Baseline,Nasopharyngeal carcinoma patients at baseline,Patients who have not received treatment yet,3,3,30 days,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,30 August 2023,Andre,Andre,Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1224;2|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:758/1/2,Study 758,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y, Teng F, Huang S, Lin Z, Yuan X, Zeng X , Yang F",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,EFO:1000058,Healthy controls at Baseline,Nasopharyngeal carcinoma patients at baseline,Patients who have not received treatment yet,3,3,30 days,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 3,30 August 2023,Andre,Andre,Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota",2|1239|91061|186826|1300|1301;2|1239,Complete,Folakunmi
bsdb:758/2/1,Study 758,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y, Teng F, Huang S, Lin Z, Yuan X, Zeng X , Yang F",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,EFO:1000058,Nasopharyngeal carcinoma patients at baseline,Nasopharyngeal carcinoma patients after treatment,Patients who have received treatment after 7 or 12 months,3,3,30 days,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 3 and within results text (under taxonomy-based characterisation of saliva microbiota, paragraph 4)",30 August 2023,Andre,"Andre,Folakunmi",Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:758/2/2,Study 758,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y, Teng F, Huang S, Lin Z, Yuan X, Zeng X , Yang F",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,EFO:1000058,Nasopharyngeal carcinoma patients at baseline,Nasopharyngeal carcinoma patients after treatment,Patients who have received treatment after 7 or 12 months,3,3,30 days,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3 and  within results text (under taxonomy-based characterisation of saliva microbiota, paragraph 4)",30 August 2023,Andre,"Andre,Folakunmi",Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:759/1/1,Study 759,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J, Vogt JK, Dalgaard MD, Pedersen O, Holmgaard K , Heegaard S",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 1,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,Dry Eye,Patients with Aqueous Deficient Dry Eye without Ocular Graft vs Host Disease,28,21,For controls- those with hx of recent (within 3 mos) use of antibiotics (local or systemic) were excluded.  ADDE patients were allowed and 7/21 had received local or systemic antibiotics within the previous 3 mos.,16S,34,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 4a,  within result text (Several genera were less abundant in ADDE, lines 8-15)",4 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Comparison of the relative abundances of genera with DESeq2 between patients with DryEye and Control,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85007|1653|1716;2|976|117743|200644|49546|237;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28216|80840|75682|149698;2|201174|1760|85006|85023|33882;2|1224|28216|80840|80864|219181;2|201174|1760|85006|1268|32207;2|1224|28211|204457|41297|13687;2|1297|188787|68933|188786|270;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:759/2/1,Study 759,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J, Vogt JK, Dalgaard MD, Pedersen O, Holmgaard K , Heegaard S",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 2,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,OGVHD,"Patients with Aqueous Deficient Dry Eye and Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,18,For controls- those with hx of recent (within 3 mos) use of antibiotics (local or systemic) were excluded.  ADDE patients were allowed and 7/21 had received local or systemic antibiotics within the previous 3 mos.,16S,34,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 4b,  within result text (Several genera were less abundant in ADDE, line 19)",4 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Comparison of the relative abundances of genera with DESeq2 between patients with OGVHD and Control,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1239|91061|186826|186828|2747;2|976|117743|200644|2762318|501783;2|1239|91061|1385|186820|1637;2|201174|1760|85006|85023|33882;2|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:759/2/2,Study 759,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J, Vogt JK, Dalgaard MD, Pedersen O, Holmgaard K , Heegaard S",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 2,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,OGVHD,"Patients with Aqueous Deficient Dry Eye and Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,18,For controls- those with hx of recent (within 3 mos) use of antibiotics (local or systemic) were excluded.  ADDE patients were allowed and 7/21 had received local or systemic antibiotics within the previous 3 mos.,16S,34,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 4b, within result text (Several genera were less abundant in ADDE, line 20)",4 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Comparison of the relative abundances of genera with DESeq2 between patients with OGVHD and Control,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,2|1239|91061|1385|186817|1386,Complete,Folakunmi
bsdb:759/3/1,Study 759,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J, Vogt JK, Dalgaard MD, Pedersen O, Holmgaard K , Heegaard S",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 3,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,ADDE,"Patients with Aqueous Deficient Dry Eye including those with and without Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,39,For controls- those with hx of recent (within 3 mos) use of antibiotics (local or systemic) were excluded.  ADDE patients were allowed and 7/21 had received local or systemic antibiotics within the previous 3 mos.,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 September 2023,Mary Bearkland,Mary Bearkland,"Fig. 5. Bacterial biomarkers identified with the LEfSe algorithm. A. Circular cladogram displaying the relation between taxa at different taxonomic levels (i.e.
phylum to genus level). Among the enriched bacteria (biomarkers) in aqueous tear-deficient dry eye (ADDE) (red) was Bacilli and for controls (green) was Pseudomonadaceae.
The size of the nodes represents the taxa abundance. B. Scores for linear discriminant analysis (LDA) with LEfSe tool for taxa with LDA score >3 and p
<0.05 are shown in the histogram. Similarly, as the cladogram demonstrated, among the bacterial biomarkers, Pseudomonas was identified for controls and Bacilli
for ADDE.",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae",2|1239|91061;2|1239;2|201174|1760|85006|85019|1696;2|1224|28211|356|212791;2|1224|1236|2887326|468;2|201174|1760|85006|85019,Complete,Folakunmi
bsdb:759/3/2,Study 759,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J, Vogt JK, Dalgaard MD, Pedersen O, Holmgaard K , Heegaard S",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 3,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,ADDE,"Patients with Aqueous Deficient Dry Eye including those with and without Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,39,For controls- those with hx of recent (within 3 mos) use of antibiotics (local or systemic) were excluded.  ADDE patients were allowed and 7/21 had received local or systemic antibiotics within the previous 3 mos.,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,4 September 2023,Mary Bearkland,Mary Bearkland,"Fig. 5. Bacterial biomarkers identified with the LEfSe algorithm. A. Circular cladogram displaying the relation between taxa at different taxonomic levels (i.e.
phylum to genus level). Among the enriched bacteria (biomarkers) in aqueous tear-deficient dry eye (ADDE) (red) was Bacilli and for controls (green) was Pseudomonadaceae.
The size of the nodes represents the taxa abundance. B. Scores for linear discriminant analysis (LDA) with LEfSe tool for taxa with LDA score >3 and p
<0.05 are shown in the histogram. Similarly, as the cladogram demonstrated, among the bacterial biomarkers, Pseudomonas was identified for controls and Bacilli
for ADDE.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",2|1239|91061|186826|186828;2|1239|91061|186826|186828|2747;2|976|117743|200644|49546;2|1224|1236|72274|135621;2|1224;2|1224|1236|72274|135621|286;2|201174|1760|85007;2|201174|1760|85007|1653;2|201174|1760|85006|1268,Complete,Folakunmi
bsdb:760/1/1,Study 760,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F, Li S, Chen W, Han Y, Yao Y, Yang L, Li Q, Xiao Q, Wei J, Liu Z, Chen T , Deng X",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Placebo control group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 Weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,increased,NA,NA,NA,Signature 1,Figure 4,14 September 2023,Yjung24,"Yjung24,Atrayees,Peace Sandy","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at
different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",increased,"k__Bacteria|p__Actinomycetota|c__Rubrobacteria,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|84995;2|201174|84995|84996;2|201174|1760|85006|1268;2|201174|84995|84996|84997;2|976|200643|171549|171550;2|1239|526524|526525|2810281;2|1239|186801|186802|31979;2|1239|186801|186802|186807;2|201174|1760|85006|1268|32207;2|201174|84995|84996|84997|42255;2|976|200643|171549|1853231|283168;2|976|200643|171549|171550|239759;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|420345;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|244127;2|1224|1236|135625|712|724,Complete,Peace Sandy
bsdb:760/1/2,Study 760,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F, Li S, Chen W, Han Y, Yao Y, Yang L, Li Q, Xiao Q, Wei J, Liu Z, Chen T , Deng X",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Placebo control group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 Weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,increased,NA,NA,NA,Signature 2,Figure 4,14 September 2023,Yjung24,"Yjung24,Peace Sandy","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota",2|1239|91061|186826|186827|46123;2|1224|1236|135625|712|713;2|1239|91061|186826|186827;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|3085642|580596;2|1239|186801|3082768|990719|990721|1935934;2|1239|91061|186826|81852;2|1239|526524|526525|128827;2|1239|91061|1385|90964|227979;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1224|1236|91347|1903414|581;2|976|200643|171549|2005525|375288;2|201174|84998|1643822|1643826|651554;2|976|200643|171549|171552|577309;2|1224|1236|72274|135621;2|1224|1236|2887326|468|497;2|1239|186801|186802|216572|1263;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201,Complete,Peace Sandy
bsdb:760/2/1,Study 760,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F, Li S, Chen W, Han Y, Yao Y, Yang L, Li Q, Xiao Q, Wei J, Liu Z, Chen T , Deng X",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer]  Patients Pre-treatment group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 Weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Fig 4,1 February 2024,Peace Sandy,Peace Sandy,"LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacteria|p__Actinomycetota|c__Rubrobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",2|976|200643|171549|171550|239759;2|1239|526524|526525|128827|118966;2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|204475;2|1224|1236|135625|712|724;2|1239|186801|186802|31979|420345;2|201174|1760|85006|1268;2|976|200643|171549|1853231|283168;2|1239|186801|186802|186807;2|1239|186801|186802|186807|2740;2|976|200643|171549|171550;2|201174|1760|85006|1268|32207;2|201174|84995|84996|84997|42255;2|201174|84995|84996|84997;2|201174|84995|84996;2|201174|84995;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281,Complete,Peace Sandy
bsdb:760/2/2,Study 760,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F, Li S, Chen W, Han Y, Yao Y, Yang L, Li Q, Xiao Q, Wei J, Liu Z, Chen T , Deng X",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer]  Patients Pre-treatment group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 Weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Fig 4,1 February 2024,Peace Sandy,Peace Sandy,"LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",decreased,"k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae|s__Opitutaceae bacterium TAV5,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|256845;2|142182|219685;2|74201|414999|415000|134623|794903;2|1239|186801;2|256845|1313211;2|1239|186801|186802;2|256845|1313211|278082;2|1224|28216|206389;2|1224|28216|80840|80864;2|1224|28216|206389|75787;2|1239|91061|186826|33958;2|256845|1313211|278082|255528;2|201174|84998|1643822|1643826|447020;2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|162290;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|830;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|841;2|1239|909932|1843488|909930|33024;2|256845|1313211|278082|255528|172900;2|200940|3031449|213115|194924|872,Complete,Peace Sandy
bsdb:760/3/1,Study 760,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F, Li S, Chen W, Han Y, Yao Y, Yang L, Li Q, Xiao Q, Wei J, Liu Z, Chen T , Deng X",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer] Patients Pre-treatment group,Placebo group,"Patients in the Placebo group routinely treated with placebo tablets instead of
probiotics",50,50,2 Weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,NA,NA,NA,Signature 1,Figure 4,14 September 2023,Yjung24,"Yjung24,Peace Sandy","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota",2|1239|91061|186826|186827|46123;2|1224|1236|135625|712|713;2|1239|91061|186826|186827;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|3085642|580596;2|1239|186801|3082768|990719|990721|1935934;2|1239|91061|186826|81852;2|1239|526524|526525|128827;2|1239|91061|1385|90964|227979;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803;2|1224|1236|91347|1903414|581;2|976|200643|171549|2005525|375288;2|201174|84998|1643822|1643826|651554;2|1224|1236|72274|135621;2|1224|1236|2887326|468|497;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201,Complete,Peace Sandy
bsdb:760/3/2,Study 760,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F, Li S, Chen W, Han Y, Yao Y, Yang L, Li Q, Xiao Q, Wei J, Liu Z, Chen T , Deng X",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer] Patients Pre-treatment group,Placebo group,"Patients in the Placebo group routinely treated with placebo tablets instead of
probiotics",50,50,2 Weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,NA,NA,NA,Signature 2,Fig 4,2 February 2024,Peace Sandy,Peace Sandy,"LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Verrucomicrobiota|c__Opitutia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",2|201174|84998|1643822|1643826|447020;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|830;2|1239|186801;2|1224|28216|80840|80864;2|1239|186801|3085636|186803|33042;2|200940|3031449|213115|194924|872;2|1239|186801|186802;2|1239|1737404|1737405|1570339|162290;2|142182|219685;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|256845|1313211;2|256845;2|74201|414999;2|1239|909932|1843488|909930|33024;2|1224|28216|206389|75787;2|1224|28216|206389;2|256845|1313211|278082|255528;2|256845|1313211|278082;2|256845|1313211|278082|255528|172900,Complete,Peace Sandy
bsdb:761/1/1,Study 761,case-control,35657343,10.1002/ijc.34145,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420782/,"Wu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA , Vogtmann E","The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study",International journal of cancer,2022,"Ghana, breast cancer, fecal microbiome, nonmalignant breast diseases, oral microbiome",Experiment 1,Ghana,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Control,Breast Health Condition,Women with breast cancer cases,419,369,1 month,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,geographic area","age,alcohol drinking,antibiotic exposure,body mass index,contraception,education level,family history of cancer,geographic area,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Suppl. Table S1,9 March 2024,Muqtadirat,"Muqtadirat,MyleeeA",Genera with higher odds ratio in breast cancer cases in comparison with control,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 1-8",2|1239|1737404|1737405|1570339|1161127;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|196081;2|976|200643|171549|2005525|195950;2|976|200643|171549|171552;2|976|200643|171549|171552|838|1486937,Complete,NA
bsdb:761/2/1,Study 761,case-control,35657343,10.1002/ijc.34145,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420782/,"Wu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA , Vogtmann E","The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study",International journal of cancer,2022,"Ghana, breast cancer, fecal microbiome, nonmalignant breast diseases, oral microbiome",Experiment 2,Ghana,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Control,Breast Health Condition,Women with non malignant cases,419,93,1 month,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,geographic area","age,alcohol drinking,antibiotic exposure,body mass index,contraception,education level,family history of cancer,geographic area,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Suppl. Table S1,10 March 2024,Muqtadirat,"Muqtadirat,MyleeeA",Genera with higher odds ratio in non malignant cases in comparison with control,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 1-8",2|976|117743|200644|2762318|59735;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|196081;2|976|200643|171549|2005525|195950;2|976|200643|171549|171552;2|976|200643|171549|171552|838|1486937,Complete,NA
bsdb:761/3/1,Study 761,case-control,35657343,10.1002/ijc.34145,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420782/,"Wu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA , Vogtmann E","The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study",International journal of cancer,2022,"Ghana, breast cancer, fecal microbiome, nonmalignant breast diseases, oral microbiome",Experiment 3,Ghana,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Non malignant,Breast cancer,Women with breast cancer cases,93,369,1 month,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,geographic area","age,alcohol drinking,antibiotic exposure,body mass index,contraception,education level,family history of cancer,geographic area,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Suppl. Table S1,10 March 2024,Muqtadirat,Muqtadirat,Genera with higher odds ratio in breast cancer cases in comparison with non malignant cases,increased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,2|1239|1737404|1737405|1570339|1161127,Complete,NA
bsdb:762/1/1,Study 762,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z, Gong Y, Chen S, Li S, Zhang Y, Zhong H, Wang Z, Chen Y, Deng Q, Jiang Y, Li L, Fu M , Yi G",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 1,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,"Patients with Dry Eye  (with or without Meibomian Gland Disease).  
Subjects were considered to have DE if a positive
dry eye survey OSDI ≥ 13 was recorded in addition
to a positive score in one or more tests (tear break-up time
≤ 10; osmolarity ≥ 308 mOsm/L or interocular difference > 8
mOsm/L; ocular surface staining > 5 corneal spots, > 9 conjunctival
spots, or lid margin ≥ 2 mm length, and 25% width).",54,35,No antibiotics for 6 months prior to study entry,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 4,9 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,Folakunmi","Taxa listed according to their linear discriminant analysis (LDA)
values determined from comparisons between the DE patients and NDE
subjects as computed by the use of the LEfSe algorithm.",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia,2|976|200643,Complete,Folakunmi
bsdb:762/1/2,Study 762,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z, Gong Y, Chen S, Li S, Zhang Y, Zhong H, Wang Z, Chen Y, Deng Q, Jiang Y, Li L, Fu M , Yi G",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 1,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,"Patients with Dry Eye  (with or without Meibomian Gland Disease).  
Subjects were considered to have DE if a positive
dry eye survey OSDI ≥ 13 was recorded in addition
to a positive score in one or more tests (tear break-up time
≤ 10; osmolarity ≥ 308 mOsm/L or interocular difference > 8
mOsm/L; ocular surface staining > 5 corneal spots, > 9 conjunctival
spots, or lid margin ≥ 2 mm length, and 25% width).",54,35,No antibiotics for 6 months prior to study entry,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 4,9 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi","Taxa listed according to their linear discriminant analysis (LDA)
values determined from comparisons between the DE patients and NDE
subjects as computed by the use of the LEfSe algorithm.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas plecoglossicida",2|1224|1236;2|1224|1236|72274|135621;2|1224;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|70775,Complete,Folakunmi
bsdb:762/2/1,Study 762,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z, Gong Y, Chen S, Li S, Zhang Y, Zhong H, Wang Z, Chen Y, Deng Q, Jiang Y, Li L, Fu M , Yi G",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 2,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Non-MGD,MGD,Patients with Dry Eye with Meibomian Gland Disease,10,25,No antibiotics for 6 months prior to study entry,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6,9 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi",Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of the LEfSe algorithm.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus pumilus",2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061;2|1239|91061|1385|186817|1386|1408,Complete,Folakunmi
bsdb:762/2/2,Study 762,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z, Gong Y, Chen S, Li S, Zhang Y, Zhong H, Wang Z, Chen Y, Deng Q, Jiang Y, Li L, Fu M , Yi G",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 2,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Non-MGD,MGD,Patients with Dry Eye with Meibomian Gland Disease,10,25,No antibiotics for 6 months prior to study entry,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6,9 September 2023,Mary Bearkland,"Mary Bearkland,Aleru002,Folakunmi",Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of LEfSe algorithm.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas",2|976|200643|171549|171552|1283313;2|976|200643|171549;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572;2|1224|1236|135614|32033|141948,Complete,Folakunmi
bsdb:763/1/1,Study 763,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X, Miao L, Deng Y, Bible PW, Hu X, Zou Y, Liu Y, Guo S, Liang J, Chen T, Peng GH, Chen W, Liang L , Wei L",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Age at assessment,EFO:0008007,Young,Old,Aged 47-84 years old,48,42,No history of antibiotics in the past 6 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6,10 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","FIGURE 6. The bacterial species with significant differences in relative
abundance between old and young groups. The LefSe program is used
to find the bacterial species that specifically distinguish the old (green)
from young (red) conjunctival microbiomes (LDA score > 3).",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium resistens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus radiodurans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Rubrivivax|s__Rubrivivax gelatinosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia|s__Wolbachia pipientis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia|s__Wolbachia sp.",2|1239|1737404|1737405|1570339|165779|33034;2|201174|1760|85007|1653|1716|169292;2|201174|1760|85007|1653|1716|38289;2|201174|1760|85007|1653|1716|258224;2|201174|1760|85007|1653|1716|43771;2|201174|1760|85009|31957|1912216|33010;2|1297|188787|118964|183710|1298|1299;2|1224|1236|91347|543|561|562;2|1239|1737404|1737405|1570339|150022|1260;2|32066|203490|203491|1129771|32067|40542;2|201174|1760|85006|1268|1269|1270;2|1224|28216|206351|481|482|485;2|1224|28216|206351|481|482|486;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1224|28216|80840|2975441|28067|28068;2|1239|91061|1385|90964|1279|1283;2|1239|91061|1385|90964|1279|28035;2|1239|91061|1385|90964|1279|1292;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|257758;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1306;2|1224|28211|766|942|953|955;2|1224|28211|766|942|953|956,Complete,Peace Sandy
bsdb:763/1/2,Study 763,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X, Miao L, Deng Y, Bible PW, Hu X, Zou Y, Liu Y, Guo S, Liang J, Chen T, Peng GH, Chen W, Liang L , Wei L",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Age at assessment,EFO:0008007,Young,Old,Aged 47-84 years old,48,42,No history of antibiotics in the past 6 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 6,10 September 2023,Mary Bearkland,Mary Bearkland,"FIGURE 6. The bacterial species with significant differences in relative
abundance between old and young groups. The LefSe program is used
to find the bacterial species that specifically distinguish the old (green)
from young (red) conjunctival microbiomes (LDA score > 3).",decreased,"k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis pulmonis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Chlorobiota|c__Chlorobiia|o__Chlorobiales|f__Chlorobiaceae|g__Chlorobium|s__Chlorobium phaeobacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria|s__Listeria monocytogenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira murdochii,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|g__Candidatus Karelsulcia,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis bovis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2|544448|2790996|2895623|2767358|2107;2|1239|91061|186826|33958|1578|47770;2|1090|191410|191411|191412|1091|1096;2|1239|91061|1385|186820|1637|1639;2|1239|91061|186826|81852|1350|1351;2|203691|203692|1643686|143786|29521|84378;2|976|117743|200644|336809;2|544448|2790996|2895623|2767358|28903;2|1224|1236|72274|135621|286|287;2|1224|28211|356|118882|234|529;2|544448|2790996|2895623|2923352|2100;2|201174|1760|85009|31957|1912216|1747,Complete,Peace Sandy
bsdb:763/2/1,Study 763,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X, Miao L, Deng Y, Bible PW, Hu X, Zou Y, Liu Y, Guo S, Liang J, Chen T, Peng GH, Chen W, Liang L , Wei L",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 2,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,Male,Female,Biological sex=female,42,48,No history of antibiotics in the past 6 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4a,24 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","FIGURE 4. Sex-differences in conjunctival microbiome of healthy adults. Male and female groups,... while no significant difference is observed in Shannon diversity index (A).  (Note- no taxon were found to be decreased in females compared to males)",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter|s__[Acidovorax] ebreus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii",2|1224|1236|91347|543|561|562;2|201174|1760|85006|1268|1269|1270;2|1224|28216|80840|80864|238749|721785;2|1239|91061|1385|90964|1279|1283;2|1224|1236|2887326|468|469|470,Complete,Peace Sandy
bsdb:763/2/2,Study 763,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X, Miao L, Deng Y, Bible PW, Hu X, Zou Y, Liu Y, Guo S, Liang J, Chen T, Peng GH, Chen W, Liang L , Wei L",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 2,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,Male,Female,Biological sex=female,42,48,No history of antibiotics in the past 6 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4a,24 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","FIGURE 4. Sex-differences in conjunctival microbiome of healthy adults. Male and female groups,... while no significant difference is observed in Shannon diversity index (A).  (Note- no taxon were found to be increased in females compared to males)",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282,Complete,Peace Sandy
bsdb:764/1/1,Study 764,case-control,29172724,10.1080/02713683.2017.1406528,NA,"Ham B, Hwang HB, Jung SH, Chang S, Kang KD , Kwon MJ",Distribution and Diversity of Ocular Microbial Communities in Diabetic Patients Compared with Healthy Subjects,Current eye research,2018,"Bacterial diversity, Bradyrhizobiaceae, Burkholderia, LFR analysis, Staphylococcus",Experiment 1,Republic of Korea,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Type II diabetes mellitus,MONDO:0005148,healthy controls,diabetic,Type 2 diabetic patients undergoing vitrectomy,16,9,No antibiotics in the 6 months prior to enrollment,16S,4,Illumina,LEfSe,0.05,NA,2.6,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5,19 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","Figure 5. Comparative analysis of the microbial communities of groups with and without diabetes at the phylum (A) and genus (B) levels using the linear
discriminant analysis (LDA) effect size (LEfSe) method. LDA scores (log 10) for the most prevalent taxa in diabetic patients are represented on the positive scale,
whereas LDA-negative scores indicate enriched taxa in the healthy controls.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Desulfuromonadaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Salinibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales,k__Eukaryota|k__Metazoa|p__Chordata|c__Lepidosauria|o__Squamata|f__Viperidae|s__Crotalinae|g__Trimeresurus|s__Trimeresurus fasciatus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae",2|1224|1236|2887326|468|469;2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|1224|1236|135624;2|1224|28211|356|82115|357;2|1224|1236|135622|72275;2|1224|1236|135622;2|201174|1760|85006|1268|1663;2|1224|28211|204458|76892|76890;2|1224|28211|204441|2829815|191;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060;2|1224|28216|80840;2|1224|1236|135613|1046;2|28221;2|1239|186801|186802|2937910|1562;2|200940|3031651|69541|213421;2|200940|3031651|69541;2|1224|1236;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|1224|1236|135622|267893;2|201174|1760|85006|85021;2|1224|1236|72274|2887365|2742;2|201174|1760|85006|1268;2|201174|1760|85006|1268|1269;2|1224|1236|2887326|468;2|1224|28211|356|82115|13159;2|201174|1760|85006|1268|57494;2|1224|1236|135619;2|1224|28216|80840|75682;2|1224|28211|204455|31989;2|1239|186801|186802|186807;2|1224|28211|356|69277;2|1224|28211|356|69277|28100;2|1239|91061|1385|186818;2|1224|1236|72274;2|1224;2|201174|1760|85010|2070;2|1224|1236|135613|1046|67575;2|1224|28211|356|82115;2|1224|28211|204455|31989|1060;2|1224|28211|204441|41295;2|201174|1760|85010|2070|1835;2|201174|1760|85006|85023|235888;2|1239|186801|68295;2759|33208|7711|8504|8509|8689|8710|8764|342873;2|976|117743|200644|2762318|343873;2|1224|1236|135613|1046,Complete,Peace Sandy
bsdb:764/1/2,Study 764,case-control,29172724,10.1080/02713683.2017.1406528,NA,"Ham B, Hwang HB, Jung SH, Chang S, Kang KD , Kwon MJ",Distribution and Diversity of Ocular Microbial Communities in Diabetic Patients Compared with Healthy Subjects,Current eye research,2018,"Bacterial diversity, Bradyrhizobiaceae, Burkholderia, LFR analysis, Staphylococcus",Experiment 1,Republic of Korea,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Type II diabetes mellitus,MONDO:0005148,healthy controls,diabetic,Type 2 diabetic patients undergoing vitrectomy,16,9,No antibiotics in the 6 months prior to enrollment,16S,4,Illumina,LEfSe,0.05,NA,2.6,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5,20 September 2023,Mary Bearkland,"Mary Bearkland,Boadiwaa","Figure 5. Comparative analysis of the microbial communities of groups with and without diabetes at the phylum (A) and genus (B) levels using the linear
discriminant analysis (LDA) effect size (LEfSe) method. LDA scores (log 10) for the most prevalent taxa in diabetic patients are represented on the positive scale,
whereas LDA-negative scores indicate enriched taxa in the healthy controls.",decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Cyanobacteriota",2|1224|28211;2|1239|91061|1385;2|1239|91061;2|1239;2|1239|186801|186802|31979;2|1117;2|1224|28211|356;2|1224|28211|356|41294;2|1224|28211|204457|41297|165696;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2759|33090|35493;2|1117,Complete,Peace Sandy
bsdb:765/1/1,Study 765,case-control,35171931,10.1371/journal.pone.0263283,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0263283,"Kunaseth J, Waiyaput W, Chanchaem P, Sawaswong V, Permpech R, Payungporn S , Sophonsritsuk A",Vaginal microbiome of women with adenomyosis: A case-control study,PloS one,2022,NA,Experiment 1,Thailand,Homo sapiens,Upper part of vagina,UBERON:0003974,Adenomyosis,EFO:1001757,Healthy controls,adenomyosis patients,"Patients with adenomoysis diagnosed using at least three diagnostic ultrasound-based criteria: globular shape uterus, asymmetric myometrial wall, thickening of the endometrial myometrial junction, hyperechoic striae along the sub-endometrial region, and presence of sub-endometrial microcyst",38,40,Not mentioned,16S,34,Illumina,LEfSe,0.05,NA,2,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Fig 4,24 September 2023,Andre,"Andre,Peace Sandy,Folakunmi",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance in the vaginal sample between adenomyosis and normal uterus.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|s__uncultured bacterium",2|201174|1760|85004|31953|419014;2|201174|84998|84999|84107;2|1224|28211|356|212791;2|1239|186801|186802|216572|216851;2|1239|909932|909929|1843491|158846;2|1224|1236|2887326|468;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|1239|909932|909929|1843491;2|1239|186801|186802|216572|292632;2|77133,Complete,Folakunmi
bsdb:765/1/2,Study 765,case-control,35171931,10.1371/journal.pone.0263283,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0263283,"Kunaseth J, Waiyaput W, Chanchaem P, Sawaswong V, Permpech R, Payungporn S , Sophonsritsuk A",Vaginal microbiome of women with adenomyosis: A case-control study,PloS one,2022,NA,Experiment 1,Thailand,Homo sapiens,Upper part of vagina,UBERON:0003974,Adenomyosis,EFO:1001757,Healthy controls,adenomyosis patients,"Patients with adenomoysis diagnosed using at least three diagnostic ultrasound-based criteria: globular shape uterus, asymmetric myometrial wall, thickening of the endometrial myometrial junction, hyperechoic striae along the sub-endometrial region, and presence of sub-endometrial microcyst",38,40,Not mentioned,16S,34,Illumina,LEfSe,0.05,NA,2,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Fig 4,24 September 2023,Andre,"Andre,Peace Sandy,Folakunmi",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance in the vaginal sample between adenomyosis and normal uterus.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|s__uncultured bacterium",2|1239|186801;2|1239|186801|186802|216572|236752;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572;2|77133,Complete,Folakunmi
bsdb:766/1/1,Study 766,case-control,32152391,https://doi.org/10.1038/s41598-020-60794-w,NA,"Kittipibul T, Puangsricharern V , Chatsuwan T",Comparison of the ocular microbiome between chronic Stevens-Johnson syndrome patients and healthy subjects,Scientific reports,2020,NA,Experiment 1,Thailand,Homo sapiens,Conjunctival sac,UBERON:0005908,Stevens-Johnson syndrome,EFO:0004276,healthy controls,Stevens-Johnson Syndrome,Stevens-Johnson Syndrome patients,20,20,Topical antibiotics within the 4 weeks prior to study entry were excluded,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1,24 September 2023,Mary Bearkland,Mary Bearkland,"Figure 1. Significant difference of taxa abundance. This figure represents the significant difference of taxonomic
level of each genus comparing between SJS patients and healthy subjects. We analyzed the proportion of each
genus by Mann-Whitney U test. The p-value less than 0.05 was defined as statistically significant difference.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Salinivibrio,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1224|1236|135623|641|51366;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|33042;2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|1578;2|32066|203490|203491|203492|848;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|91061|1385|186817|1386;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|577309;2|1224|1236|2887326|468|469;2|1239|186801|186802|216572|1263;2|1239|909932|909929|1843491|158846;2|976|200643|171549|1853231|283168;2|1239|91061|1385|90964|1279;2|1224|1236|135622|267888|53246;2|1224|1236|91347|1903409|551;2|1224|1236|72274|135621|286;2|201174|84998|84999|84107|102106;2157|28890|183925|2158|2159|2172;2|1239|909932|1843489|31977|29465;2|1224|1236|135614|32033|141948;2|1239|186801|3085636|186803|841;2|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:766/1/2,Study 766,case-control,32152391,https://doi.org/10.1038/s41598-020-60794-w,NA,"Kittipibul T, Puangsricharern V , Chatsuwan T",Comparison of the ocular microbiome between chronic Stevens-Johnson syndrome patients and healthy subjects,Scientific reports,2020,NA,Experiment 1,Thailand,Homo sapiens,Conjunctival sac,UBERON:0005908,Stevens-Johnson syndrome,EFO:0004276,healthy controls,Stevens-Johnson Syndrome,Stevens-Johnson Syndrome patients,20,20,Topical antibiotics within the 4 weeks prior to study entry were excluded,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 1,24 September 2023,Mary Bearkland,Mary Bearkland,"Figure 1. Significant difference of taxa abundance. This figure represents the significant difference of taxonomic
level of each genus comparing between SJS patients and healthy subjects. We analyzed the proportion of each
genus by Mann-Whitney U test. The p-value less than 0.05 was defined as statistically significant difference.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Cohaesibacteraceae|g__Cohaesibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Fusibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Tenacibaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Methylophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",2|1224|1236|135622|267890|22;2|1224|28211|356|655351|655352;2|1239|186801|186802|31979|1485;2|1239|186801|186802|543313|76008;2|976|117743|200644|49546|104267;2|1224|1236|72273|135616|40222;2|32066|203490|203491|203492|180162;2|29547|3031852|213849|2808963|28196;2|1224|1236|135623|641|662,Complete,Peace Sandy
bsdb:767/1/1,Study 767,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S, Nalbantoğlu ÖU, Bayraktar A, Ercan FB, Gündoğdu A, Velioğlu HA, Göl MF, Soylu AE, Koç F, Gülpınar EA, Kadak KS, Arıkan M, Mardinoğlu A, Koçak M, Köseoğlu E , Hanoğlu L",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Alzheimer's disease patients,"Patients with Alzheimer's disease, mostly exhibiting mild to very mild dementia",51,47,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,diet,"age,sex",NA,increased,increased,unchanged,unchanged,NA,Signature 1,Supplementary Table S2A and Supplementary Table S2CC,24 October 2023,Joan Chuks,"Joan Chuks,Peace Sandy",Differentially Abundant Genus level Taxa Between Alzheimer's disease Patients and Non-demented control groups Detected by Limma-Voom Model (Age and Sex Adjusted),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|815|816;2|201174|84998|84999|84107|102106;2|1224|1236|91347|543|1940338;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|1869337;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|1239|526524|526525|128827,Complete,Peace Sandy
bsdb:767/1/2,Study 767,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S, Nalbantoğlu ÖU, Bayraktar A, Ercan FB, Gündoğdu A, Velioğlu HA, Göl MF, Soylu AE, Koç F, Gülpınar EA, Kadak KS, Arıkan M, Mardinoğlu A, Koçak M, Köseoğlu E , Hanoğlu L",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Alzheimer's disease patients,"Patients with Alzheimer's disease, mostly exhibiting mild to very mild dementia",51,47,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,diet,"age,sex",NA,increased,increased,unchanged,unchanged,NA,Signature 2,Supplementary Table S2A and Supplementary Table S2CC,24 October 2023,Joan Chuks,"Joan Chuks,Iram jamshed,Peace Sandy",Differentially Abundant Genus level Taxa Between Alzheimer's disease Patients and Non-demented control groups Detected by Limma-Voom Model (Age and Sex Adjusted),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes",2|1239|186801|186802|3085642|580596;2|1239|526524|526525|128827;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|544448|31969,Complete,Peace Sandy
bsdb:767/2/1,Study 767,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S, Nalbantoğlu ÖU, Bayraktar A, Ercan FB, Gündoğdu A, Velioğlu HA, Göl MF, Soylu AE, Koç F, Gülpınar EA, Kadak KS, Arıkan M, Mardinoğlu A, Koçak M, Köseoğlu E , Hanoğlu L",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 2,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Mild Cognitive Impairment group,Amnestic patients with mild cognitive impairment (MCI),51,27,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,NA,increased,increased,Signature 1,Supplementary Table S2D and Supplementary Table S2B,24 October 2023,Joan Chuks,"Joan Chuks,Peace Sandy,Welile","Differentially Abundant Genus level Taxa Between mild cognitive impairment (MCI)
and Non-demented Control (C) groups Detected by Limma-Voom Model (Age and Sex Adjusted)",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|526524|526525|128827|1774107;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803;2|976|200643|171549|2005473;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|976|200643|171549|171550;2|1224|28216|80840|995019|40544;2|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:767/2/2,Study 767,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S, Nalbantoğlu ÖU, Bayraktar A, Ercan FB, Gündoğdu A, Velioğlu HA, Göl MF, Soylu AE, Koç F, Gülpınar EA, Kadak KS, Arıkan M, Mardinoğlu A, Koçak M, Köseoğlu E , Hanoğlu L",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 2,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Mild Cognitive Impairment group,Amnestic patients with mild cognitive impairment (MCI),51,27,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,NA,increased,increased,Signature 2,Supplementary Table S2D,24 October 2023,Joan Chuks,"Joan Chuks,ChiomaBlessing,Peace Sandy",Differentially Abundant Genus level Taxa Between mild cognitive impairment (MCI) and Non-demented Control (C) groups Detected by Limma-Voom Model (Age and Sex Adjusted),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella sp.",2|1239|186801|186802|3085642|580596;2|1224|28216|80840|995019|577310;2|1239|186801|186802|216572|3068309;2|544448|31969;2|1239|186801|186802|31979|1485|59620;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|297314;2|1239|186801|3085636|186803|841;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827;2|1239|186801|3085636|186803;2|1224|28216|80840|995019|577310|2049037,Complete,Peace Sandy
bsdb:768/1/1,Study 768,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J, Guo Y, Liu J, Guo F, Du L, Yang Y, Li X , Ma Y",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Mismatch repair cancer syndrome,MONDO:0031219,proficient DNA mismatch repair (pMMR) CRC,deficient DNA mismatch repair (dMMR) CRC,dMMR in colorectal cancer (CRC) characterized by robust immune environment,207,21,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 1,"Table S2, Figure 2c",16 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) in CRC,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp. AONIH1,k__Bacteria|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus|s__Acidithiobacillus ferrivorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp. RAC01,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinoalloteichus|s__Actinoalloteichus hoggarensis,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter|s__Aminobacter aminovorans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter|s__Aminobacter sp. MSH1,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Amycolatopsis|s__Amycolatopsis albispora,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum propionicum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Aquitalea|s__Aquitalea sp. USM4,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Leadbetterellaceae|g__Arcticibacterium|s__Arcticibacterium luteifluviistationis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus|s__Azoarcus sp. DN11,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus|s__Azoarcus sp. KH32C,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae|g__Azospira|s__Azospira oryzae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum brasilense,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. TSH100,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum thermophilum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus velezensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium CF,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella|s__Bordetella genomosp. 8,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium diazoefficiens,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium erythrophlei,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium guangdongense,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium lablabi,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Trinickia|s__Trinickia violacea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia stabilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia thailandensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium JOSHI_001,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides|s__Candidatus Azobacteroides pseudotrichonymphae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Candidatus Desulfovibrio trichonymphae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter flavus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Cereibacter|s__Cereibacter sphaeroides,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Christiangramia|s__Christiangramia fulva,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Chromobacterium|s__Chromobacterium violaceum,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium shandongense,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. 6424,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Collimonas|s__Collimonas pratensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium|s__Coriobacterium glomerans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Croceicoccus|s__Croceicoccus naphthovorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus necator,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus taiwanensis,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus actinosclerus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfatibacillaceae|g__Desulfatibacillum|s__Desulfatibacillum aliphaticivorans,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus oralis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfococcaceae|g__Desulfococcus|s__Desulfococcus multivorans,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfocurvibacter|s__Desulfocurvibacter africanus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium baculatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum|s__Desulfotomaculum nigrificans,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. G11,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Nitratidesulfovibrio|s__Nitratidesulfovibrio vulgaris,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia|s__Devosia sp. A16,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya chrysanthemi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya fangzhongdai,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter|s__Dyadobacter fermentans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia|s__Elizabethkingia miricola,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Ensifer|s__Ensifer adhaerens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Erythrobacter|s__Erythrobacter litoralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Ferrimonadaceae|g__Ferrimonas|s__Ferrimonas balearica,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola|s__Fluviicola taffensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Frigidibacter|s__Frigidibacter mobilis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Geoalkalibacteraceae|g__Geoalkalibacter|s__Geoalkalibacter subterraneus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sp. M18,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sp. M21,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sulfurreducens,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geotalea|s__Geotalea daltonii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Gluconobacter|s__Gluconobacter oxydans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia|s__Gordonia sp. YC-JH1,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter massiliensis (ex Traore et al. 2017),k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus|s__Halobacillus halophilus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter psoromatis,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter radiodurans,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sedentarius,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. APR13,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. DG25A,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. DG25B,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Immundisolibacterales|f__Immundisolibacteraceae|g__Immundisolibacter|s__Immundisolibacter cernigliae,k__Bacteria|p__Kiritimatiellota|c__Kiritimatiellia|o__Kiritimatiellales|f__Kiritimatiellaceae|g__Kiritimatiella|s__Kiritimatiella glycovorans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Kitasatospora|s__Kitasatospora sp. MMS16-BH015,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus pentosus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Magnetospirillum|s__Magnetospirillum gryphiswaldense,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Magnetospirillaceae|g__Paramagnetospirillum|s__Paramagnetospirillum magneticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter nauticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinobacterium|s__Marinobacterium aestuarii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae|g__Martelella|s__Martelella endophytica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia oculi,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia sp. YMA4,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia violaceinigra,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Megalodesulfovibrio|s__Megalodesulfovibrio gigas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium ciceri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium loti,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium sp. Pch-S,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga|s__Microvirga sp. 17 mud 1-3,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Aquaspirillaceae|g__Microvirgula|s__Microvirgula aerodenitrificans,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter sp. PAMC 26640,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria animaloris,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Neobacillus|s__Neobacillus mesonae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsaceae|g__Nocardiopsis|s__Nocardiopsis dassonvillei,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium resinovorum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio alaskensis,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae|s__Opitutaceae bacterium TAV5,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus chitinolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus ihbetae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus kribbensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus larvae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus lutimineralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus polymyxa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus sp. CAA11,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Paludisphaera|s__Paludisphaera borealis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea|s__Pandoraea oxalativorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea|s__Pandoraea sp. XY-2,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea vagans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia terrae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Parvibaculaceae|g__Parvibaculum|s__Parvibaculum lavamentivorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Paucibacter sp. KCTC 42545,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium|s__Pectobacterium carotovorum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Desulfuromonadaceae|g__Pelobacter|s__Pelobacter propionicus,k__Bacteria|p__Chlorobiota|c__Chlorobiia|o__Chlorobiales|f__Chlorobiaceae|g__Pelodictyon|s__Pelodictyon luteolum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus ivorii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Phaeobacter|s__Phaeobacter gallaeciensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter|s__Phreatobacter cathodiphilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Pigmentiphaga|s__Pigmentiphaga sp. H8,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces|s__Planctomyces sp. SH-PL62,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas crevioricanis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio aespoeensis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio profundus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella|s__Pseudoduganella armeniaca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brassicacearum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas entomophila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas knackmussii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas protegens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. LTJR-52,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium etli,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium jaguaris,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter|s__Rhodobacter xanthinilyticus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas|s__Rhodopseudomonas palustris,k__Bacteria|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|s__Rhodothermaceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Rufibacter|s__Rufibacter radiotolerans,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Runella|s__Runella rosea,k__Bacteria|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Salinibacteraceae|g__Salinibacter|s__Salinibacter ruber,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Salipiger|s__Salipiger profundus,k__Bacteria|p__Myxococcota|o__Polyangiales|f__Sandaracinaceae|g__Sandaracinus|s__Sandaracinus amylolyticus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia fonticola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium fredii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium meliloti,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium sp. RAC02,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta|s__Sphaerochaeta globosa,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium baderi,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta|s__Spirochaeta africana,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma pollinicola,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma radiotolerans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Staphylospora|s__Staphylospora marina,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces bingchenggensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces cadmiisoli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces dengpaensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces olivoreticuli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. endophyte_N2,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiohalomonadales|f__Thiohalomonadaceae|g__Sulfurivermis|s__Sulfurivermis fontis,k__Bacteria|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae|g__Syntrophobacter|s__Syntrophobacter fumaroxidans,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Syntrophotaleaceae|g__Syntrophotalea|s__Syntrophotalea acetylenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera humireducens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Thiobacillaceae|g__Thiobacillus|s__Thiobacillus denitrificans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Thiomonas|s__Thiomonas intermedia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Geminicoccales|f__Geminicoccaceae|g__Tistrella|s__Tistrella mobilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus|s__Tumebacillus avium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sp. H121,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. HW608,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PMC12,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|s__Victivallales bacterium CCUG 44730,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Xanthobacter|s__Xanthobacter autotrophicus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas translucens",2|1224|28216|80840|506|222|1758194;2|1224|1807140|225057|225058|119977|160808;2|1224|28216|80840|80864|12916|1842533;2|201174|1760|85010|2070|65496|1470176;2|74201|203494|48461|1647988|239934|239935;2|1224|28211|356|69277|31988|83263;2|1224|28211|356|69277|31988|374606;2|201174|1760|85010|2070|1813|1804986;2|1239|186801|3085636|3118652|2039240|28446;2|1224|28216|206351|1499392|407217|1590041;2|976|768503|768507|3141702|2173039|1784714;2|1224|28216|206389|2008794|12960|356837;2|1224|28216|206389|2008794|12960|748247;2|1224|28216|206389|75787|146937|146939;2|1224|28211|204441|2829815|191|192;2|1224|28211|204441|2829815|191|652764;2|1224|28211|204441|2829815|191|2202148;2|1239|91061|1385|186817|1386|492670;2|976|200643|171549|1400053;2|976|200643|171549|2005519|397864|397865;2|201174|1760|85004|31953|1678|1683;2|1224|28216|80840|506|517|1416806;2|1224|28211|356|41294|374|1355477;2|1224|28211|356|41294|374|1437360;2|1224|28211|356|41294|374|1325090;2|1224|28211|356|41294|374|722472;2|1224|28216|80840|119060|2571160|2571746;2|1224|28216|80840|119060|32008|95485;2|1224|28216|80840|119060|32008|57975;2|1224|28216|80840|864051;2|976|200643|171549|511434|511435;2|200940|3031449|213115|194924|872|1725232;2|976|117743|200644|49546|1016|45243;2|1224|28211|204458|76892|75|1679497;2|1224|28211|204455|31989|1653176|1063;2|976|117743|200644|49546|292691|2126553;2|1224|28216|206351|1499392|535|536;2|976|117743|200644|2762318|59732|1493872;2|976|117743|200644|2762318|59732|2039166;2|1224|28216|80840|75682|202907|279113;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107|33870|33871;2|201174|1760|85007|1653|1716|38289;2|1224|28211|204457|335929|1295327|1348774;2|1224|28216|80840|119060|106589|119219;2|1224|28216|80840|119060|106589|106590;2|1224|28216|80840|119060|106589|164546;2|1297|188787|118964|183710|1298|1768108;2|200940|3024418|213118|3031627|218207|218208;2|200940|3031451|3024411|213121|893|1986146;2|200940|3024418|213118|2931039|896|897;2|200940|3031449|213115|194924|2582840|873;2|200940|3031449|213115|213116|898|899;2|1239|186801|186802|2937910|1562|1565;2|200940|3031449|213115|194924|872|876;2|200940|3031449|213115|194924|872|631220;2|200940|3031449|213115|194924|2802295|881;2|1224|28211|356|2831106|46913|1736675;2|1224|1236|91347|1903410|204037|556;2|1224|1236|91347|1903410|204037|1778540;2|976|768503|768507|2896860|120831|94254;2|1224|28216|206351|481|538|539;2|976|117743|200644|2762318|308865|172045;2|1224|28211|356|82115|106591|106592;2|1224|1236|91347|543|547|61645;2|1224|1236|91347|543|547|881260;2|1224|1236|91347|543|547|2027919;2|1224|1236|91347|543|547|158836;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|81852|1350|160453;2|1224|28211|204457|335929|1041|39960;2|1224|1236|135622|267892|44011|44012;2|1239|186801|3082720|3118655|44259|143361;2|976|117743|200644|1853230|332102|191579;2|1224|28211|204455|31989|1775705|1335048;2|32066|203490|203491|203492|848|851;2|200940|3031651|69541|3031665|392332|483547;2|200940|3031651|3031668|213422|28231|443143;2|200940|3031651|3031668|213422|28231|443144;2|200940|3031651|3031668|213422|28231|35554;2|200940|3031651|3031668|213422|2910589|1203471;2|1224|28211|204441|433|441|442;2|201174|1760|85007|85026|2053|2059875;2|201174|84998|1643822|1643826|644652|1841863;2|201174|84998|1643822|1643826|644652|471189;2|201174|84998|1643822|1643826|644652|1335613;2|1239|91061|1385|186817|45667|1570;2|29547|3031852|213849|72293|209|210;2|976|200643|171549|171552|2974257|76123;2|976|768503|768507|1853232|89966|1484116;2|976|768503|768507|1853232|89966|2496028;2|976|768503|768507|1853232|89966|1411621;2|976|768503|768507|1853232|89966|1356852;2|976|768503|768507|1853232|89966|1385663;2|976|768503|768507|1853232|89966|1385664;2|1224|1236|1934945|1934946|1934947|1810504;2|134625|1921781|1921782|1921783|1921784|1307763;2|201174|1760|85011|2062|2063|2018025;2|1239|91061|186826|33958|2767842|1589;2|1224|28216|80840|119060|47670|47671;2|1224|28211|204441|41295|13134|55518;2|1224|28211|204441|3036766|3031148|84159;2|1224|1236|72274|2887365|2742|2743;2|1224|1236|135619|135620|48075|1821621;2|1224|28211|356|255475|293088|1486262;2|1224|28216|80840|75682|149698|945844;2|1224|28216|80840|75682|149698|1593482;2|1224|28216|80840|75682|149698|2045208;2|200940|3031449|213115|194924|2910978|879;2|1224|28211|356|69277|68287|39645;2|1224|28211|356|69277|68287|381;2|1224|28211|356|69277|68287|2082387;2|1224|28211|356|119045|186650|2082949;2|1224|28216|206351|2897176|57479|57480;2|976|117747|200666|84566|423349|1300914;2|976|200643|171549|2005473|1918540|1796646;2|1224|28216|206351|481|482|326522;2|1224|28216|206351|481|482|487;2|1239|91061|1385|186817|2675232|1193713;2|201174|1760|85012|83676|2013|2014;2|1224|28211|204457|41297|165696|158500;2|976|200643|171549|1853231|283168|28118;2|200940|3031449|213115|194924|2909705|58180;2|74201|414999|415000|134623|794903;2|1239|91061|1385|186822|44249|79263;2|1239|91061|1385|186822|44249|1870820;2|1239|91061|1385|186822|44249|172713;2|1239|91061|1385|186822|44249|1464;2|1239|91061|1385|186822|44249|2707005;2|1239|91061|1385|186822|44249|1406;2|1239|91061|1385|186822|44249|1532905;2|203682|203683|2691356|1763524|1763521|1387353;2|1224|28216|80840|119060|93217|573737;2|1224|28216|80840|119060|93217|2518599;2|1224|1236|91347|1903409|53335|549;2|1224|1236|91347|1903409|53335|470934;2|1224|28216|80840|119060|1822464|311230;2|1224|28216|80840|119060|1822464|36873;2|1224|28211|356|2813035|256616|256618;2|1224|28216|80840|2975441|93681|1768242;2|1224|1236|91347|1903410|122277|554;2|200940|3031651|69541|213421|18|29543;2|1090|191410|191411|191412|1099|1100;2|1239|1737404|1737405|1570339|2981628|54006;2|1224|28211|204455|2854170|302485|60890;2|1224|28211|356|2843305|1632780|1868589;2|1224|28216|80840|506|152267|2488560;2|203682|203683|112|126|118|1636152;2|976|200643|171549|171551|836|36874;2|976|200643|171549|171551|836|393921;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|28131;2|200940|3031449|213115|194924|2035811|182210;2|200940|3031449|213115|194924|2035811|57320;2|1224|28216|80840|75682|1522432|2072590;2|1224|1236|72274|135621|286|930166;2|1224|1236|72274|135621|286|312306;2|1224|1236|72274|135621|286|294;2|1224|1236|72274|135621|286|65741;2|1224|1236|72274|135621|286|1392877;2|1224|1236|72274|135621|286|380021;2|1224|1236|72274|135621|286|2479392;2|1224|28211|356|82115|379|29449;2|1224|28211|356|82115|379|1312183;2|1224|28211|204455|31989|1060|1850250;2|1224|28211|356|41294|1073|1076;2|1853220|1853222|1853224|563843|2026787;2|201174|1760|85006|1268|32207|2047;2|976|768503|768507|1853232|1379908|1379910;2|976|768503|768507|2896860|105|2259595;2|1853220|1853222|1853224|1853225|146918|146919;2|1224|28211|204455|2854170|263377|1229727;2|2818505|3031712|1055686|1055688|927083;2|1239|909932|909929|1843491|970|69823;2|1224|1236|91347|1903411|613|47917;2|1224|1236|91347|1903411|613|615;2|1224|28211|356|82115|28105|380;2|1224|28211|356|82115|28105|382;2|1224|28211|356|82115|28105|1842534;2|203691|203692|136|2791015|399320|1131703;2|1224|28211|204457|41297|165695|1332080;2|203691|203692|136|137|146|46355;2|976|768503|768507|89373|107|2057025;2|976|768503|768507|89373|107|1379870;2|1239|91061|1385|186824|2689589|2490858;2|1239|91061|186826|1300|1301|1336;2|1239|91061|186826|1300|1301|1338;2|1239|91061|186826|1300|1301|150055;2|1239|91061|186826|1300|1301|1305;2|201174|1760|85011|2062|1883|379067;2|201174|1760|85011|2062|1883|2184053;2|201174|1760|85011|2062|1883|2049881;2|201174|1760|85011|2062|1883|68246;2|201174|1760|85011|2062|1883|2153485;2|1224|1236|72274|135621|2901164|316;2|1224|1236|3084968|3084969|2034504|1972068;2|200940|3024408|213462|213465|29526|119484;2|200940|3031651|69541|2812024|2812025|29542;2|976|200643|171549|2005525|195950|712710;2|1224|28216|206389|2008794|33057|1134435;2|1224|28216|32003|2008790|919|36861;2|1224|28216|80840|32012|926;2|1224|28211|3108222|2066434|171436|171437;2|1239|91061|1385|186823|432330|1903704;2|1239|526524|526525|2810281|191303|1712675;2|1224|28216|80840|80864|34072|1034889;2|1224|28216|80840|80864|34072|2126319;2|256845|1313211|278082|2094242;2|1224|28211|356|335928|279|280;2|1224|1236|135614|32033|338|343,Complete,Folakunmi
bsdb:768/1/2,Study 768,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J, Guo Y, Liu J, Guo F, Du L, Yang Y, Li X , Ma Y",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Mismatch repair cancer syndrome,MONDO:0031219,proficient DNA mismatch repair (pMMR) CRC,deficient DNA mismatch repair (dMMR) CRC,dMMR in colorectal cancer (CRC) characterized by robust immune environment,207,21,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table S2,16 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) in CRC,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans",2|1239|186801|186802|216572|946234|292800;2|1239|91061|1385|539738|1378|1379,Complete,Folakunmi
bsdb:768/2/1,Study 768,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J, Guo Y, Liu J, Guo F, Du L, Yang Y, Li X , Ma Y",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls (CTRL),deficient DNA mismatch repair (dMMR) CRC,dMMR in colorectal cancer (CRC) characterized by robust immune environment,227,21,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2c,16 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between deficient DNA mismatch repair (dMMR) in CRC and healthy controls (CTRL),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus velezensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",2|1239|91061|1385|186817|1386|492670;2|976|200643|171549|2005519|397864|397865;2|200940|3031449|213115|194924|872|876;2|32066|203490|203491|203492|848|851;2|976|200643|171549|171552|2974257|76123;2|976|200643|171549|2005473|1918540|1796646;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171551|836|36874;2|976|200643|171549|171552|838|28131,Complete,Folakunmi
bsdb:768/3/1,Study 768,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J, Guo Y, Liu J, Guo F, Du L, Yang Y, Li X , Ma Y",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls (CTRL),proficient DNA mismatch repair (pMMR) CRC,pMMR in colorectal cancer (CRC) characterized by immunosuppressive tumor microenvironment,227,207,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2c,16 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between proficient DNA mismatch repair (pMMR) in CRC and healthy controls (CTRL),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,2|1239|186801|186802|216572|946234|292800,Complete,Folakunmi
bsdb:768/3/2,Study 768,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J, Guo Y, Liu J, Guo F, Du L, Yang Y, Li X , Ma Y",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls (CTRL),proficient DNA mismatch repair (pMMR) CRC,pMMR in colorectal cancer (CRC) characterized by immunosuppressive tumor microenvironment,227,207,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2c,16 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between proficient DNA mismatch repair (pMMR) in CRC and healthy controls (CTRL),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum propionicum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae",2|1239|186801|3085636|3118652|2039240|28446;2|201174|84998|84999|84107|102106|74426;2|201174|84998|1643822|1643826|644652|471189,Complete,Folakunmi
bsdb:769/1/1,Study 769,time series / longitudinal observational,36894532,10.1038/s41467-023-36781-w,https://pubmed.ncbi.nlm.nih.gov/36894532/,"Sukumar S, Wang F, Simpson CA, Willet CE, Chew T, Hughes TE, Bockmann MR, Sadsad R, Martin FE, Lydecker HW, Browne GV, Davis KM, Bui M, Martinez E , Adler CJ",Development of the oral resistome during the first decade of life,Nature communications,2023,NA,Experiment 1,Australia,Homo sapiens,Mouth,UBERON:0000165,Dental caries,EFO:0003819,T1 - Timepoint 1 - (T1. edentulous (no teeth)),T2 - Timepoint 2,Samples (1.6 ± 0.4 years) at T2 (primary/deciduous/baby teeth only),139,180,3 Months,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4 C,23 February 2024,Peace Sandy,Peace Sandy,"Vector loadings for ARGs, functional pathways and species that contribute to discrimination  of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus wangshanyuanii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus himalayensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus marmotae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parauberis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pluranimalium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus urinalis",2|1239|91061|186826|81852|1350|2005703;2|1239|91061|186826|1300|1301|1888195;2|1239|91061|186826|1300|1301|1825069;2|1239|91061|186826|1300|1301|1348;2|1239|91061|186826|1300|1301|82348;2|1239|91061|186826|1300|1301|149016,Complete,Peace Sandy
bsdb:769/2/1,Study 769,time series / longitudinal observational,36894532,10.1038/s41467-023-36781-w,https://pubmed.ncbi.nlm.nih.gov/36894532/,"Sukumar S, Wang F, Simpson CA, Willet CE, Chew T, Hughes TE, Bockmann MR, Sadsad R, Martin FE, Lydecker HW, Browne GV, Davis KM, Bui M, Martinez E , Adler CJ",Development of the oral resistome during the first decade of life,Nature communications,2023,NA,Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Dental caries,EFO:0003819,T1 - Timepoint 1 - (T1. edentulous (no teeth)),T3 - Timepoint 3,"Samples at T3 (mixed dentition, 8.5 ± 1.2 years old)",139,211,3 Months,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4 C,23 February 2024,Peace Sandy,Peace Sandy,"Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus",2|201174|1760|2037|2049|1654|29317;2|201174|1760|2037|2049|1654|1656,Complete,Peace Sandy
bsdb:769/2/2,Study 769,time series / longitudinal observational,36894532,10.1038/s41467-023-36781-w,https://pubmed.ncbi.nlm.nih.gov/36894532/,"Sukumar S, Wang F, Simpson CA, Willet CE, Chew T, Hughes TE, Bockmann MR, Sadsad R, Martin FE, Lydecker HW, Browne GV, Davis KM, Bui M, Martinez E , Adler CJ",Development of the oral resistome during the first decade of life,Nature communications,2023,NA,Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Dental caries,EFO:0003819,T1 - Timepoint 1 - (T1. edentulous (no teeth)),T3 - Timepoint 3,"Samples at T3 (mixed dentition, 8.5 ± 1.2 years old)",139,211,3 Months,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4 C,23 February 2024,Peace Sandy,Peace Sandy,"Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus wangshanyuanii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus himalayensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus marmotae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parauberis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pluranimalium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus urinalis",2|1239|91061|186826|81852|1350|2005703;2|1239|91061|186826|1300|1301|1888195;2|1239|91061|186826|1300|1301|1825069;2|1239|91061|186826|1300|1301|1348;2|1239|91061|186826|1300|1301|82348;2|1239|91061|186826|1300|1301|149016,Complete,Peace Sandy
bsdb:769/3/1,Study 769,time series / longitudinal observational,36894532,10.1038/s41467-023-36781-w,https://pubmed.ncbi.nlm.nih.gov/36894532/,"Sukumar S, Wang F, Simpson CA, Willet CE, Chew T, Hughes TE, Bockmann MR, Sadsad R, Martin FE, Lydecker HW, Browne GV, Davis KM, Bui M, Martinez E , Adler CJ",Development of the oral resistome during the first decade of life,Nature communications,2023,NA,Experiment 3,Australia,Homo sapiens,Mouth,UBERON:0000165,Dental caries,EFO:0003819,T2 - Timepoint 2,T3 - Timepoint 3,"Samples at T3 (mixed dentition, 8.5 ± 1.2 years old)",180,211,3 Months,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4 C,23 February 2024,Peace Sandy,Peace Sandy,"Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed.For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus",2|201174|1760|2037|2049|1654|29317;2|201174|1760|2037|2049|1654|1656,Complete,Peace Sandy
bsdb:770/1/1,Study 770,case-control,37762390,10.3390/ijms241814091,NA,"Schlegel I, De Goüyon Matignon de Pontourade CMF, Lincke JB, Keller I, Zinkernagel MS , Zysset-Burri DC",The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease,International journal of molecular sciences,2023,"chromatography–tandem mass spectrometry, dry eye disease, ocular surface microbiome, tear proteome, whole-metagenome shotgun sequencing",Experiment 1,Switzerland,Homo sapiens,Eyelid,UBERON:0001711,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,Dry Eye Disease diagnosis,10,10,Antibiotics within the past 3 months,WMS,NA,Illumina,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,1 October 2023,Mary Bearkland,Mary Bearkland,"Figure 4c. The distinct taxonomical and functional composition of the ocular surface microbiome between DED patients and healthy controls.  The relative abundances
of taxa associated with DED (Mann–Whitney test). Mean values and
standard deviations are shown.",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,2|201174|1760|85009|31957,Complete,ChiomaBlessing
bsdb:770/2/1,Study 770,case-control,37762390,10.3390/ijms241814091,NA,"Schlegel I, De Goüyon Matignon de Pontourade CMF, Lincke JB, Keller I, Zinkernagel MS , Zysset-Burri DC",The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease,International journal of molecular sciences,2023,"chromatography–tandem mass spectrometry, dry eye disease, ocular surface microbiome, tear proteome, whole-metagenome shotgun sequencing",Experiment 2,Switzerland,Homo sapiens,Palpebral conjunctiva,UBERON:0001812,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,Dry Eye Disease diagnosis,10,10,Antibiotics within the past 3 months,WMS,NA,Illumina,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,1 October 2023,Mary Bearkland,Mary Bearkland,"Figure 4. The distinct taxonomical composition of the ocular surface microbiome between DED patients and healthy controls.  The relative abundances
of taxa (c) associated with DED (Mann–Whitney test). Mean values and
standard deviations are shown.",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,2|201174|1760|85007|1653|1716|38304,Complete,ChiomaBlessing
bsdb:771/1/1,Study 771,case-control,32106294,10.1167/iovs.61.2.47,NA,"Deng Y, Wen X, Hu X, Zou Y, Zhao C, Chen X, Miao L, Li X, Deng X, Bible PW, Ke H, Situ J, Guo S, Liang J, Chen T, Zou B, Liu Y, Chen W, Wu K, Zhang M, Jin ZB, Liang L , Wei L","Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities",Investigative ophthalmology & visual science,2020,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Health study participation,EFO:0010130,Guangzhou healthy volunteers,Bejing healthy volunteers,Healthy nonsmokers from Bejing,48,20,6 months prior to enrollment,WMS,NA,Illumina,LEfSe,NA,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 October 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy",Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Cereibacter|s__Cereibacter sphaeroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia|s__Gordonia polyisoprenivorans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium sp.",2|1239|91061|1385|186817|1386|1396;2|1224|28211|356|118882|234|529;2|1224|28211|204455|31989|1653176|1063;2|201174|1760|85007|1653|1716|169292;2|201174|1760|85007|1653|1716|38289;2|201174|1760|85007|1653|1716|43771;2|1224|28216|80840|80864|80865|80866;2|1224|28216|80840|80864|80865|1886637;2|1239|91061|186826|81852|1350|1351;2|1224|1236|91347|543|561|562;2|201174|1760|85007|85026|2053|84595;2|201174|1760|85006|2805426|57499|1276;2|201174|1760|85006|1268|1269|1270;2|1224|28216|206351|481|482|487;2|976|200643|171549|171551|836|837;2|1224|1236|72274|135621|286|287;2|1224|28216|80840|119060|48736|329;2|1224|28211|356|82115|379|391,Complete,Peace Sandy
bsdb:771/1/2,Study 771,case-control,32106294,10.1167/iovs.61.2.47,NA,"Deng Y, Wen X, Hu X, Zou Y, Zhao C, Chen X, Miao L, Li X, Deng X, Bible PW, Ke H, Situ J, Guo S, Liang J, Chen T, Zou B, Liu Y, Chen W, Wu K, Zhang M, Jin ZB, Liang L , Wei L","Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities",Investigative ophthalmology & visual science,2020,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Health study participation,EFO:0010130,Guangzhou healthy volunteers,Bejing healthy volunteers,Healthy nonsmokers from Bejing,48,20,6 months prior to enrollment,WMS,NA,Illumina,LEfSe,NA,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,1 October 2023,Mary Bearkland,Mary Bearkland,Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria|s__Listeria monocytogenes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mendocina,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira murdochii,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|g__Candidatus Karelsulcia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis bovis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter|s__[Acidovorax] ebreus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2|1239|91061|1385|186820|1637|1639;2|1224|1236|72274|135621|286|300;2|203691|203692|1643686|143786|29521|84378;2|976|117743|200644|336809;2|1224|1236|135614|32033|40323|40324;2|544448|2790996|2895623|2767358|28903;2|1224|28216|80840|80864|12916|1872122;2|1224|28216|80840|80864|238749|721785;2|544448|2790996|2895623|2923352|2100;2|201174|1760|85009|31957|1912216|1747,Complete,Peace Sandy
bsdb:772/1/NA,Study 772,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q , Pan Y",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 1,United States of America,Felis catus,Feces,UBERON:0001988,Obesity,EFO:0001073,LN cats at T1,OW cats at T1,Overweight domestic felines that have an excess accumulation of body fat at the end of T1 (baseline feeding),19,20,NA,16S,34,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:772/2/1,Study 772,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q , Pan Y",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 2,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T1(end of baseline feeding),CON-fed OW cats at T2 (end of intervention),Overweight domestic felines placed on the control diet at T2 (end of intervention),20,10,NA,16S,34,Illumina,"Kruskall-Wallis,Dunn's test",0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S4,5 October 2023,Deacme,"Deacme,Folakunmi",Increased abundance in CON-fed OW cats at T2 (end of intervention),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|201174|84998|84999|84107;2|976|200643|171549|171551;2|976|200643|171549|171550,Complete,Folakunmi
bsdb:772/3/1,Study 772,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q , Pan Y",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 3,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T1(end of baseline feeding),HPLC-fed OW cats at T2 (end of intervention),Overweight domestic felines placed on the HPLC diet at T2 (end of intervention),20,10,NA,16S,34,Illumina,"Kruskall-Wallis,Dunn's test",0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S4,5 October 2023,Deacme,"Deacme,Folakunmi",Increased abundance in HPLC-fed OW cats at T2 (end of intervention),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|31979;2|201174|84998|84999|84107;2|1239|186801|186802|541000;2|1239|186801|3082720|186804|2743582|89152;2|1239|186801|186802|186807;2|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:772/3/2,Study 772,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q , Pan Y",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 3,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T1(end of baseline feeding),HPLC-fed OW cats at T2 (end of intervention),Overweight domestic felines placed on the HPLC diet at T2 (end of intervention),20,10,NA,16S,34,Illumina,"Kruskall-Wallis,Dunn's test",0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S4,10 October 2023,Deacme,"Deacme,Folakunmi",Decreased abundance in HPLC-fed OW cats at T2 (end of intervention),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|976|200643|171549|815|909656|310297,Complete,Folakunmi
bsdb:772/4/1,Study 772,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q , Pan Y",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 4,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T2 (end of intervention),HPLC-fed OW cats at T2 (end of intervention),HPLC-fed overweight domestic felines at T2 (end of intervention),10,10,NA,16S,34,Illumina,"Kruskall-Wallis,Dunn's test",0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Table S4, Table 3, Text results (Dietary Intervention Changes Gut Microbiota in OW Cats)",10 October 2023,Deacme,"Deacme,Folakunmi",Increased abundance in HPLC-fed OW cats at T2 (end of intervention),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis",2|1239|186801|186802|31979;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3082720|186804|2743582|89152,Complete,Folakunmi
bsdb:772/4/2,Study 772,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q , Pan Y",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 4,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T2 (end of intervention),HPLC-fed OW cats at T2 (end of intervention),HPLC-fed overweight domestic felines at T2 (end of intervention),10,10,NA,16S,34,Illumina,"Kruskall-Wallis,Dunn's test",0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Table S4, Table 3, Text results (Dietary Intervention Changes Gut Microbiota in OW Cats)",10 October 2023,Deacme,"Deacme,Folakunmi",Decreased abundance in HPLC-fed OW cats at T2 (end of intervention),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|906;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171551;2|976|200643|171549|171550;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Folakunmi
bsdb:773/1/1,Study 773,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y, Gilbreath TM, Kukutla P, Yan G , Xu J",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 1,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Gut microbiome measurement,EFO:0007874,Pupal (Triplicates),Newly emerged adult guts,"1-day-old adult, no feeding (triplicates)",9,6,NIL,16S,123,Roche454,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table S5,20 February 2024,Peace Sandy,Peace Sandy,"Differentially abundant families between pupal and newly emerged adult guts

The differential abundant taxa between collections were detected with Metastats",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",2|1224|1236|91347|543;2|201174|1760|85009|31957,Complete,Peace Sandy
bsdb:773/1/2,Study 773,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y, Gilbreath TM, Kukutla P, Yan G , Xu J",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 1,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Gut microbiome measurement,EFO:0007874,Pupal (Triplicates),Newly emerged adult guts,"1-day-old adult, no feeding (triplicates)",9,6,NIL,16S,123,Roche454,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table S5,20 February 2024,Peace Sandy,Peace Sandy,"Differentially abundant families between pupal and newly emerged adult guts 

The differential abundant taxa between collections were detected with Metastats",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae",2|1224|28216|80840|80864;2|1224|28211|204457|335929;2|1224|28211|204455|31989;2|1224|1236|135624|84642;2|1224|1236|135614|1775411,Complete,Peace Sandy
bsdb:773/2/1,Study 773,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y, Gilbreath TM, Kukutla P, Yan G , Xu J",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 2,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Gut microbiome measurement,EFO:0007874,"Sugar fed mosquito - 3-day-old,sugar (triplicates)",Blood fed mosquito - 2 days post blood meal (triplicates),Blood-fed mosquito at different time points,6,6,NIL,16S,123,Roche454,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Table S7 and Table S6,20 February 2024,Peace Sandy,Peace Sandy,"Differentially abundant genera before and after a blood meal

Differentially abundant families before and after a blood meal",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1224|1236|91347|543|547;2|976|117743|200644|2762318|308865;2|1224|1236|91347|543;2|1224|1236|135624|84642;2|1224|1236|72274|135621,Complete,Peace Sandy
bsdb:773/2/2,Study 773,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y, Gilbreath TM, Kukutla P, Yan G , Xu J",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 2,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Gut microbiome measurement,EFO:0007874,"Sugar fed mosquito - 3-day-old,sugar (triplicates)",Blood fed mosquito - 2 days post blood meal (triplicates),Blood-fed mosquito at different time points,6,6,NIL,16S,123,Roche454,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,Table S7 and Table S6,20 February 2024,Peace Sandy,Peace Sandy,"Differentially abundant genera before and after a blood meal

Differentially abundant families before and after a blood meal",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1224|28216|80840|80864;2|976|117743|200644|49546;2|1224|1236|2887326|468;2|201174|1760|85009|31957;2|1224|1236|91347|543|160674;2|1224|28211|204457|41297;2|1224|1236|135614|32033,Complete,Peace Sandy
bsdb:774/1/1,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 1,"United States of America,United Kingdom,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS1 (Non-irritable bowel syndrome 1),IBS-C (IBS-Constipation),"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool)",180,180,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, b and c and Supplemental. Table 3",25 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-C and Non-IBS1,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|s__bacterium FCS020,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|s__bacterium ND3007",2|201174;2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|653683;2|1239|186801|3085636|186803|207244;2|1239;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|33042;2|201174|1760|85007|1653|1716;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|877420;2|1239|186801|3085656|3085657|2039302;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|216572|292632;2|1224|1236|135624|83763|83770;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|216572|39492;2|1451755;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003;2|1452070,Complete,Folakunmi
bsdb:774/1/2,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 1,"United States of America,United Kingdom,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS1 (Non-irritable bowel syndrome 1),IBS-C (IBS-Constipation),"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool)",180,180,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, b and c and Supplemental Table 3",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,Joan Chuks",Differential microbial abundance between IBS-C and Non-IBS1,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Diplocloster",2|74201|203494|48461|1647988|239934;2|976|200643|171549|2005519|397864;2|1239|186801|3082768|990719|990721;2|1239|186801;2|1239|186801|186802|543314|2137877;2|1224|28216|80840|80864|80865;2|200940|3031449|213115|194924|872;2|1239|526524|526525|128827|1472649;2|1239|186801|3085636|186803|1432051;2|1224|1236|91347|543|1940338;2|1239|186801|186802|186806|1730;2|1239|526524|526525|128827|1573534;2|1239|1737404|1737405|1570339|150022;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1918511;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|216572|596767;2|1239|186801|186802|1392389;2|1239|1980693;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1508657;2|200940;2|1239|526524|526525|128827|1522;2|1239|186801|3085636|186803|2918511,Complete,Folakunmi
bsdb:774/2/1,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 2,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS2 (Non-irritable bowel syndrome 2),IBS-D (IBS-Diarrhea),"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool)",302,302,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 2a, b and c and Supplemental. Table 4",26 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-D and Non-IBS2,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|s__bacterium ND3007,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",2|1224|28216|80840|506|222;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|976|200643|171549|2005519|397864;2|201174|1760|85004|31953|1678;2|976|200643|171549|1853231|574697;2|1239|186801|3085636|186803|830;2|29547|3031852|213849|72294|194;2|544448|1912503|2975519;2|1239|186801|3082768|990719;2|1239|186801|186802|543314|2137877;2|1239|186801|3085636|186803|33042;2|1117;2|1224|28216|206389|2008795|73029;2|200940|3031449|213115|194924|872;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|216851;2|1239|186801|186802|1686313;2|1239|186801|186802|216572|596767;2|256845;2|976|200643|171549|2005473;2|976|200643|171549|1853231|283168;2|1224|28216|80840|75682|846;2|1224|28216|80840|995019|577310;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|201174|1760|2037|2049|184869;2|1239|909932|1843489|31977|29465;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|216572|39492;2|1452070;2|256845;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003;2|1239|186801|244328,Complete,Folakunmi
bsdb:774/2/2,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 2,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS2 (Non-irritable bowel syndrome 2),IBS-D (IBS-Diarrhea),"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool)",302,302,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 2a, b and c and Supplemental Table 4",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Iram jamshed,Folakunmi",Differential microbial abundance between IBS-D and Non-IBS2,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae",2|1239|91061|186826|186827|46123;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|946234;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|2569097|39488;2|1224|28211|204458|76892|41275;2|1239|186801|3085636|1185407,Complete,Folakunmi
bsdb:774/3/1,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 3,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS3 (Non-irritable bowel syndrome 3),IBS-U (IBS-Unclassified),"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool",460,460,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,unchanged,Signature 1,"Figure 2a, b and c and Supplemental. Table 5",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential microbial abundance between IBS-U and Non-IBS3,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|s__uncultured Erysipelotrichia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|29547|3031852|213849|72294|194;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|216572|216851;2|1239|186801|186802|1686313;2|1239|1737404|1737405|1570339|150022;2|1239|186801|3085636|186803|1407607;2|1239|91061|1385|539738|1378;2|1239|526524|526525|128827|1573535;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|201174|1760|2037|2049|184869;2|256845;2|1239|526524|666559;2|1239|186801|3085636|186803|297314;2|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:774/3/2,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 3,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS3 (Non-irritable bowel syndrome 3),IBS-U (IBS-Unclassified),"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool",460,460,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,unchanged,Signature 2,IBS-U (IBS-Unclassified),26 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential microbial abundance between IBS-U and Non-IBS3,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Pseudomonadota",2|1224|1236|91347|543|1940338;2|1224|1236|72274|135621|286;2|1239|909932|1843488|909930|40840;2|1239|186801|3085636|186803|2316020|33039;2|1224,Complete,Folakunmi
bsdb:774/4/1,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 4,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,IBS patients without depression,"IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)","IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)",134,134,6 months,16S,4,Illumina,MaAsLin2,0.05,FALSE,NA,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3C, Results (text)",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Atrayees","Differential microbial abundance between IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U) and IBS patients without depression",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae",2|201174|1760|85004|31953|1678;2|976|200643|171549|1853231|574697;2|1224|28216|80840|995019|40544;2|1239|186801|186802|3085642,Complete,Folakunmi
bsdb:774/4/2,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 4,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,IBS patients without depression,"IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)","IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)",134,134,6 months,16S,4,Illumina,MaAsLin2,0.05,FALSE,NA,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3C, Results (text)",27 October 2023,ChiomaBlessing,ChiomaBlessing,"Differential microbial abundance between IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U) and IBS patients without depression",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,2|1224|1236|91347|1903414|583,Complete,Folakunmi
bsdb:774/5/1,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 5,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-C (IBS-Constipation) Validation Cohort,"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool) in the Validation Cohort",44,44,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental. Figure 5C,27 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-C and Non-IBS (Validation cohort),decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota",2|1239;2|201174,Complete,Folakunmi
bsdb:774/5/2,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 5,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-C (IBS-Constipation) Validation Cohort,"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool) in the Validation Cohort",44,44,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-C and Non-IBS (Validation cohort),increased,k__Bacteria|p__Verrucomicrobiota,2|74201,Complete,Folakunmi
bsdb:774/6/1,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 6,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-D (IBS-Diarrhea) Validation Cohort,"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool) in the Validation Cohort",48,48,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-D and Non-IBS (Validation cohort),decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Campylobacterota",2|201174;2|1239;2|29547,Complete,Folakunmi
bsdb:774/6/2,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 6,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-D (IBS-Diarrhea) Validation Cohort,"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool) in the Validation Cohort",48,48,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-D and Non-IBS (Validation cohort),increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Folakunmi
bsdb:774/7/1,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 7,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-U (IBS-Unclassified) Validation Cohort,"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool in the Validation Cohort",61,61,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-U and Non-IBS (Validation cohort),decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota",2|1239;2|201174,Complete,Folakunmi
bsdb:774/7/2,Study 774,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK , Ng SC",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 7,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-U (IBS-Unclassified) Validation Cohort,"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool in the Validation Cohort",61,61,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between IBS-U and Non-IBS (Validation cohort),increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,Folakunmi
bsdb:775/1/1,Study 775,case-control,36631533,10.1038/s41598-023-27436-3,NA,"Shrode RL, Knobbe JE, Cady N, Yadav M, Hoang J, Cherwin C, Curry M, Garje R, Vikas P, Sugg S, Phadke S, Filardo E , Mangalam AK",Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls (HC),Breast cancer (BC),"All BC patients eligible for this study were diagnosed with invasive BC of any stage, and recruited from the Breast Molecular Epidemiology Resource (BMER) of the Holden Comprehensive Cancer Center (HCCC)",19,22,Antibiotic use within four weeks of sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,race,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,3 October 2023,ChiomaBlessing,"ChiomaBlessing,Peace Sandy","Bacteria significantly increased in patients with breast cancer compared to healthy controls. (a–f) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 6 features were significantly higher in abundance in the breast cancer cohort compared to the healthy controls (p ≤ 0.05, q ≤ .15). Significance: * < 0.05 and ** < 0.01.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|572511;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|128827|1573534;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:775/1/2,Study 775,case-control,36631533,10.1038/s41598-023-27436-3,NA,"Shrode RL, Knobbe JE, Cady N, Yadav M, Hoang J, Cherwin C, Curry M, Garje R, Vikas P, Sugg S, Phadke S, Filardo E , Mangalam AK",Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls (HC),Breast cancer (BC),"All BC patients eligible for this study were diagnosed with invasive BC of any stage, and recruited from the Breast Molecular Epidemiology Resource (BMER) of the Holden Comprehensive Cancer Center (HCCC)",19,22,Antibiotic use within four weeks of sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,race,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,3 October 2023,ChiomaBlessing,"ChiomaBlessing,Peace Sandy","Bacteria significantly decreased in patients with breast cancer compared to healthy controls. (a–h) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 8 features weresignificantly lower in abundance in the breast cancer cohort compared to the healthy controls (p ≤ 0.05, q ≤ 0.15). Significance: * < 0.05, ** < 0.01, and *** < 0.001.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|976|200643|171549|171550|239759|1872444;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1506553|1926283;2|1239|186801|3085636|186803|28050|28052;2|1239|186801|186802|216572|459786|1945593;2|976|200643|171549|2005525|375288|46503;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|297314,Complete,Peace Sandy
bsdb:776/1/1,Study 776,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P, Chen Y, Zhao J, Zhang G, Chen J, Wang J , Zhang H",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 1,China,Homo sapiens,Female urethra,UBERON:0001334,Overactive bladder,EFO:1000781,Asymptomatic controls,Overactive Bladder (OAB) patients,"Adult patients aged 18 or above, diagnosed with OAB",25,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,4 October 2023,Ojotuleonalo,Ojotuleonalo,Urinary microbiomes that were significantly more increased in the samples of female patients with OAB (Over Active Bladder) compared to the control samples from asymptomatic women,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus",2|1239|91061|1385|90964|1279;2|32066|203490|203491|1129771|168808;2|1224|1236|91347|1903414|583;2|1239|1737404|1737405|1570339|31983;2|1239|91061|1385|539738|1378;2|544448|31969|2085|2092|2093;2|1239|91061|186826|186827|1375,Complete,Folakunmi
bsdb:776/1/2,Study 776,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P, Chen Y, Zhao J, Zhang G, Chen J, Wang J , Zhang H",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 1,China,Homo sapiens,Female urethra,UBERON:0001334,Overactive bladder,EFO:1000781,Asymptomatic controls,Overactive Bladder (OAB) patients,"Adult patients aged 18 or above, diagnosed with OAB",25,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,4 October 2023,Ojotuleonalo,Ojotuleonalo,Urinary microbiomes that were significantly more decreased in the samples of female patients with OAB (Over Active Bladder) compared to the control samples from asymptomatic women,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",2|1239|1737404|1737405|1570339|165779;2|29547|3031852|213849|72294|194;2|1239|909932|1843489|31977|39948;2|1239|91061|186826|81852|1350;2|1239|1737404|1737405|1570339|150022;2|32066|203490|203491|203492|848;2|508458|649775|649776|3029088|428711;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1224|28211|204457|41297|165696;2|976|200643|171549|171552|838;2|508458|649775|649776|3029088|638847;2|544448|2790996|2790998|2129,Complete,Folakunmi
bsdb:776/2/1,Study 776,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P, Chen Y, Zhao J, Zhang G, Chen J, Wang J , Zhang H",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 2,China,Homo sapiens,Female urethra,UBERON:0001334,Anxiety,EFO:0005230,Overactive Bladder (OAB) without anxiety,Overactive Bladder (OAB) with anxiety,"Adult patients aged 18 or above, diagnosed with OAB and have anxiety",18,12,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,increased,increased,increased,increased,NA,NA,Signature 1,Figure 5C,8 October 2023,Ojotuleonalo,"Ojotuleonalo,Peace Sandy,Folakunmi",Urinary microbiomes that were significantly more increased in the samples of female patients with OAB (Over Active Bladder) with anxiety compared to the samples of female patients with OAB without anxiety,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae|g__Leptolyngbya,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|201174|1760|2037|2049|76833;2|1239|91061|1385|186823|29330;2|1239|1737404|1737405|1570339|162290;2|1239|1737404|1737405|1570339|31983;2|1117|3028117|3079749|1890438|47251;2|976|200643|171549|171551|836;2|32066|203490|203491|1129771|168808,Complete,Folakunmi
bsdb:776/2/2,Study 776,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P, Chen Y, Zhao J, Zhang G, Chen J, Wang J , Zhang H",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 2,China,Homo sapiens,Female urethra,UBERON:0001334,Anxiety,EFO:0005230,Overactive Bladder (OAB) without anxiety,Overactive Bladder (OAB) with anxiety,"Adult patients aged 18 or above, diagnosed with OAB and have anxiety",18,12,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,increased,increased,increased,increased,NA,NA,Signature 2,Figure 5C,8 October 2023,Ojotuleonalo,"Ojotuleonalo,Peace Sandy,Folakunmi",Urinary microbiomes that were significantly more decreased in the samples of female patients with OAB (Over Active Bladder) with anxiety compared to the samples of female patients with OAB without anxiety.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Cryocola,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter",2|1224|28211|356|82115|357;2|1224|28216|80840|119060|32008;2|201174|84998|84999|84107|102106;2|201174|1760|85006|85023|205841;2157|28890|183925|2158|2159|2172;2|1224|1236|2887326|468|497,Complete,Folakunmi
bsdb:776/3/1,Study 776,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P, Chen Y, Zhao J, Zhang G, Chen J, Wang J , Zhang H",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 3,China,Homo sapiens,Female urethra,UBERON:0001334,Depressive disorder,MONDO:0002050,Overactive Bladder (OAB) without depression,Overactive Bladder (OAB) with depression,"Adult patients aged 18 or above, diagnosed with OAB and have anxiety",16,14,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,increased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5D,18 January 2024,Folakunmi,Folakunmi,Urinary microbiomes that were significantly decreased in the samples of female patients with OAB (Over Active Bladder) with depression compared to the samples of female patients with OAB without depression,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D",2|1239|186801|186802|31979|1485;2|201174|1760|2037|2049|76833;2|976|117747|200666|84566|84567;2|1239|186801|3085636|186803|100132|507843,Complete,Folakunmi
bsdb:777/1/1,Study 777,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B , Al-Ali AK",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 1,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis (UC),"Patients diagnosed with inflammatory bowel disease (IBD) through colonoscopy examinations, for ulcerative colitis (UC)",124,84,2 months,16S,123456789,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File 14: Table S2,5 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between ulcerative colitis (UC) and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Eukaryota|k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichuridae|g__Trichuris|s__Trichuris trichiura",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815|2212467;2|976|200643|171549|2030927;2|976|200643|171549|815|816|46506;2|1239|186801|3085636|186803|189330|39486;2|976|200643|171549|2005525|375288|328812;2|976|200643|171549|171552|577309|454154;2|976|200643|171549|815|909656|310298;2|976|200643|171549|171552|2974251|165179;2759|33208|6231|119088|6329|119093|36086|36087,Complete,Svetlana up
bsdb:777/1/2,Study 777,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B , Al-Ali AK",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 1,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis (UC),"Patients diagnosed with inflammatory bowel disease (IBD) through colonoscopy examinations, for ulcerative colitis (UC)",124,84,2 months,16S,123456789,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File 14: Table S2,5 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between ulcerative colitis (UC) and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas kerstersii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Myrtales|f__Lythraceae|g__Punica|s__Punica granatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacteria|s__bacterium NLAE-zl-H31",2|976|200643|171549|815|816|28116;2|1239|186801|3085636|186803|572511|1322;2|1239|186801|186802|31979|1898204;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|186802|31979|1485|1502;2|1224|28216|80840|80864|283|225992;2|1239|909932|1843489|31977|39948|218538;2|1239|909932|1843489|31977|39948|309120;2|1239|909932|1843489|31977|39948|308994;2|1239|186801|3085636|186803|189330|39486;2|1239|91061|186826|81852|1350|53345;2|1224|1236|91347|543|561|1884818;2|1239|909932|909929|1843491|158846|437897;2|976|200643|171549|2005525|375288|387661;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171552|2974251|28135;2759|33090|35493|3398|41944|3928|22662|22663;2|1239|186801|3085636|186803|1506577|2053632;2|1201630,Complete,Svetlana up
bsdb:777/2/1,Study 777,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B , Al-Ali AK",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 2,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",124,135,2 months,16S,123456789,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File 15: Table S3,5 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between Crohn's disease (CD) and healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Myrtales|f__Lythraceae|g__Punica|s__Punica granatum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Eukaryota|k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichuridae|g__Trichuris|s__Trichuris trichiura",2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|46506;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|189330|39486;2|1239|91061|186826|33958|1578|1579;2|1239|91061|186826|33958|1578|1596;2|976|200643|171549|171552|2974265|363265;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|2049047;2759|33090|35493|3398|41944|3928|22662|22663;2|976|200643|171549|171552|2974251|165179;2759|33208|6231|119088|6329|119093|36086|36087,Complete,Svetlana up
bsdb:777/2/2,Study 777,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B , Al-Ali AK",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 2,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",124,135,2 months,16S,123456789,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary File 15: Table S3, Figure 4: left plot",5 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between Crohn's disease (CD) and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Myrtales|f__Lythraceae|g__Punica|s__Punica granatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacteria|s__bacterium NLAE-zl-H31,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|976|200643|171549|815|816|28116;2|1239|186801|3085636|186803|572511|1322;2|1239|186801|186802|31979|1898204;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|186802|31979|1485|1492;2|1239|186801|186802|31979|1485|1502;2|1239|909932|1843489|31977|39948|218538;2|1239|909932|1843489|31977|39948|309120;2|1239|909932|1843489|31977|39948|308994;2|1239|186801|3085636|186803|189330|39486;2|1239|91061|186826|81852|1350|53345;2|1224|1236|91347|543|561|1884818;2|1239|909932|909929|1843491|158846|437897;2|976|200643|171549|2005525|375288|387661;2|976|200643|171549|171551|836|28123;2759|33090|35493|3398|41944|3928|22662|22663;2|1239|91061|186826|1300|1301|150055;2|1239|186801|3085636|186803|1506577|2053632;2|1201630;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:777/3/1,Study 777,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B , Al-Ali AK",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 3,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,ulcerative colitis (UC),Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",84,135,2 months,16S,123456789,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4: right plot,8 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD),increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:777/3/2,Study 777,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B , Al-Ali AK",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 3,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,ulcerative colitis (UC),Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",84,135,2 months,16S,123456789,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Plot 2",8 October 2023,ChiomaBlessing,"ChiomaBlessing,Peace Sandy",Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD),decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__uncultured Lachnospira sp.,k__Bacteria|s__uncultured bacterium,k__Archaea|p__Candidatus Bathyarchaeota",2|74201|203494|48461|1647988|239934;2|1239|186801|3085636|186803|653683;2|976|200643|171549|1853231|574697;2|95818|2093818|2093825|2171986;2|1239|186801|3082768|990719|2054177;2|1239|186801|186802|186806|1730|290054;2|32066|203490|203491|203492|848;2|1239|186801|186802|216572|1892380;2|1239|909932|909929|1843491|158846;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|28050|446043;2|77133;2157|928852,Complete,Svetlana up
bsdb:778/1/1,Study 778,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu ZF, Zou K, Wu GN, Jin ZJ, Xiang CJ, Xu S, Wang YH, Wu XY, Chen C, Xu Z, Li WS, Yao XQ, Zhang JF , Liu FK",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 1,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,Superficial gastritis,Gastric cancer (GC),Gastric microbiome in paired tumor and paracancerous tissue samples from GC patients undergoing surgical treatment,64,96,1 month,16S,345,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figure 2B,14 October 2023,Chikamso,"Chikamso,ChiomaBlessing",Cladogram representation of the gastric microbiota taxa associated with superficial gastritis (group 0) an gastric cancer (group1),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rudaea,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales",2|1224|1236|135624|84642;2|1224|1236|135624|84642|642;2|29547|3031852|213849|72294|194;2|29547|3031852|213849;2|29547;2|976|1853228|1853229|563835;2|976|1853228|1853229;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|201174|1760|85007;2|201174|1760|85007|85025;2|976|200643|171549|171552|838;2|1224|1236|135614|1775411;2|201174|1760|85007|85025|1827;2|1224|1236|135614|1775411|886360;2|976|1853228|1853229|563835|504481;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|135614,Complete,ChiomaBlessing
bsdb:778/1/2,Study 778,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu ZF, Zou K, Wu GN, Jin ZJ, Xiang CJ, Xu S, Wang YH, Wu XY, Chen C, Xu Z, Li WS, Yao XQ, Zhang JF , Liu FK",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 1,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,Superficial gastritis,Gastric cancer (GC),Gastric microbiome in paired tumor and paracancerous tissue samples from GC patients undergoing surgical treatment,64,96,1 month,16S,345,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figure 2B,14 October 2023,Chikamso,"Chikamso,ChiomaBlessing",Cladogram representation of the gastric microbiota taxa associated with superficial gastritis (group 0) and gastric cancer (group 1).,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|976|200643|171549|171552|1283313;2|201174|1760|85006|1268|1663;2|976|200643|171549;2|976|200643;2|976;2|1224|28216;2|1224|28211|356|41294|374;2|1224|28211|204458|76892|41275;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|363464;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28211|356;2|32066|203490|203491|1129771|32067;2|201174|1760|85006|1268;2|201174|1760|85006;2|1239|909932;2|1224|28216|206351|481|482;2|1224|1236|135625|712;2|1224|1236|135625;2;2|1224|28211|356|69277|28100;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1224|28211|356|82115;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1224|28211|356|335928,Complete,ChiomaBlessing
bsdb:778/2/1,Study 778,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu ZF, Zou K, Wu GN, Jin ZJ, Xiang CJ, Xu S, Wang YH, Wu XY, Chen C, Xu Z, Li WS, Yao XQ, Zhang JF , Liu FK",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 2,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,non-tumor tissues of gastric cancer patients,tumor tissues of gastric cancer patients,Gastric microbiome in tumor tissue samples from GC patients undergoing surgical treatment,78,18,1 month,16S,345,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary figure 3A,22 October 2023,Chikamso,Chikamso,Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA scores >3.0),decreased,"k__Bacteria|p__Actinomycetota|c__Nitriliruptoria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",2|201174|908620;2|1224|28211|356|69277|68287;2|1224|28211|356|41294|374;2|1224|28211|356|335928;2|1224|1236|2887326|468;2|1224|28211|356|82115;2|1224|1236|72274;2|1224|28211|356,Complete,ChiomaBlessing
bsdb:778/2/2,Study 778,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu ZF, Zou K, Wu GN, Jin ZJ, Xiang CJ, Xu S, Wang YH, Wu XY, Chen C, Xu Z, Li WS, Yao XQ, Zhang JF , Liu FK",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 2,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,non-tumor tissues of gastric cancer patients,tumor tissues of gastric cancer patients,Gastric microbiome in tumor tissue samples from GC patients undergoing surgical treatment,78,18,1 month,16S,345,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Supplementary figure 3A,22 October 2023,Chikamso,Chikamso,Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA >3.0),increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Fusobacteriota",2|1239|91061;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|91061|186826;2|1224|28216|206351|481;2|32066,Complete,ChiomaBlessing
bsdb:779/1/1,Study 779,"cross-sectional observational, not case-control",37468867,10.1186/s12916-023-02972-x,NA,"Zhang D, Weng S, Xia C, Ren Y, Liu Z, Xu Y, Yang X, Wu R, Peng L, Sun L, Zhu J, Liang X, Jia Y, Wang H, Chen Q, Liu D, Chen Y, Guo H, Han X, Jin Z, Chen C, Yang X, Li Z , Huang H",Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites,BMC medicine,2023,"Coronavirus, Gut microbiome, Microbial functions, Serum metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Post-COVID-19 disorder,MONDO:0100320,healthy controls and mild COVID-19 patients,long COVID-19,patients with gastrointestinal symptoms associated with long COVID-19 at 3 months follow-up,70,45,3 months before enrollment,WMS,NA,Illumina,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3H,8 October 2023,Chiwendeee,"Chiwendeee,Folakunmi",The top 20 microbial species with significantly lower relative abundance in fecal samples of follow-up patients compared with normal samples or mild patients.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. ICM33,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Candidatus Saccharibacteria|s__Candidatus Saccharibacteria bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. KLE 1280",2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|838|28132;2|1224|28216|206351|481|482|484;2|1239|91061|186826|1300|1301|28037;2|976|200643|171549|171552|1283313|1872471;2|1224|28216|206351|481|482|28449;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171552|1283313|712469;2|32066|203490|203491|203492|848|2663009;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|171552|838|28131;2|1239|91061|186826|1300|1301|1303;2|976|200643|171549|171552|838|1161412;2|976|200643|171549|171552|838|60133;2|1239|91061|186826|1300|1301|1313;2|1239|909932|1843489|31977|29465|1110546;2|95818|2026720;2|1239|91061|186826|1300|1301|68892;2|201174|1760|2037|2049|1654|936548;2|976|200643|171549|171551|836|997829,Complete,Folakunmi
bsdb:779/2/1,Study 779,"cross-sectional observational, not case-control",37468867,10.1186/s12916-023-02972-x,NA,"Zhang D, Weng S, Xia C, Ren Y, Liu Z, Xu Y, Yang X, Wu R, Peng L, Sun L, Zhu J, Liang X, Jia Y, Wang H, Chen Q, Liu D, Chen Y, Guo H, Han X, Jin Z, Chen C, Yang X, Li Z , Huang H",Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites,BMC medicine,2023,"Coronavirus, Gut microbiome, Microbial functions, Serum metabolomics",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Post-COVID-19 disorder,MONDO:0100320,healthy controls and mild COVID-19 patients,long COVID-19,patients with gastrointestinal symptoms associated with long COVID-19 at 3 months follow-up,70,45,3 months before enrollment,WMS,NA,Illumina,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4K,23 February 2024,Folakunmi,Folakunmi,The top 20 microbial species with significantly high relative abundance in saliva samples of follow-up patients compared to normal samples or mild patients.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis",2|976|200643|171549|171551|836|1583331;2|1224|28216|206351|481|482|28449;2|1224|28216|206351|481|482|484;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465|423477;2|1224|1236|135625|712|724|729;2|1239|909932|1843489|31977|29465|1110546;2|976|200643|171549|171552|838|60133;2|1224|28216|80840|119060|47670|47671;2|1239|91061|186826|1300|1301|1304;2|976|200643|171549|171552|838|1177574;2|201174|1760|85006|1268|32207|43675;2|1224|28216|206351|481|482|495;2|976|200643|171549|171551|836|837,Complete,Folakunmi
bsdb:780/1/1,Study 780,"cross-sectional observational, not case-control",36760344,10.1136/gpsych-2022-100893,NA,"Sun Y, Ju P, Xue T, Ali U, Cui D , Chen J",Alteration of faecal microbiota balance related to long-term deep meditation,General psychiatry,2023,"Healthy Lifestyle, Mental Health, Psychosomatic Medicine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,Control group,Meditation group,Tibetan Buddhist monks that performed meditation practices of Samatha and Vipassana for at least 2 hours a day for 3 to 30 years.,19,37,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.6,"age,alcohol drinking,diet,sex,smoking status",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4,5 October 2023,Nwajei Edgar,"Nwajei Edgar,Deacme",Relative abundances of gut microbiota and linear discriminant analysis (LDA) effect size (LEfSe) in the meditation and control groups.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria",2|1239|186801|186802|216572|216851;2|1239|909932|909929|1843491|158846;2|976|200643|171549|171552|838;2|976|200643|171549|815|816;2|976|200643|171549;2|1224|28216|80840|995019;2|1224|28216|80840;2|1224|28216,Complete,Folakunmi
bsdb:780/1/2,Study 780,"cross-sectional observational, not case-control",36760344,10.1136/gpsych-2022-100893,NA,"Sun Y, Ju P, Xue T, Ali U, Cui D , Chen J",Alteration of faecal microbiota balance related to long-term deep meditation,General psychiatry,2023,"Healthy Lifestyle, Mental Health, Psychosomatic Medicine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,Control group,Meditation group,Tibetan Buddhist monks that performed meditation practices of Samatha and Vipassana for at least 2 hours a day for 3 to 30 years.,19,37,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.6,"age,alcohol drinking,diet,sex,smoking status",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4,5 October 2023,Nwajei Edgar,"Nwajei Edgar,Deacme,Folakunmi",Relative abundances of gut microbiota and linear discriminant analysis (LDA) effect size (LEfSe) in the meditation and control groups.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|201174|1760|85004|31953|1678;2|95818;2|201174|84998|84999|84107|102106;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|841;2759|33090|35493;2|1239|909932|1843489|31977;2|201174;2|1224|1236,Complete,Folakunmi
bsdb:782/1/1,Study 782,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J, Jing Q, Li J, Hua M, Di L, Song C, Huang Y, Wang J, Chen C , Wu AR",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,samples from Healthy patients,Pharyngeal samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",39,174,NA,PCR,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 1-4)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi",Altered microbial composition associated with disease severity,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1224|28216|80840|119060|32008;2|29547|3031852|213849|72294|194;2|1224|1236|91347|543|561;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|201174|1760|85006|1268|1269;2|1224|28216|206351|481|482;2|1239|909932|909929|1843491|970;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Folakunmi
bsdb:782/1/2,Study 782,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J, Jing Q, Li J, Hua M, Di L, Song C, Huang Y, Wang J, Chen C , Wu AR",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,samples from Healthy patients,Pharyngeal samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",39,174,NA,PCR,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 1-4)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi",Altered microbial composition associated with disease severity,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:782/2/1,Study 782,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J, Jing Q, Li J, Hua M, Di L, Song C, Huang Y, Wang J, Chen C , Wu AR",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,COVID-19,MONDO:0100096,samples from Healthy patients,Sputum samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria",15,235,Not Specified,PCR,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 5-7)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi",Altered microbial composition associated with disease severity,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|117743|200644|49546|1016;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:782/2/2,Study 782,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J, Jing Q, Li J, Hua M, Di L, Song C, Huang Y, Wang J, Chen C , Wu AR",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,COVID-19,MONDO:0100096,samples from Healthy patients,Sputum samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria",15,235,Not Specified,PCR,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 5-7)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi",Altered microbial composition associated with disease severity,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1224|28216|80840|80864|80865;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Folakunmi
bsdb:782/3/1,Study 782,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J, Jing Q, Li J, Hua M, Di L, Song C, Huang Y, Wang J, Chen C , Wu AR",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,samples from Healthy patients,Feces samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",40,112,N/A,PCR,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 13-16)  Description: Altered microbial composition associated with disease severity",27 October 2023,MyleeeA,"MyleeeA,Folakunmi",Altered microbial composition associated with disease severity,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236|135619|28256|2745;2|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:782/3/2,Study 782,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J, Jing Q, Li J, Hua M, Di L, Song C, Huang Y, Wang J, Chen C , Wu AR",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,samples from Healthy patients,Feces samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",40,112,N/A,PCR,NA,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 13-16)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi",Altered microbial composition associated with disease severity.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|84111;2|1239|186801|3085636|186803|2719313;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|28050;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:784/1/1,Study 784,time series / longitudinal observational,37438797,10.1186/s13073-023-01202-6,NA,"Nguyen LH, Okin D, Drew DA, Battista VM, Jesudasen SJ, Kuntz TM, Bhosle A, Thompson KN, Reinicke T, Lo CH, Woo JE, Caraballo A, Berra L, Vieira J, Huang CY, Das Adhikari U, Kim M, Sui HY, Magicheva-Gupta M, McIver L, Goldberg MB, Kwon DS, Huttenhower C, Chan AT , Lai PS",Metagenomic assessment of gut microbial communities and risk of severe COVID-19,Genome medicine,2023,"Machine learning, Microbiome, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Moderate COVID-19,Severe COVID-19,Hospitalized patients with severe Covid-19,48,79,NIL,PCR,NA,Illumina,Random Forest Analysis,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,comorbidity,ethnic group,race,sequence read depth",NA,NA,NA,NA,decreased,NA,Signature 1,Fig. 3a,23 February 2024,Peace Sandy,"Peace Sandy,ChiomaBlessing",Stool-based classifier for COVID-19 disease severity showing the differential abundance among patients with severe/critical COVID-19 compared to patients with mild/moderate COVID-19,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,2|1239|91061|186826|81852|1350|1351,Complete,Peace Sandy
bsdb:784/1/2,Study 784,time series / longitudinal observational,37438797,10.1186/s13073-023-01202-6,NA,"Nguyen LH, Okin D, Drew DA, Battista VM, Jesudasen SJ, Kuntz TM, Bhosle A, Thompson KN, Reinicke T, Lo CH, Woo JE, Caraballo A, Berra L, Vieira J, Huang CY, Das Adhikari U, Kim M, Sui HY, Magicheva-Gupta M, McIver L, Goldberg MB, Kwon DS, Huttenhower C, Chan AT , Lai PS",Metagenomic assessment of gut microbial communities and risk of severe COVID-19,Genome medicine,2023,"Machine learning, Microbiome, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Moderate COVID-19,Severe COVID-19,Hospitalized patients with severe Covid-19,48,79,NIL,PCR,NA,Illumina,Random Forest Analysis,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,comorbidity,ethnic group,race,sequence read depth",NA,NA,NA,NA,decreased,NA,Signature 2,Fig. 3a,23 February 2024,Peace Sandy,"Peace Sandy,ChiomaBlessing",Stool-based classifier for COVID-19 disease severity showing the differential abundance among patients with severe/critical COVID-19 compared to patients with mild/moderate COVID-19,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HPA0247,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|201174|1760|2037|2049|1654|544580;2|201174|1760|2037|2049|1654|1203556;2|201174|84998|1643822|1643826|447020|446660;2|201174|84998|1643822|1643826|447020|446660|394340;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|3085642|2048137|1628085;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244|649756;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|572511|418240;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107|102106|147206;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|216851|853;2|1239|1262989;2|1239|1262988;2|1239|186801|3085636|186803|1407607|1150298;2|1239|91061|1385|539738|1378|84135;2|1239|186801|186802|204475|745368;2|1239|186801|3085636|186803|28050|39485;2|1239|91061|186826|1300|1357|1358;2|1239|186801|3085656|3085657|2039302|1981510;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|841|301302;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|201174|1760|85006|1268|32207|43675;2|1239|186801|186802|216572|1263|1160721;2|1239|186801|186802|216572|1263|40518;2|201174|1760|2037|2049|2529408|1660;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|39492;2|1239|186801|3085636|186803|2316020|33039,Complete,Peace Sandy
bsdb:785/1/1,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy control individual,Ulcerative colitis patient,Patients diagnosed with ulcerative colitis from 3 different academic hospitals in Korea.,100,70,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4a,24 November 2023,Yjung24,"Yjung24,Atrayees","Taxa list according to linear discriminate analysis values determined from comparisons between HC and UC patients. HC, healthy control individuals; UC, ulcerative colitis.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus vulgaris,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|201174|1760|85004|31953|1678|1689;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|186802|216572|946234|292800;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|28050|39485;2|1224|1236|91347|1903414|583|585;2|1239|909932|1843489|31977|29465|39778;2|976|200643|171549|2005525|375288,Complete,Peace Sandy
bsdb:785/1/2,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy control individual,Ulcerative colitis patient,Patients diagnosed with ulcerative colitis from 3 different academic hospitals in Korea.,100,70,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 4a,24 November 2023,Yjung24,Yjung24,"Taxa list according to linear discriminate analysis values determined from comparisons between HC and UC patients. HC, healthy control individuals; UC, ulcerative colitis.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum|s__Bifidobacterium pullorum subsp. gallinarum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|1239|909932|909929|1843491|158846|491921;2|976|200643|171549|171550|239759|28117;2|201174|1760|85004|31953|1678|1694;2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803|189330|88431;2|976|200643|171549|2005525|375288|46503;2|201174|1760|85004|31953|1678|78448|78344;2|201174|84998|84999|84107|102106|74426;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|186802|216572|292632|214851;2|1239|186801|3085636|186803|2316020|592978;2|1239|91061|186826|33958|2767887|1623;2|201174|84998|84999|84107|1473205|1473216;2|74201|203494|48461|1647988|239934|239935,Complete,Peace Sandy
bsdb:785/2/1,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy control individual,Crohn's disease patient,Patients diagnosed with Crohn's disease from 3 different academic hospitals in Korea.,100,39,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4b,24 November 2023,Yjung24,"Yjung24,Peace Sandy","Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fragi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|201174|1760|85004|31953|1678|1689;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|2719313|1531;2|1224|1236|91347|543|561|562;2|1239|186801|3085636|186803|2005355|1912855;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1243|1246;2|1239|186801|3085636|186803|2316020|33038;2|1239|909932|1843489|31977|906|907;2|1224|1236|72274|135621|286|296;2|1239|91061|186826|1300|1301|315405;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|39778,Complete,Peace Sandy
bsdb:785/2/2,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy control individual,Crohn's disease patient,Patients diagnosed with Crohn's disease from 3 different academic hospitals in Korea.,100,39,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 4b,24 November 2023,Yjung24,"Yjung24,Peace Sandy","Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum|s__Bifidobacterium pullorum subsp. gallinarum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia cecicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|976|200643|171549|171550|239759|28117;2|201174|1760|85004|31953|1678|1694;2|201174|1760|85004|31953|1678|78448|78344;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|216572|216851|853;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|3085636|186803|2316020|592978;2|976|200643|171549|2005525|375288|46503;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|3085636|186803|841|842;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|292632|214851;2|1239|186801|186802|216572|39492,Complete,Peace Sandy
bsdb:785/3/1,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with mild ulcerative colitis,Patients with moderate to severe ulcerative colitis,"patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",37,18,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5a,24 November 2023,Yjung24,Yjung24,Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius",2|1239|186801|3082720|186804|1870884|1496;2|1239|91061|186826|33958|2767887|1624,Complete,Peace Sandy
bsdb:785/3/2,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with mild ulcerative colitis,Patients with moderate to severe ulcerative colitis,"patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",37,18,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5a,24 November 2023,Yjung24,"Yjung24,Atrayees",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|815|816|85831;2|976|200643|171549|815|816|47678;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|186802|404402|404403;2|1239|186801|186802|216572|1263|40519;2|1239|91061|186826|1300|1301|1313;2|1239|526524|526525|128827|1522;2|976|200643|171549|171550|239759,Complete,Peace Sandy
bsdb:785/4/1,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with remission ulcerative colitis (symptoms of UC are reduced or inapparent),Patients with moderate to severe ulcerative colitis,"Patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",15,18,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5b,24 November 2023,Yjung24,Yjung24,Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe UC and remission (B).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus plantarum",2|1239|91061|186826|1300|1357|1358;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3082720|186804|1870884|1496;2|1239|91061|186826|33958|46255|1583;2|1239|186801|3085636|186803|207244|649756;2|1239|526524|526525|2810280|3025755|29348;2|1239|91061|186826|33958|1243|1246;2|1239|91061|186826|1300|1357|1365,Complete,Peace Sandy
bsdb:785/4/2,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with remission ulcerative colitis (symptoms of UC are reduced or inapparent),Patients with moderate to severe ulcerative colitis,"Patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",15,18,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5b,24 November 2023,Yjung24,"Yjung24,Atrayees",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe UC and remission (B).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas paravirosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|815|816|85831;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|246787;2|200940|3031449|213115|194924|35832|35833;2|976|200643|171549|1853231|574697|1472417;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|216572|1263|40519;2|1239|91061|186826|1300|1301|1305;2|976|200643|171549|171550|239759;2|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:785/5/1,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,"Pancolitis,Distal colitis","EFO:0005623,EFO:0005626",patients with proctitis ulcerative colitis,patients with left sided or extensive ulcerative colitis,patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea defined as left sided (distal colitis) or extensive (pancolitis).,21,28,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 5c,25 November 2023,Yjung24,Yjung24,Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between left sided or extensive UC and proctitis.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|201174|1760|85004|31953|1678|1681;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|207244|649756;2|1239|91061|186826|33958|2759736|1597;2|1239|186801|3085636|186803|2316020|33038,Complete,Peace Sandy
bsdb:785/5/2,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,"Pancolitis,Distal colitis","EFO:0005623,EFO:0005626",patients with proctitis ulcerative colitis,patients with left sided or extensive ulcerative colitis,patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea defined as left sided (distal colitis) or extensive (pancolitis).,21,28,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 5c,25 November 2023,Yjung24,"Yjung24,Atrayees",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between left sided or extensive UC and proctitis.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter|s__Tractidigestivibacter scatoligenes",2|976|200643|171549|171550|239759|2585118;2|976|200643|171549|171550|239759|1288121;2|1239|186801|186802|404402|404403;2|976|200643|171549|171552|2974265|363265;2|1239|91061|186826|33958|2767887|1623;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171552|577309|454154;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179;2|201174|84998|84999|84107|1473205|1473216;2|201174|84998|1643822|1643826|84108|572010;2|1239|186801|186802|216572|44748;2|201174|84998|84999|1643824|2847313|1299998,Complete,Peace Sandy
bsdb:785/6/1,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,patients with remission Crohn's disease,patients with active Crohn's disease,"Patients diagnosed with Crohn's disease (CD) from 3 different academic hospitals in Korea. The severity of disease was assessed by the Crohn’s Disease Activity Index CD. Active status including mild, moderate, severe forms of CD. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",24,15,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6a,25 November 2023,Yjung24,Yjung24,Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between remission and active CD (A).,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus",2|1239|909932|1843488|909930|33024|626940;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|97478;2|976|200643|171549|171551|836|28123;2|1239|186801|3085636|186803|33042|116085,Complete,Peace Sandy
bsdb:785/6/2,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,patients with remission Crohn's disease,patients with active Crohn's disease,"Patients diagnosed with Crohn's disease (CD) from 3 different academic hospitals in Korea. The severity of disease was assessed by the Crohn’s Disease Activity Index CD. Active status including mild, moderate, severe forms of CD. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",24,15,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6a,25 November 2023,Yjung24,Yjung24,Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between remission and active CD (A).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus",2|976|200643|171549|815|816|820;2|201174|84998|1643822|1643826|84111|84112;2|1239|526524|526525|128827|1522;2|1239|186801|186802|216572|946234|292800;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|3085636|186803|572511|1532;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|815|909656|310297;2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|2005525|375288|823;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|3085636|186803|2316020|342942,Complete,Peace Sandy
bsdb:785/7/1,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Ileocolitis,EFO:0005624,patients with small bowel Crohn's disease,patients with ileocolonic Crohn's disease,Patients diagnosed with ileocolonic Crohn's disease (CD) from 3 different academic hospitals in Korea.,17,17,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,25 November 2023,Yjung24,Yjung24,Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between ileocolonic and small bowel CD (B).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",2|1239|91061|186826|33958|1578|1596;2|976|200643|171549|815|816|28116;2|1239|91061|186826|33958|46255|1583,Complete,Peace Sandy
bsdb:785/7/2,Study 785,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin SY, Kim Y, Kim WS, Moon JM, Lee KM, Jung SA, Park H, Huh EY, Kim BC, Lee SC , Choi CH",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Ileocolitis,EFO:0005624,patients with small bowel Crohn's disease,patients with ileocolonic Crohn's disease,Patients diagnosed with ileocolonic Crohn's disease (CD) from 3 different academic hospitals in Korea.,17,17,"Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.",16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,25 November 2023,Yjung24,Yjung24,Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between ileocolonic and small bowel CD (B).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",2|1239|186801|3085636|186803|572511|1532;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|2719313|1531,Complete,Peace Sandy
bsdb:786/1/1,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls - based on GA- map,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",38,22,4 weeks,16S,3456789,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy","Differentially abundant bacteria – pre-T2D vs. healthy, GA-map® 131-plex",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|186801|3085636|186803|189330;2|1224;2|1224|1236|91347;2|1224|1236|91347|543|1940338,Complete,Peace Sandy
bsdb:786/1/2,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls - based on GA- map,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",38,22,4 weeks,16S,3456789,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy","Differentially abundant bacteria – pre-T2D vs. healthy, GA-map® 131-plex",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|216851|853;2|1239|909932|1843489|31977|39948|218538;2|1239|909932|1843489|31977|29465;2|1224|28216|80840|995019|40544|40545,Complete,Peace Sandy
bsdb:786/2/1,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",48,22,4 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,11 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter|s__Neglectibacter timonensis",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1432051;2|1239|186801|3085636|186803|1432051|1720294;2|1239|186801|186802|216572|1924105;2|1239|186801|186802|216572|1924105|1776382,Complete,Peace Sandy
bsdb:786/2/2,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",48,22,4 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,11 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola",2|1239|186801|186802|216572|459786|351091;2|976|200643|171549|815|909656|310298,Complete,Peace Sandy
bsdb:786/3/1,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Type 2 Diabetes - T2D,Patients with  Type 2 diabetes (T2D),48,16,4 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,12 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",2|1239|186801|3085636|186803|189330;2|1224|1236|91347;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1239|526524;2|1239|526524|526525|128827;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281|191303|154288,Complete,Peace Sandy
bsdb:786/3/2,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Type 2 Diabetes - T2D,Patients with  Type 2 diabetes (T2D),48,16,4 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,12 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,2|1239|186801|3085636|3118652|2039240,Complete,Peace Sandy
bsdb:786/4/1,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Pre- Type 2 Diabetes individuals,Type 2 Diabetes - T2D Patients,Patients with Type 2 Diabetes,22,16,4 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,24 January 2024,Peace Sandy,Peace Sandy,"Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|88431;2|1239|526524|526525|128827;2|1239|526524;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281|191303|154288,Complete,Peace Sandy
bsdb:786/4/2,Study 786,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A , Casèn C",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Pre- Type 2 Diabetes individuals,Type 2 Diabetes - T2D Patients,Patients with Type 2 Diabetes,22,16,4 weeks,16S,123456789,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,24 January 2024,Peace Sandy,Peace Sandy,"Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter|s__Neglectibacter timonensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061;2|1239|186801|3085636|186803|1432051;2|1239|186801|3085636|186803|1432051|1720294;2|1239|91061|186826;2|1239|186801|186802|216572|1924105;2|1239|186801|186802|216572|1924105|1776382;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:787/1/1,Study 787,"cross-sectional observational, not case-control",35305613,10.1186/s12894-022-00990-0,NA,"Li K, Chen C, Zeng J, Wen Y, Chen W, Zhao J , Wu P",Interplay between bladder microbiota and overactive bladder symptom severity: a cross-sectional study,BMC urology,2022,"Bladder microbiota, Overactive bladder, Severity of OAB symptom, Urinary microbiome",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Overactive bladder,EFO:1000781,Mild Overactive Bladder,Moderate/Severe Overactive Bladder,Adult patients with Overactive Bladder Symptom Score greater than five (OABSS > 5).,17,53,4 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,"age,body mass index,hypertension,race",NA,unchanged,increased,increased,increased,NA,increased,Signature 1,Table 2,23 October 2023,Deacme,"Deacme,Chinelsy",Increased abundance of bacteria in moderate/severe overactive bladder patients.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|201174|1760|85004|31953;2|1224|28211|356|119045;2|976|200643|171549|171552;2|1239|91061|1385|90964,Complete,Chinelsy
bsdb:787/1/2,Study 787,"cross-sectional observational, not case-control",35305613,10.1186/s12894-022-00990-0,NA,"Li K, Chen C, Zeng J, Wen Y, Chen W, Zhao J , Wu P",Interplay between bladder microbiota and overactive bladder symptom severity: a cross-sectional study,BMC urology,2022,"Bladder microbiota, Overactive bladder, Severity of OAB symptom, Urinary microbiome",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Overactive bladder,EFO:1000781,Mild Overactive Bladder,Moderate/Severe Overactive Bladder,Adult patients with Overactive Bladder Symptom Score greater than five (OABSS > 5).,17,53,4 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,"age,body mass index,hypertension,race",NA,unchanged,increased,increased,increased,NA,increased,Signature 2,Table 2,23 October 2023,Deacme,Deacme,Decreased abundance of bacteria in moderate/severe overactive bladder patients.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",2|1239|91061|186826|33958;2|1239|91061|186826|81852;2|1239|91061|186826|1300;2|1224|1236|2887326|468;2|1224|28211|204457|41297,Complete,Chinelsy
bsdb:788/1/1,Study 788,time series / longitudinal observational,32630754,https://doi.org/10.3390/ani10071127,NA,"Kim DH, Kim MH, Kim SB, Son JK, Lee JH, Joo SS, Gu BH, Park T, Park BY , Kim ET",Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment,Animals : an open access journal from MDPI,2020,"Holstein, Jersey, KEGG pathways, heat stress, ruminal microbiome",Experiment 1,Republic of Korea,Bos taurus,Rumen,UBERON:0007365,Response to heat,GO:0009408,Holstein cows under normal condition,Holstein cows under heat stress condition,"Holstein cows under heat stress condition. The measurement of the respiration rate and rectal temperature in May was considered as the normal condition, while  measurement of the respiration rate and rectal temperature in August was considered the heat stress condition.",8,8,none,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,figure 4B,23 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa in Holstein cows under heat stress condition compared to cows under normal conditions,increased,"k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria,k__Bacteria|p__Fibrobacterota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas arboricola",2|65842|204430|218872|204431;2|65842|204430|218872;2|65842|204430;2|65842;2|1224|1236|135614|32033|338|56448,Complete,ChiomaBlessing
bsdb:788/1/2,Study 788,time series / longitudinal observational,32630754,https://doi.org/10.3390/ani10071127,NA,"Kim DH, Kim MH, Kim SB, Son JK, Lee JH, Joo SS, Gu BH, Park T, Park BY , Kim ET",Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment,Animals : an open access journal from MDPI,2020,"Holstein, Jersey, KEGG pathways, heat stress, ruminal microbiome",Experiment 1,Republic of Korea,Bos taurus,Rumen,UBERON:0007365,Response to heat,GO:0009408,Holstein cows under normal condition,Holstein cows under heat stress condition,"Holstein cows under heat stress condition. The measurement of the respiration rate and rectal temperature in May was considered as the normal condition, while  measurement of the respiration rate and rectal temperature in August was considered the heat stress condition.",8,8,none,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,figure 4B,24 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa in Holstein cows under heat stress condition compared to cows under normal conditions,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium P7,2|1239|186801|186802|216572|1200751,Complete,ChiomaBlessing
bsdb:788/2/1,Study 788,time series / longitudinal observational,32630754,https://doi.org/10.3390/ani10071127,NA,"Kim DH, Kim MH, Kim SB, Son JK, Lee JH, Joo SS, Gu BH, Park T, Park BY , Kim ET",Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment,Animals : an open access journal from MDPI,2020,"Holstein, Jersey, KEGG pathways, heat stress, ruminal microbiome",Experiment 2,Republic of Korea,Bos taurus,Rumen,UBERON:0007365,Ruminative stress response,EFO:0009857,Jersey cows under normal condition,Jersey cows under heat stress condition,"Jersey cows under heat stress condition. The measurement of the respiration rate and rectal temperature in May was considered as the normal condition, while  measurement of the respiration rate and rectal temperature in August was considered the heat stress condition.",8,8,none,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,figure 4C,23 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa in Jersey cows under heat stress condition compared to Jersey cows under normal conditions,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Tissierellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas arboricola",2|1239|91061|1385|186817|1386|1396;2|1239|91061|1385|186817|1386;2|203691|203692|1643686|143786;2|203691|203692|1643686;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1491;2|1117;2|29547|3031852;2|976|117743;2|32066|203490;2|544448|31969;2|544448|31969|2085;2|544448;2|976|117747;2|1239|91061|1385|90964|1279;2|1239|1737404;2|1224|1236|135614|32033|338|56448,Complete,ChiomaBlessing
bsdb:788/2/2,Study 788,time series / longitudinal observational,32630754,https://doi.org/10.3390/ani10071127,NA,"Kim DH, Kim MH, Kim SB, Son JK, Lee JH, Joo SS, Gu BH, Park T, Park BY , Kim ET",Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment,Animals : an open access journal from MDPI,2020,"Holstein, Jersey, KEGG pathways, heat stress, ruminal microbiome",Experiment 2,Republic of Korea,Bos taurus,Rumen,UBERON:0007365,Ruminative stress response,EFO:0009857,Jersey cows under normal condition,Jersey cows under heat stress condition,"Jersey cows under heat stress condition. The measurement of the respiration rate and rectal temperature in May was considered as the normal condition, while  measurement of the respiration rate and rectal temperature in August was considered the heat stress condition.",8,8,none,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,figure 4C + 4A,24 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa in Jersey cows under heat stress condition compared to Jersey cows under normal conditions,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium WCE2004",2|201174|1760;2|201174;2|201174|1760|85004;2|201174|84998;2|1239|186801|186802;2|201174|1760|85011;2|201174|1760|85008;2|1224|1236|72274|135621|286;2|201174|1760|85010;2|201174|1760|85011|2062|1883;2|1239|526524|526525|128827|118966;2|976|200643|171549|1945890,Complete,ChiomaBlessing
bsdb:789/1/1,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Prediagnostic (PD),Samples donated prior to breast cancer diagnosis,49,15,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3b,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Differentially abundant taxa in Prediagnostic group versus Healthy group,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",2|1224|28216|80840|2975441|196013;2|32066|203490|203491|203492|848;2|1224|1236|91347|1903409|53335;2|1239|186801|3082720|186804|1501226;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301|1306,Complete,ChiomaBlessing
bsdb:789/1/2,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Prediagnostic (PD),Samples donated prior to breast cancer diagnosis,49,15,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3b,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Differentially abundant taxa in Prediagnostic group versus Healthy group,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,2|201174|1760|85007|1653|1716,Complete,ChiomaBlessing
bsdb:789/2/1,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Adjacent normal (AN),samples donated after breast cancer diagnosis (AN),49,49,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3c,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Differentially abundant taxa in Adjacent normal group versus Healthy group,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes|s__Atopostipes sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus|s__Oceanobacillus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pseudogracilibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella|s__Tissierella sp.",2|1224|28216|80840|506|507|512;2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|186828|292480|1872652;2|201174|1760|85007|1653|1716;2|1224|28216|80840|75682|75654;2|1239|91061|186826|81852|1350|35783;2|1224|28216|80840|75682|963|1890675;2|1224|1236|91347|543|570;2|1239|91061|1385|186817|182709|1871622;2|1224|1236|91347|1903414|583;2|1239|91061|1385|186817|1494958;2|1224|1236|72274|135621|286|306;2|1239|1737404|1737405|1737406|41273|41274,Complete,ChiomaBlessing
bsdb:789/2/2,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Adjacent normal (AN),samples donated after breast cancer diagnosis (AN),49,49,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3c,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Differentially abundant taxa in Adjacent normal group versus Healthy group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Iodobacter|s__Iodobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus",2|1224|1236|2887326|468|469|472;2|201174|1760|85006|1268|1663;2|976|200643|171549|815|816;2|1224|28211|356|41294|374;2|1239|91061|1385|186820|2755;2|1239|91061|186826|186828|2747|48221;2|201174|1760|85007|1653|1716|1720;2|201174|1760|85009|31957|1912216;2|1224|28216|206351|2897177|32014|1915058;2|1239|91061|186826|1300|1357;2|1224|1236|135623|641|657;2|1224|1236|72274|135621|286|306;2|201174|84995|84996|84997|42255;2|1239|186801|186802|216572|1263;2|1224|1236|91347|1903411|613;2|1239|91061|1385|90964|1279|29387;2|1239|91061|186826|81852|2737,Complete,ChiomaBlessing
bsdb:789/3/1,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Tumor (T),Samples donated after breast cancer diagnosis (tumor),49,46,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3d,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Differentially abundant taxa in Tumor group versus Healthy group,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pseudogracilibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.",2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|81852|1350|35783;2|1224|28216|80840|75682|963|1890675;2|1239|91061|1385|186817|1494958;2|1224|1236|72274|135621|286|306;2|201174|1760|85007|85025|1827;2|1239|91061|1385|90964|1279|29387,Complete,ChiomaBlessing
bsdb:789/3/2,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Tumor (T),Samples donated after breast cancer diagnosis (tumor),49,46,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3d,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing",Differentially abundant taxa in Tumor group versus Healthy group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix|s__Brochothrix sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Iodobacter|s__Iodobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus",2|1224|1236|2887326|468|469;2|201174|1760|85006|1268|1663;2|976|200643|171549|815|816;2|200940|3031449|213115|194924|35832;2|1224|28211|356|41294|374|376;2|1239|91061|1385|186820|2755|1993875;2|1239|91061|186826|186828|2747|48221;2|201174|1760|85007|1653|1716|1720;2|1224|28216|206351|2897177|32014|1915058;2|1239|91061|186826|1300|1357;2|201174|1760|85007|2805586|1847725;2|976|200643|171549|2005473;2|1224|1236|135623|641|657;2|1224|1236|72274|135621|286|306;2|1224|28211|204455|2854170|295418;2|1224|1236|91347|1903411|613;2|1239|91061|1385|90964|1279|29387;2|1297|188787|68933|188786|270;2|1239|91061|186826|81852|2737,Complete,ChiomaBlessing
bsdb:789/4/NA,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 4,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Prediagnostic (PD),Tumor (T),Samples donated after breast cancer diagnosis (tumor),15,46,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:789/5/NA,Study 789,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N , Stiemsma LT",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 5,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Adjacent Normal (AN),Tumor (T),Samples donated after breast cancer diagnosis (tumor),49,46,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:790/1/1,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy controls,Inflammatory bowel disease patients,Patients under 18 years old diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,75,107,Six Months,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 December 2023,Yjung24,Yjung24,Bacterial species exhibiting deviating abundances between patient and control groups. IBD vs Healthy.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|201174|1760|85004|31953|1678|1683;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|1686;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3082768|990719|990721|626937;2|1239|186801|186802|216572|1535;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|186806|1730|39496;2|1239|91061|186826|33958|1578|1579;2|1239|91061|186826|33958|2759736|1597;2157|28890|183925|2158|2159|2172|2173;2|976|200643|171549|171552|577309|454154;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|841|301301;2|1239|186801|186802|216572|1263|40518;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1308;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|171550|239759|328813;2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|909656|357276;2|976|200643|171549|2005519|397864|487174;2|1239|186801|3082720|186804|1505657|261299;2|74201|203494|48461|1647988|239934|239935,Complete,Chloe
bsdb:790/2/1,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy children,Non-inflammatory bowel disease symptomatic controls,patients under 18 years presented with symptoms of inflammatory bowel disease (Crohn's Disease or ulcerative colitis) but did not meet the criteria for IBD and who had a  macroscopically and histologically normal mucosa and normal MRI examination from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,75,50,antibiotics use within the last six months of study for healthy controls (group 0),PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 December 2023,Yjung24,Yjung24,Bacterial species exhibiting deviating abundances between patient and control groups. Non-IBD vs. Healthy.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",2|201174|1760|85004|31953|1678|1683;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|186802|216572|39492;2|1239|186801|186802|216572|1263|40518;2|1239|91061|186826|1300|1301|1308;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|909656|357276,Complete,Chloe
bsdb:790/2/2,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy children,Non-inflammatory bowel disease symptomatic controls,patients under 18 years presented with symptoms of inflammatory bowel disease (Crohn's Disease or ulcerative colitis) but did not meet the criteria for IBD and who had a  macroscopically and histologically normal mucosa and normal MRI examination from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,75,50,antibiotics use within the last six months of study for healthy controls (group 0),PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 December 2023,Yjung24,Yjung24,Bacterial species exhibiting deviating abundances between patient and control groups. Non-IBD vs. Healthy.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri",2|1239|91061|186826|81852|1350|1352;2|1224|1236|91347|543|544|545,Complete,Chloe
bsdb:790/3/1,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,non-inflammatory bowel disease symptomatic controls,inflammatory bowel disease patients,patients under 18 diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,50,110,antibiotics use within the last six months of study for healthy controls (group 0),PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 December 2023,Yjung24,Yjung24,Bacterial species exhibiting deviating abundances between patient and control groups.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|976|200643|171549|171552|577309|454154;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1683;2|201174|1760|85004|31953|1678|1681;2|1239|186801|3082768|990719|990721|626937;2|1239|186801|186802|216572|1535;2|200940|3031449|213115|194924|872|901;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|216572|39492;2|1239|186801|186802|186806|1730|39496;2|1239|91061|186826|33958|1578|1579;2|1239|91061|186826|33958|2759736|1597;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|841|301301;2|1239|186801|186802|216572|1263|40518;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|46506;2|74201|203494|48461|1647988|239934|239935,Complete,Chloe
bsdb:790/3/2,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,non-inflammatory bowel disease symptomatic controls,inflammatory bowel disease patients,patients under 18 diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,50,110,antibiotics use within the last six months of study for healthy controls (group 0),PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 December 2023,Yjung24,Yjung24,Bacterial species exhibiting deviating abundances between patient and control groups. IBD vs. Non-IBD.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,2|1224|1236|135625|712|724|729,Complete,Chloe
bsdb:790/4/1,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Crohn's Disease patients with inflammatory phenotypes,Crohn's Disease patients with stricturing and/or penetrating phenotypes,patients under 18 diagnosed with Crohn's Disease with stricturing and/or penetrating phenotypes,53,27,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Section 3.4 (text),10 December 2023,Yjung24,Yjung24,"The CD patients had a significantly lower abundance for five bacterial species and a
higher abundance for five bacterial species. The CD patients with stricturing and/or penetrating phenotypes had a lower abundance of four species and a higher abundance of Escherichia coli (p = 0.010) compared to the CD patients
with an inflammatory phenotype.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis",2|1239|186801|3082768|990719|990721|626937;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|841|301301,Complete,Chloe
bsdb:790/4/2,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Crohn's Disease patients with inflammatory phenotypes,Crohn's Disease patients with stricturing and/or penetrating phenotypes,patients under 18 diagnosed with Crohn's Disease with stricturing and/or penetrating phenotypes,53,27,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Section 3.4 (text),10 December 2023,Yjung24,Yjung24,The CD patients had a significantly lower abundance for five bacterial species and a higher abundance for five bacterial species. The CD patients with stricturing and/or penetrating phenotypes had a lower abundance of four species and a higher abundance of Escherichia coli (p = 0.010) compared to the CD patients with an inflammatory phenotype.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,2|1224|1236|91347|543|561|562,Complete,Chloe
bsdb:790/5/1,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Inflammatory bowel disease patients treated with conventional therapy,Inflammatory bowel disease patients treated with biological therapy,58% of inflammatory bowel disease patients were later treated with biologic therapy due to failure to induce remission with conventional treatments or relapse after primary induction.,46,64,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 December 2023,Yjung24,Yjung24,"Bacterial species exhibiting deviating abundances between medical therapy groups and
between groups with high and low calprotectin levels.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara",2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1681;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40518;2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|246787;2|976|200643|171549|171552|577309|454154,Complete,Chloe
bsdb:790/5/2,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Inflammatory bowel disease patients treated with conventional therapy,Inflammatory bowel disease patients treated with biological therapy,58% of inflammatory bowel disease patients were later treated with biologic therapy due to failure to induce remission with conventional treatments or relapse after primary induction.,46,64,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 December 2023,Yjung24,Yjung24,"Bacterial species exhibiting deviating abundances between medical therapy groups and
between groups with high and low calprotectin levels.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|815|909656|821,Complete,Chloe
bsdb:790/6/1,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 6,Norway,Homo sapiens,Feces,UBERON:0001988,Increased inflammatory response,HP:0012649,Inflammatory bowel disease patients with fecal calprotectin levels < 1000 mg/kg,Inflammatory bowel disease patients with fecal calprotectin levels > 1000 mg/kg,Inflammatory bowel disease patients with higher fecal protectin levels (31 with CD and 12 with UC had above 1000 mg/kg).,67,43,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 December 2023,Yjung24,Yjung24,"Bacterial species exhibiting deviating abundances between medical therapy groups and
between groups with high and low calprotectin levels.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis",2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|841|166486;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|2005519|397864|487174,Complete,Chloe
bsdb:790/7/1,Study 790,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C, Småstuen MC , Moen AEF","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 7,Norway,Homo sapiens,Feces,UBERON:0001988,Increased inflammatory response,HP:0012649,Inflammatory bowel disease patients receiving one biologic or conventional therapy,Inflammatory bowel disease patients receiving second class of biologic drug,A subset of the IBD patients receiving biologic therapy needed further treatment escalation to a second class of biologics.,88,22,antibiotics use within the last six months of study for healthy controls (group 0),PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text: Page 6 Paragraph 2,21 January 2024,Yjung24,Yjung24,"A subset of the IBD patients receiving biologic therapy needed further treatment escalation to a second class of biologics. These patients had a significantly lower abundance of Bifidobacterium bifidum, Roseburia hominis and Bacteroides xylanisolvens compared to the IBD patients who received one biologic or conventional therapy.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens",2|201174|1760|85004|31953|1678|1681;2|1239|186801|3085636|186803|841|301301;2|976|200643|171549|815|816|371601,Complete,NA
bsdb:791/1/1,Study 791,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM , Cotter PD",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 1,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Full-term Birth,Preterm Birth,Pregnant women who delivered before 37 weeks’ gestation.,41,8,Women currently on antibiotic treatment.,WMS,NA,Illumina,"T-Test,Linear Regression",0.25,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2b + Figure 2C,7 October 2023,Joan Chuks,"Joan Chuks,ChiomaBlessing",Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__Coriobacteriales bacterium DNF00809,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella greenwoodii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera lornae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacteria|p__Bacillota|c__Tissierellia|s__Tissierellia bacterium KA00581,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S7-1-8",2|1239|91061|186826|186827|1375|87541;2|201174|84998|84999|1588753;2|1239|909932|1843489|31977|39948|309120;2|201174|84998|84999|1643824|2767327|82135;2|201174|1760|85004|31953|2701|2914925;2|201174|1760|85004|31953|2701|2702;2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171552|52228|1703337;2|976|200643|171549|171552|2974257|386414;2|1239|186801|3085636|186803|1898203;2|1239|909932|1843489|31977|906|699218;2|976|200643|171549|171552|838|419005;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|470565;2|201174|1760|85004|31953|196081|230143;2|32066|203490|203491|1129771|168808|40543;2|32066|203490|203491|1129771|168808|187101;2|1239|1737404|1588751;2|1239|186801|3085636|186803|1213720;2|976|200643|171549|171552|838|1284775,Complete,ChiomaBlessing
bsdb:791/1/2,Study 791,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM , Cotter PD",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 1,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Full-term Birth,Preterm Birth,Pregnant women who delivered before 37 weeks’ gestation.,41,8,Women currently on antibiotic treatment.,WMS,NA,Illumina,"T-Test,Linear Regression",0.25,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2b + Figure 2C,7 October 2023,Joan Chuks,"Joan Chuks,ChiomaBlessing",Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",2|201174|1760|85004|31953|1678|1685;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1578|33959,Complete,ChiomaBlessing
bsdb:791/2/1,Study 791,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM , Cotter PD",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 2,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Low-risk controls,Risk Group,Pregnant women with either a history of previous spontaneous preterm birth (risk_PTB) or women with risk factors for preterm birth but who delivered full term (risk_FTB),14,35,Women currently on antibiotic treatment.,WMS,NA,Illumina,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,27 October 2023,Joan Chuks,Joan Chuks,Differentially abundant species within the Risk group.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,2|201174|1760|85004|31953|1678|1685,Complete,ChiomaBlessing
bsdb:791/2/2,Study 791,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM , Cotter PD",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 2,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Low-risk controls,Risk Group,Pregnant women with either a history of previous spontaneous preterm birth (risk_PTB) or women with risk factors for preterm birth but who delivered full term (risk_FTB),14,35,Women currently on antibiotic treatment.,WMS,NA,Illumina,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C,27 October 2023,Joan Chuks,Joan Chuks,Differentially abundant species within the Risk group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator|s__Caloramator mitchellensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. 852013-50091_SCH5140682,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",2|1239|186801|186802|31979|44258|908809;2|201174|1760|85007|1762|1763|1834109;2|1224|1236|135614|32033|40323|40324,Complete,ChiomaBlessing
bsdb:791/3/1,Study 791,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM , Cotter PD",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 3,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,No Previous Preterm birth,Previous Preterm birth,Pregnant women with a history of previous spontaneous preterm birth (PTB),20,29,Women currently on antibiotic treatment.,WMS,NA,Illumina,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,27 October 2023,Joan Chuks,Joan Chuks,Differentially abundant species for Previous Preterm birth(PTB) group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator|s__Caloramator mitchellensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. 852013-50091_SCH5140682,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus|s__Virgibacillus profundi,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Desulfuromonadaceae|g__Desulfuromonas|s__Desulfuromonas acetexigens",2|976|200643|171549|815|816|246787;2|1239|186801|186802|31979|44258|908809;2|201174|1760|85007|1762|1763|1834109;2|1224|1236|135614|32033|40323|40324;2|1239|91061|186826|33958|2759736|47715;2|1239|91061|1385|186817|84406|2024555;2|200940|3031651|69541|213421|890|38815,Complete,ChiomaBlessing
bsdb:791/3/2,Study 791,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM , Cotter PD",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 3,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,No Previous Preterm birth,Previous Preterm birth,Pregnant women with a history of previous spontaneous preterm birth (PTB),20,29,Women currently on antibiotic treatment.,WMS,NA,Illumina,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C,27 October 2023,Joan Chuks,Joan Chuks,Differentially abundant species for Previous Preterm birth(PTB) group,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis",2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816|1682,Complete,ChiomaBlessing
bsdb:792/1/1,Study 792,"cross-sectional observational, not case-control",30631088,http://dx.doi.org/10.1038/s41598-018-37208-z,NA,"Jana Mittelstrass, Joy Bergelson, Mathew W. Horton",Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome,Scientific reports,2019,"Arabidopsis thaliana, bacteria, fungi, microbiome, roots, leaves, field experiment",Experiment 1,United States of America,Arabidopsis thaliana,Accessory nerve root,UBERON:0014615,Root,PO:0009005,Control group (Leaves),Test group (Roots),"The leaf microbiome, representing the microbial communities associated with the leaves of the Arabidopsis plants.",4,4,NIL,16S,567,Roche454,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 1,6 October 2023,Spykelionel,"Spykelionel,Peace Sandy","The top 10 differentially enriched genera from each kingdom and their preferred habitats. 
The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|g__Tetracladium",2|1224|28216|80840|75682|149698;2759|4751|1913637|2212732|214503|4854|4855;2759|4751|4890|147548|5178|164535,Complete,Peace Sandy
bsdb:792/1/2,Study 792,"cross-sectional observational, not case-control",30631088,http://dx.doi.org/10.1038/s41598-018-37208-z,NA,"Jana Mittelstrass, Joy Bergelson, Mathew W. Horton",Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome,Scientific reports,2019,"Arabidopsis thaliana, bacteria, fungi, microbiome, roots, leaves, field experiment",Experiment 1,United States of America,Arabidopsis thaliana,Accessory nerve root,UBERON:0014615,Root,PO:0009005,Control group (Leaves),Test group (Roots),"The leaf microbiome, representing the microbial communities associated with the leaves of the Arabidopsis plants.",4,4,NIL,16S,567,Roche454,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Table 1,6 October 2023,Spykelionel,"Spykelionel,Peace Sandy","The top 10 differentially enriched genera from each kingdom and their preferred habitats. The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Discinellaceae|g__Articulospora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Plectosphaerella",2|1224|28216|80840|75682|29580;2|1224|1236|72274|135621|286;2759|4751|4890|147541|92860|28556|5598;2759|4751|4890|147548|5178|2794838|253308;2759|4751|4890|147541|2726946|452563|5498;2759|4751|4890|147550|1028384|1033978|40657,Complete,Peace Sandy
bsdb:793/1/1,Study 793,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B, Satizabal C, Kautz TF, Wadop YN, Muhammad JAS, Vasquez E, Mathews J, Gireud-Goss M, Saklad AR, Himali J, Beiser A, Cavazos JE, Mahaney MC, Maestre G, DeCarli C, Shipp EL, Vasan RS , Seshadri S",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the PSMD marker,674,108,unspecified,16S,4,Illumina,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table S4, S5, S6",14 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Peace Sandy,Folakunmi,Welile","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|3082768|990719|270497;2|1239|186801|186802|31979|1485|1960653;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|119852|119853;2|1239|526524|526525|128827,Complete,Folakunmi
bsdb:793/1/2,Study 793,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B, Satizabal C, Kautz TF, Wadop YN, Muhammad JAS, Vasquez E, Mathews J, Gireud-Goss M, Saklad AR, Himali J, Beiser A, Cavazos JE, Mahaney MC, Maestre G, DeCarli C, Shipp EL, Vasan RS , Seshadri S",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the PSMD marker,674,108,unspecified,16S,4,Illumina,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table S4, S5, S6",14 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Peace Sandy,Folakunmi","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",decreased,"k__Bacteria|p__Candidatus Poribacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",2|265317;2|1239|186801|186802|31979|1485;2157|28890|183925|2158|2159|2172;2|256845|1313211|278082|255528|172900,Complete,Folakunmi
bsdb:793/2/1,Study 793,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B, Satizabal C, Kautz TF, Wadop YN, Muhammad JAS, Vasquez E, Mathews J, Gireud-Goss M, Saklad AR, Himali J, Beiser A, Cavazos JE, Mahaney MC, Maestre G, DeCarli C, Shipp EL, Vasan RS , Seshadri S",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the WMH marker,832,136,unspecified,16S,4,Illumina,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Pseudomonadota",2|1239|186801|3082768|990719|990721;2|1239|186801|3085636|186803|2719313|358742;2|1224,Complete,Folakunmi
bsdb:793/2/2,Study 793,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B, Satizabal C, Kautz TF, Wadop YN, Muhammad JAS, Vasquez E, Mathews J, Gireud-Goss M, Saklad AR, Himali J, Beiser A, Cavazos JE, Mahaney MC, Maestre G, DeCarli C, Shipp EL, Vasan RS , Seshadri S",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the WMH marker,832,136,unspecified,16S,4,Illumina,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi,Welile","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaerosinus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Candidatus Parcubacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea glycerini,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|201174;2|1239|909932|909929|1843490|151037;2|1239;2|976|200643;2|976|200643|171549|2005519|397864;2|976|200643|171549|2005519|397864|487174;2|221216;2|1239|526524|526525|2810280|135858;2|1239|526524|526525|2810280|135858|100886;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1960653;2|1239|186801|3085636|186803|1763508|1763509;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|2316020|46228;2|1239|526524|526525|128827,Complete,Folakunmi
bsdb:793/3/1,Study 793,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B, Satizabal C, Kautz TF, Wadop YN, Muhammad JAS, Vasquez E, Mathews J, Gireud-Goss M, Saklad AR, Himali J, Beiser A, Cavazos JE, Mahaney MC, Maestre G, DeCarli C, Shipp EL, Vasan RS , Seshadri S",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the EF marker,822,121,unspecified,16S,4,Illumina,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis",2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979|1485|1960653;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|3085636|186803|2719313|460384,Complete,Folakunmi
bsdb:793/3/2,Study 793,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B, Satizabal C, Kautz TF, Wadop YN, Muhammad JAS, Vasquez E, Mathews J, Gireud-Goss M, Saklad AR, Himali J, Beiser A, Cavazos JE, Mahaney MC, Maestre G, DeCarli C, Shipp EL, Vasan RS , Seshadri S",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the EF marker,822,121,unspecified,16S,4,Illumina,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Candidatus Parcubacteria,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|976|200643|171549|171550|239759;2|1239;2|221216;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|2316020|46228,Complete,Folakunmi
bsdb:794/1/1,Study 794,case-control,36389150,10.3389/fcimb.2022.1036946,NA,"Xiong H, Wang J, Chang Z, Hu H, Yuan Z, Zhu Y, Hu Z, Wang C, Liu Y, Wang Y, Wang G , Tang Q",Gut microbiota display alternative profiles in patients with early-onset colorectal cancer,Frontiers in cellular and infection microbiology,2022,"16S rRNA, colorectal cancer, early onset, functional annotation, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,EOCRC (Early-onset Colorectal cancer) patients,Colorectal cancer diagnosed before the age of 50 years.,31,24,"3 months, including probiotics and corticosteroids use.",16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,NA,3.5,"age,alcohol drinking,body mass index,sex",NA,NA,decreased,NA,increased,NA,NA,Signature 1,Figure 3,17 October 2023,Deacme,"Deacme,Yjung24,Davvve,Folakunmi",Differentially abundant taxa in Early onset colorectal cancer (EOCR) when compared to healthy controls as obtained by LEfSe analysis. Kruskal-wallis test was also performed on the abundance of bacteria in the three groups at different levels to verify the results of LEfSe analysis.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Tissierellia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|976|200643|171549|1840213;2|1239|909932|909929|1843491|158846;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1239|1737404;2|1239|186801|3085636|186803|2316020|33038,Complete,Folakunmi
bsdb:794/3/1,Study 794,case-control,36389150,10.3389/fcimb.2022.1036946,NA,"Xiong H, Wang J, Chang Z, Hu H, Yuan Z, Zhu Y, Hu Z, Wang C, Liu Y, Wang Y, Wang G , Tang Q",Gut microbiota display alternative profiles in patients with early-onset colorectal cancer,Frontiers in cellular and infection microbiology,2022,"16S rRNA, colorectal cancer, early onset, functional annotation, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,LOCRC (Late onset colorectal cancer),Late onset colorectal cancer (diagnosed >=50 years of age),31,43,"3 months, including probiotics and corticosteroids use.",16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,NA,3.5,"age,alcohol drinking,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,19 October 2023,Yjung24,"Yjung24,ChiomaBlessing,Folakunmi",Differentially abundant taxa in Late onset colorectal cancer (LOCR) when compared to healthy controls as obtained by LEfSe analysis. Kruskal-wallis test was also performed on the abundance of bacteria in the three groups at different levels to verify the results of LEfSe analysis.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|909932|1843488|909930;2|976|200643|171549|171550|239759;2|976|200643|171549;2|976|200643;2|976;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552;2|976|200643|171549|171550;2|976|200643|171549|2005525;2|1224|1236|91347|543;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:795/1/1,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 1,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva","UBERON:0008310,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Individuals who carry pneumococci in the nasopharynx,47,12,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S2.,9 October 2023,Karen254.,"Karen254.,Chloe,Peace Sandy",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra",2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|257758;2|1239|91061|186826|1300|1301|28037;2|1224|1236|135625|712|724|727;2|32066|203490|203491|203492|848|851;2|1239|1737404|1737405|1570339|543311|33033,Complete,Peace Sandy
bsdb:795/1/2,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 1,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva","UBERON:0008310,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Individuals who carry pneumococci in the nasopharynx,47,12,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S2,9 October 2023,Karen254.,"Karen254.,Chloe,Peace Sandy",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis",2|1224|1236|135625|712|724|735;2|1224|28216|206351|481|482|490;2|1239|1737404|1737405|1570339|165779;2|1239|91061|1385|90964|1279|28035;2|976|200643|171549|171552|2974257|28127,Complete,Peace Sandy
bsdb:795/2/1,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 2,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva","UBERON:0008310,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,non- smokers,Smokers,The nasopharyngeal area of smokers,20,5,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table S3,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the nasopharyngeal microbiota of smokers and non-smokers.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum",2|1239|91061|1385|186817|1386;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465|39777;2|1224|28216|80840|119060|32008;2|32066|203490|203491|203492|848|859,Complete,Peace Sandy
bsdb:795/2/2,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 2,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva","UBERON:0008310,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,non- smokers,Smokers,The nasopharyngeal area of smokers,20,5,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table S3,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the nasopharyngeal microbiota of smokers and non-smokers,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella|s__Lawsonella clevelandensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter gracilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis",2|1224|1236|135625|712|724|735;2|1224|1236|135625|712|724|1078480;2|201174|1760|85007|1653|1716|43769;2|201174|1760|85007|2805586|1847725|1528099;2|1224|28216|80840|80864|281915|230310;2|1239|91061|186826|186828|29393|29394;2|32066|203490|203491|203492|848|851;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|171552|2974257|28127,Complete,Peace Sandy
bsdb:795/3/1,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 3,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva","UBERON:0008310,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,No contact with children,Contact with children,The nasopharyngeal microbiota of individuals that  regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,Signature 1,Table S4,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the nasopharyngeal microbiota of individuals that have and do not have regular contact with children.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum",2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|28037;2|1224|1236|2887326|468|475|480;2|1224|1236|135625|712|724|727;2|32066|203490|203491|203492|848|851,Complete,Peace Sandy
bsdb:795/3/2,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 3,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva","UBERON:0008310,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,No contact with children,Contact with children,The nasopharyngeal microbiota of individuals that  regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,Signature 2,Table S4,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the nasopharyngeal microbiota of individuals that have and do not have regular contact with children.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. FARSPH,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus|s__Dermacoccus nishinomiyaensis",2|1239|91061|1385|90964|1279|28035;2|1224|28211|204457|41297|13687|2219696;2|201174|1760|85006|145357|57495|1274,Complete,Peace Sandy
bsdb:795/4/1,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 4,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Oropharyngeal microbiota of pneumococcal carriers,47,12,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S5,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the oropharyngeal microbiota of pneumococcal carriers and non-carriers.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|1239|91061|186826|1300|1301|1313;2|976|117743|200644|49546|1016;2|1239|1737404|1737405|1570339|543311|33033;2|29547|3031852|213849|72294|194|204;2|976|117743|200644|49546|1016|45242;2|1239|186801|3085636|186803|297314;2|976|117743|200644|49546|1016|1019;2|976|200643|171549|2005525|195950,Complete,Peace Sandy
bsdb:795/4/2,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 4,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Oropharyngeal microbiota of pneumococcal carriers,47,12,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S5,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the oropharyngeal microbiota of pneumococcal carriers and non-carriers.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|s__uncultured bacterium",2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|1283313|76122;2|77133,Complete,Peace Sandy
bsdb:795/5/1,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 5,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Non- smokers,Smokers,Oropharyngeal microbiota of smokers,20,5,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table S6,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the oropharyngeal microbiota of smokers and non-smokers.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus",2|1239|91061|1385|186817|1386;2|1239|91061|186826|1300|1301|1313;2|1224|28216|80840|119060|32008;2|1239|909932|909929|1843491|970|69823;2|1224|1236|135625|712|724|736,Complete,Peace Sandy
bsdb:795/5/2,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 5,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Non- smokers,Smokers,Oropharyngeal microbiota of smokers,20,5,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table S6,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the oropharyngeal microbiota of smokers and non-smokers.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia dentalis",2|1224|28216|206351|481|482;2|1224|1236|135625|712|724|735;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|171552|2974257|228603;2|29547|3031852|213849|72294|194|204;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157;2|1224|28216|80840|119060|47670|2490857,Complete,Peace Sandy
bsdb:795/6/1,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 6,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,No Contact with Children,Contact with children,Oropharyngeal microbiota of individuals that have regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table S7,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the oropharyngeal microbiota of individuals that have and do not have regular contact with children.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum",2|1239|91061|186826|1300|1301|1313;2|1224|1236|135625|712|724|735;2|32066|203490|203491|203492|848|851;2|201174|1760|85006|1268|32207|43675;2|1224|1236|135625|712|416916|739;2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|265975|1501332,Complete,Peace Sandy
bsdb:795/6/2,Study 795,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo AC, Lança J, Almeida ST, Hilty M , Sá-Leão R","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 6,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,No Contact with Children,Contact with children,Oropharyngeal microbiota of individuals that have regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table S7,10 February 2024,Peace Sandy,Peace Sandy,Bacteria (ASV) differentially present in the oropharyngeal microbiota of individuals that have and do not have regular contact with children,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|1283313|671218;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|1224|28216|206351|481|482,Complete,Peace Sandy
bsdb:796/1/1,Study 796,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G, Pimentel M, Barlow GM , Mathur R",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 1,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),Group 4- oldest age group (66 to 80 years old. elderly people),This is the oldest age advanced group from the study,32,82,None.,16S,34,Illumina,PLS-DA (Partial least square discriminant analysis),1e-4,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Figure S6 + Results (text): Page 6, under sub-heading ""Microbiome differences are most pronounced between younger (group 1) and elderly (group 4) adults.""",19 October 2023,Davvve,"Davvve,ChiomaBlessing",Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1239|186801|186802|31979;2|200940|3031449|213115|194924;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:796/1/2,Study 796,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G, Pimentel M, Barlow GM , Mathur R",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 1,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),Group 4- oldest age group (66 to 80 years old. elderly people),This is the oldest age advanced group from the study,32,82,None.,16S,34,Illumina,PLS-DA (Partial least square discriminant analysis),1e-4,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure S6,30 January 2024,ChiomaBlessing,ChiomaBlessing,Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|201174|1760|2037|2049;2|1239|91061|186826|186828;2|1239|526524|526525|128827;2|1239|186801|3085636|186803;2|32066|203490|203491|1129771;2|1224|1236|2887326|468;2|976|200643|171549|171552|577309;2|1239|186801|3082720|186804;2|976|200643|171549|171551;2|976|200643|171549|171552;2|1224|1236|72274|135621;2|203691|203692|136|137;2|1239|1737404|1737405|1737406;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|171552|577309,Complete,ChiomaBlessing
bsdb:796/2/1,Study 796,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G, Pimentel M, Barlow GM , Mathur R",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 2,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),"Group 2, 3 and 4 - older age groups (36 to 50 years old; 51 to 65 years old and 66 to 80 years old.)","These are the remaining 3 groups of subjects grouped according to advancing chronological age (N= 41, 36 to 50 years old; N= 96, 51 to 65 years old and N= 82, 66 to 80 years old).",32,219,None.,16S,34,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S2,30 January 2024,ChiomaBlessing,ChiomaBlessing,"Facultative and strict anaerobic genera in the duodenal microbiome of older subjects from groups 2, 3, and 4, when compared to group 1",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1224|1236|135625|712|713;2|976|200643|171549|815|816;2|1224|1236|91347|543|561;2|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:796/2/2,Study 796,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G, Pimentel M, Barlow GM , Mathur R",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 2,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),"Group 2, 3 and 4 - older age groups (36 to 50 years old; 51 to 65 years old and 66 to 80 years old.)","These are the remaining 3 groups of subjects grouped according to advancing chronological age (N= 41, 36 to 50 years old; N= 96, 51 to 65 years old and N= 82, 66 to 80 years old).",32,219,None.,16S,34,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S2,30 January 2024,ChiomaBlessing,ChiomaBlessing,"Facultative and strict anaerobic genera in the duodenal microbiome of older subjects from groups 2, 3, and 4, when compared to group 1",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,2|1224|1236|135614|32033,Complete,ChiomaBlessing
bsdb:797/1/1,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,Active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,9,22,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,8 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Genera that were found to be differentially more abundant in Never smokers vs Active smokers using  DESeq2.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28211|356|119045|407;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:797/1/2,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,Active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,9,22,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 2,table 3,8 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Genera that were found to be differentially more abundant in Never smokers vs Active smokers using  DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia sp. 1-6,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|28216|80840|119060|32008|36773;2|1224|28216|80840|119060|48736|1221567;2|1224|28216|80840|2975441|335058;2|1224|1236|135614|32033|40323,Complete,Folakunmi
bsdb:797/2/1,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 2,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,former smokers,subjects that are abstinent of tobacco use for at least 12months,9,24,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Genera that were found to be differentially more abundant in Never smokers vs former smokers using  DESeq2.,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia sp. 1-6,2|1224|28216|80840|119060|48736|1221567,Complete,Folakunmi
bsdb:797/2/2,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 2,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,former smokers,subjects that are abstinent of tobacco use for at least 12months,9,24,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 2,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Genera that were found to be differentially more abundant in Never smokers vs former smokers using  DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:797/3/1,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 3,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,former smokers,active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,24,22,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Genera that were found to be differentially more abundant in former smokers vs Active smokers using  DESeq2.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482,Complete,Folakunmi
bsdb:797/3/2,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 3,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,former smokers,active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,24,22,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 2,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Genera that were found to be differentially more abundant in former smokers vs active smokers using  DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|1213720,Complete,Folakunmi
bsdb:797/4/1,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 4,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Active smokers & former smokers,Never smokers,Participants who have never smoked,46,9,use of antibiotics within 12weeks prior to study,16S,678,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,Fig 5,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using  LEFse.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|28211;2|1239;2|976|200643|171549;2|976|200643;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1224|1236|135625|712|724;2|1224|28211|356;2|1224|28216|80840|119060|47670;2|1239|909932|1843489|31977|906;2|1224|28211|356|119045;2|1224|28211|356|119045|407;2|1239|186801|3082720|3030910|86331;2|1239|909932;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Folakunmi
bsdb:797/5/1,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 5,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,never smokers & former smokers,Active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,33,22,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,9 October 2023,OdigiriGreat,OdigiriGreat,Genera that were found to be differentially more abundant in Never smokers and former smokers vs Active smokers using  DESeq2.,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,2|1224|28216|80840|80864|80865,Complete,Folakunmi
bsdb:797/6/1,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 6,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Active smokers & former smokers,Never smokers,Participants who have smoked at least one cigarette within 3days of enrolment,46,9,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,increased,NA,Signature 1,table 3,16 February 2024,Folakunmi,Folakunmi,Genera that were found to be differentially more abundant in Active  smokers and former smokers vs Never smokers using DESeq2.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,2|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:797/7/1,Study 797,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K , Narasimhan G",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 7,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Active smokers & former smokers,never smokers,Participants who have never smoked,46,9,use of antibiotics within 12weeks prior to study,16S,678,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,increased,NA,Signature 1,table 3,16 February 2024,Folakunmi,Folakunmi,Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using DESeq2.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,2|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:798/1/1,Study 798,case-control,35722326,10.3389/fmicb.2022.888681,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200618/,"Huang L, Li X, Zheng B, Li P, Wei D, Huang C, Sun L , Li H",Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection,Frontiers in microbiology,2022,"16S rRNA, next generation sequencing (NGS), recurrent urinary tract infection (RUTI), standard urine culture, urinary microbiota",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic controls,Recurrent Urinary Tract Infection (RUTI) patients,Women with clinically diagnosed RUTI with negative Standard Urine Cultures (SUCs),44,67,Patients with antibiotic treatment in the previous 48 hours (2 days) and their symptoms relieved.,16S,34,Illumina,LEfSe,0.05,FALSE,3,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 5,7 October 2023,Aleru002,Aleru002,"Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae",2|1239|1737404|1737405|1570339|165779;2|1224|28216;2|1224|28216|80840|119060;2|1224|28216|80840;2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|906;2|201174|1760|85007;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552;2|1224;2|1224|28216|80840|119060|48736;2|201174|1760|2037|2049|1653174;2|1239|1737404|1737405|1570339|162289;2|201174|1760|2037;2|201174|1760|2037|2049;2|29547|3031852;2|29547|3031852|213849;2|29547|3031852|213849|72294;2|29547|3031852|213849|72294|194;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|1224|28211|356|212791;2|201174|1760|85007|1653,Complete,Svetlana up
bsdb:798/1/2,Study 798,case-control,35722326,10.3389/fmicb.2022.888681,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200618/,"Huang L, Li X, Zheng B, Li P, Wei D, Huang C, Sun L , Li H",Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection,Frontiers in microbiology,2022,"16S rRNA, next generation sequencing (NGS), recurrent urinary tract infection (RUTI), standard urine culture, urinary microbiota",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic controls,Recurrent Urinary Tract Infection (RUTI) patients,Women with clinically diagnosed RUTI with negative Standard Urine Cultures (SUCs),44,67,Patients with antibiotic treatment in the previous 48 hours (2 days) and their symptoms relieved.,16S,34,Illumina,LEfSe,0.05,FALSE,3,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 5,7 October 2023,Aleru002,Aleru002,"Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Phaseolus|s__Phaseolus acutifolius,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota",2|1224|1236|2887326|468|469;2|976|200643|171549|171550|239759;2|1239|91061;2|1239|1737404|1582879;2|201174|1760|85004|31953|2701;2|1239|186801|3085636|186803|877420;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1596;2|32066|203490|203491|1129771;2759|33090|35493|3398|72025|3803|3814|3883|33129;2|32066|203490|203491|1129771|168808;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1313;2|1239,Complete,Svetlana up
bsdb:799/1/1,Study 799,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W , Forslund SK",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals with COPD,HIV-positive individuals diagnosed with COPD,The exposed group (Group 1) consists of individuals with both HIV infection and COPD.,50,50,Antibiotic use within 2 weeks,16S,34,Illumina,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 1,Table 4.,27 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Mean relative abundance of phyla and genera in HIV-positive individuals diagnosed with COPD versus HIV-negative individuals with COPD,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Candidatus Saccharibacteria|s__Candidatus Saccharibacteria bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|s__bacterium,k__Bacteria|p__Candidatus Saccharibacteria|s__uncultured Candidatus Saccharibacteria bacterium,k__Bacteria|p__Pseudomonadota|s__unidentified proteobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.",2|201174;2|1224|1236|135625|712|416916;2|201174|1760|85009|31957|2801844;2|1239;2|1239|91061|1385|186817|1386;2|95818|2026720;2|1224|1236|135615|868|2717;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186806|1730;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|976|200643|171549|1840213|1840214;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|33958|2742598;2|1224|1236|2887326|468|475;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838;2|201174|1760|85009|31957|1743;2|1224;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|909932|909929|1843491|970;2|203691;2|1239|91061|186826|1300|1301;2|508458;2|976|200643|171549|2005525|195950;2|1869227;2|95818|179883;2|1224|2722;2|1239|186801|186802|186806|1730|142586,Complete,Chinelsy
bsdb:799/1/2,Study 799,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W , Forslund SK",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals with COPD,HIV-positive individuals diagnosed with COPD,The exposed group (Group 1) consists of individuals with both HIV infection and COPD.,50,50,Antibiotic use within 2 weeks,16S,34,Illumina,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 2,Table 4.,27 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,Welile",Mean relative abundance of phyla and genera in HIV-positive individuals diagnosed with COPD versus HIV-negative individuals with COPD,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured actinomycete,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus",2|1239|91061|186826|186827|46123;2|544448|31969|186329|2146|2147;2|1224|1236|135625|712|713;2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|156454;2|201174|84998|84999|1643824|1380;2|976;2|976|117743|200644|2762318|59735;2|29547|3031852|213849|72294|194;2|29547;2|95818|2093818|2093825|2171986|1331051;2|976|117743|200644|49546|1016;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186806|1730|142586;2|508458|649775|649776|3029087|1434006;2|32066;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|59823;2|1239|909932|909929;2|1224|28216|206351|481|71;2|1239|526524|526525|128827|123375;2|1239|186801|3085636|186803|1213720;2|32066|203490|203491|1129771|34104;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|1239|91061;2|976|200643|171549;2|976|200643;2|363464;2|95818|2093818|2093825;2|95818|2093818;2|1239|526524|526525|128827;2|1224|1236;2|1239|186801|3085636|186803;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|1239|186801|244328;2|201174|1760|2037|100235;2|95818|2093818|2093819|2093822|2093823|2093824,Complete,Chinelsy
bsdb:799/2/1,Study 799,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W , Forslund SK",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 2,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals (without COPD),HIV-positive individuals (without COPD),The exposed group (Group 1) consists of individuals with HIV infection but without COPD.,50,50,Antibiotic use within 2 weeks,16S,34,Illumina,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 1,Table 4.,28 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,Welile",Mean relative abundance of phyla and genera in HIV-positive individuals without COPD versus HIV-negative individuals without COPD,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Synergistota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Candidatus Saccharibacteria|s__uncultured Candidatus Saccharibacteria bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured actinomycete,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus",2|1224|1236|135625|712|713;2|201174|1760|2037|2049|1654;2|201174;2|976|200643|171549|171552|1283313;2|1239|186801|3082720|3030910|2060094;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|186817|1386;2|976;2|1239|186801|3085636|186803|830;2|29547|3031852|213849|72294|194;2|29547;2|95818|2093818|2093825|2171986|1331051;2|976|117743|200644|49546|1016;2|1239|186801|3085636|186803|43996;2|201174|1760|85007|1653|1716;2|1117;2|1239|186801|186802|186806|1730;2|32066|203490|203491;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1224|1236|2887326|468|475;2|1239|186801|3085636|186803|265975;2;2|1239|186801|3082720|3118655|1913599;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|59823;2|201174|1760|85009|31957|1743;2|1224;2|1239|909932|909929|1843491;2|1239|909932|909929;2|1239|909932|909929|1843491|970;2|1239|526524|526525|128827|123375;2|203691;2|1239|186801|3085636|186803|1213720;2|32066|203490|203491|1129771|34104;2|508458;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|95818|179883;2|201174|1760|2037|100235;2|95818|2093818|2093819|2093822|2093823|2093824,Complete,Chinelsy
bsdb:799/2/2,Study 799,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W , Forslund SK",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 2,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals (without COPD),HIV-positive individuals (without COPD),The exposed group (Group 1) consists of individuals with HIV infection but without COPD.,50,50,Antibiotic use within 2 weeks,16S,34,Illumina,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 2,Table 4.,28 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Mean relative abundance of phyla and genera in HIV-positive individuals without COPD versus HIV-negative individuals without COPD,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota,k__Bacteria|p__Candidatus Saccharibacteria|s__Candidatus Saccharibacteria bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.",2|1239|91061|186826|186827|46123;2|1224|1236|135625|712|416916;2|201174|1760|85009|31957|2801844;2|1239;2|95818|2026720;2|1239|186801|3082720|3118655|44259;2|508458|649775|649776|3029087|1434006;2|32066;2|32066|203490|203491|203492|848;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186806|1730|142586,Complete,Chinelsy
bsdb:800/1/1,Study 800,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi FR, Vogel SC, Thomason ME, Callaghan BL , Brito NH",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pre-pandemic group with covariates controlled for,pandemic group with covariates controlled for,"healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic with covariates ( diet(average fat intake), child sex, still breastfeeding at sample collection, and birth mode) controlled for.",34,20,no antibiotic within a month preceding stool collection.,16S,NA,Illumina,MaAsLin2,0.25,TRUE,NA,NA,"breast feeding,delivery procedure,diet,sex",NA,unchanged,decreased,NA,NA,NA,Signature 1,"figure 6, figure 7",10 October 2023,Folakunmi,Folakunmi,differential analysis of gut microbiome by pandemic group with covariates controlled for.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|1224|1236|135625|712|724;2|1224|1236|135625|712,Complete,ChiomaBlessing
bsdb:800/2/1,Study 800,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi FR, Vogel SC, Thomason ME, Callaghan BL , Brito NH",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pre-pandemic group without covariates controlled for,pandemic group without covariates controlled for,healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic without controlling for covariates.,34,20,no antibiotic within a month preceding stool collection.,16S,NA,Illumina,MaAsLin2,0.25,TRUE,NA,NA,"age,breast feeding,delivery procedure,diet",NA,unchanged,decreased,NA,NA,NA,Signature 1,"Supplementary information: Page 5, under sub-heading- “Differential abundance of gut microbiome by pandemic group without controlling for covariates”",10 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differential abundance of gut microbiome by pandemic group without controlling for covariates.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,2|1224|1236|135625|712,Complete,ChiomaBlessing
bsdb:800/2/2,Study 800,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi FR, Vogel SC, Thomason ME, Callaghan BL , Brito NH",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pre-pandemic group without covariates controlled for,pandemic group without covariates controlled for,healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic without controlling for covariates.,34,20,no antibiotic within a month preceding stool collection.,16S,NA,Illumina,MaAsLin2,0.25,TRUE,NA,NA,"age,breast feeding,delivery procedure,diet",NA,unchanged,decreased,NA,NA,NA,Signature 2,"Supplementary information: Page 5, under sub-heading- “Differential abundance of gut microbiome by pandemic group without controlling for covariates”",11 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differential abundance of gut microbiome by pandemic group without controlling for covariates.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,ChiomaBlessing
bsdb:800/3/1,Study 800,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi FR, Vogel SC, Thomason ME, Callaghan BL , Brito NH",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pandemic group (without covariates),pandemic group according to the number of days,"Healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic according to the number of days since the pandemic began. Due to the small sample size of the during pandemic group (N = 20), analyses restricted to this group did not include any covariates.",34,20,no antibiotic within a month preceding stool collection.,16S,NA,Illumina,MaAsLin2,0.25,TRUE,NA,NA,"breast feeding,delivery procedure,diet,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Results within text: Page 4, under sub-heading ""Differential abundance of gut microbiota by days since the start of the pandemic among the pandemic group"".",11 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differential abundance of gut microbiota by days since the start of the pandemic among the pandemic group.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,ChiomaBlessing
bsdb:801/1/1,Study 801,prospective cohort,32320621,10.1164/rccm.201911-2202OC,NA,"Mac Aogáin M, Lau KJX, Cai Z, Kumar Narayana J, Purbojati RW, Drautz-Moses DI, Gaultier NE, Jaggi TK, Tiew PY, Ong TH, Siyue Koh M, Lim Yick Hou A, Abisheganaden JA, Tsaneva-Atanasova K, Schuster SC , Chotirmall SH",Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease,American journal of respiratory and critical care medicine,2020,"antimicrobial resistance, macrolides, metagenomics, resistome, respiratory disease",Experiment 1,Singapore,Homo sapiens,Sputum,UBERON:0007311,Respiratory system disease,EFO:0000684,Non-diseased/ healthy individuals (ND),Diseased individuals (D),"Patients with a range of chronic respiratory disease states (severe asthma, chronic obstructive pulmonary disease- COPD, and bronchiectasis)",13,41,None,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,decreased,unchanged,NA,NA,Signature 1,Supplemental. fig. E3D and Supplemental fig. E3E,22 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between diseased (D) and nondiseased (ND)/ healthy individuals,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",2|201174|1760|85009|31957|2801844;2|201174|1760|85004|31953|1678;2|201174|1760|85007|1653|1716;2|1224|1236|91347|543|561;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1239|91061|1385|186822|44249;2|1224|1236|72274|135621|286;2|1224|1236|2887326|468|497;2|976|200643|171549|2005525|195950;2|201174|1760|85006|1268|32207|43675,Complete,NA
bsdb:801/1/2,Study 801,prospective cohort,32320621,10.1164/rccm.201911-2202OC,NA,"Mac Aogáin M, Lau KJX, Cai Z, Kumar Narayana J, Purbojati RW, Drautz-Moses DI, Gaultier NE, Jaggi TK, Tiew PY, Ong TH, Siyue Koh M, Lim Yick Hou A, Abisheganaden JA, Tsaneva-Atanasova K, Schuster SC , Chotirmall SH",Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease,American journal of respiratory and critical care medicine,2020,"antimicrobial resistance, macrolides, metagenomics, resistome, respiratory disease",Experiment 1,Singapore,Homo sapiens,Sputum,UBERON:0007311,Respiratory system disease,EFO:0000684,Non-diseased/ healthy individuals (ND),Diseased individuals (D),"Patients with a range of chronic respiratory disease states (severe asthma, chronic obstructive pulmonary disease- COPD, and bronchiectasis)",13,41,None,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,decreased,unchanged,NA,NA,Signature 2,Supplemental. fig. E3D and Supplemental fig. E3E,22 October 2023,ChiomaBlessing,ChiomaBlessing,Differential microbial abundance between diseased (D) and nondiseased (ND)/ healthy individuals,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|1737404|1737405|1570339|543311;2|544448|31969|2085|2092|2093;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|39948;2|32066|203490|203491|1129771|32067;2|1239|186801|3082720|3030910|86331;2|201174|84998|84999|1643824|1380;2|1224|1236|135625|712|416916;2|1239|526524|526525|128827|123375;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|43996;2|1224|28216|80840|119060|47670;2|201174|1760|2037|2049|76833;2|29547|3031852|213849|72294|194;2|1239|186801|3085636|186803|1164882;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|1283313;2|1239|186801|186802|31979|1485;2|200940|3031449|213115|213116|898;2|32066|203490|203491|203492|848;2|203691|203692|136|2845253|157;2|976|200643|171549|171552|838,Complete,NA
bsdb:802/1/1,Study 802,laboratory experiment,37220908,10.5483/BMBRep.2023-0068,NA,"Jeong SM, Jin EJ, Wei S, Bae JH, Ji Y, Jo Y, Jeong JH, Im SJ , Ryu D",The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model,BMB reports,2023,NA,Experiment 1,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Cachexia,HP:0004326,Healthy controls,cachexia-induced mice,All mice that were induced with cancer cachexia (Lewis lung cancer cells).,3,4,NA,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Fig 3,8 October 2023,Grace og,"Grace og,Peace Sandy",Differential abundance analysis of gut microbiota by DESeq2. (B) Microbes of significantly different abundance in genus level by DESeq2 analysis between groups expressed in log2 fold change.,increased,"k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter",2|877428;2|1239|186801|3085636|186803|248744;2|1239|526524|526525|128827;2|1239|186801|186802|31979|49082;2|1239|91061|186826|1300|1301;2|1239|186801|186802|31979|1485;2|201174|84998|1643822|1643826|1926677,Complete,Peace Sandy
bsdb:802/1/2,Study 802,laboratory experiment,37220908,10.5483/BMBRep.2023-0068,NA,"Jeong SM, Jin EJ, Wei S, Bae JH, Ji Y, Jo Y, Jeong JH, Im SJ , Ryu D",The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model,BMB reports,2023,NA,Experiment 1,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Cachexia,HP:0004326,Healthy controls,cachexia-induced mice,All mice that were induced with cancer cachexia (Lewis lung cancer cells).,3,4,NA,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Fig 3,8 October 2023,Grace og,"Grace og,Hodan Issah,Peace Sandy",Differential abundance analysis of gut microbiota by DESeq2. (B) Microbes of significantly different abundance in genus level by DESeq2 analysis between groups expressed in log2 fold change.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter",2|1239|186801|3082720|186804|1501226;2|1239|91061|186826|1300|1357;2|1239|526524|526525|2810281|191303;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|1263;2|1239|186801|186802|1980681,Complete,Peace Sandy
bsdb:803/1/1,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 1,Egypt,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,Egyptian Samples with Colorectal Cancer,Egyptian Patients with colocrectal cancer,17,17,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2A,12 October 2023,Chloe 256,"Chloe 256,Peace Sandy,Folakunmi","Fig.2A  shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in Egyptians.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Abyssicoccaceae|g__Abyssicoccus|s__Abyssicoccus albus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella|s__Tissierella creatinophila",2|1239|91061|1385|3076164|1955413|1817405;2|201174|1760|85004|31953|1678|1694;2|201174|1760|85007|1653|1716|161879;2|201174|1760|85009|31957|1912216|1747;2|1239|186801|186802;2|201174|1760|85006|1268|57493;2|1239|91061|186826|33958|1578|1587;2|1239|1737404|1737405|1737406|41273|79681,Complete,Folakunmi
bsdb:803/1/2,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 1,Egypt,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,Egyptian Samples with Colorectal Cancer,Egyptian Patients with colocrectal cancer,17,17,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2A,12 October 2023,Chloe 256,"Chloe 256,Peace Sandy","Figure 2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in egyptians.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria",2|201174|1760|2037;2|1239|91061|1385|33986;2|201174|1760|85006|1268|57493|71999;2|201174|1760|85006|1268|1269;2|1224|28216|206351|481|482;2|1224|1236|72274|135621|286|33069;2|201174|1760|85006|1268|32207|172042,Complete,Folakunmi
bsdb:803/2/1,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 2,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,African American Samples with Colorectal Cancer,African American Patients with Colorectal cancer.,18,18,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2B,13 October 2023,Chloe 256,Chloe 256,"Figure 2B shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African Americans.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter",2|1239|186801|186802|31979|1485|1502;2|201174|1760|85004|31953|2701;2|1239|91061|186826|186828|117563;2|1224|28211|204455|31989|1060,Complete,Folakunmi
bsdb:803/2/2,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 2,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,African American Samples with Colorectal Cancer,African American Patients with Colorectal cancer.,18,18,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2B,13 October 2023,Chloe 256,Chloe 256,"Figure 2B shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African American",decreased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,2|1224|28211|356|41294|374,Complete,Folakunmi
bsdb:803/3/1,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 3,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,European American Samples with Colorectal Cancer,European American Patients with colorectal cancer,19,19,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2C,13 October 2023,Chloe 256,Chloe 256,"Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.",increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,2|1224|28216|80840|75682|149698,Complete,Folakunmi
bsdb:803/3/2,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 3,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,European American Samples with Colorectal Cancer,European American Patients with colorectal cancer,19,19,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2C,13 October 2023,Chloe 256,"Chloe 256,Iram jamshed","Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",2|1239|186801|186802|204475|745368;2|200940|3031651|3031668|213422|28231;2|976|200643|171549|171552|2974251|165179;2|1239|186801|3085636|186803|2316020|33038,Complete,Folakunmi
bsdb:803/4/1,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 4,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"KeNyaN, African American and Egyptians patients",Tumor samples of European American,sample of European Americans patients,53,19,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,14 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi",Differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|544448|31969|186332|186333|2086;2|976|200643|171549|815|816|28116;2|1239|186801|186802|31979|1485|1502;2|1224|28216|80840|80864;2|201174|84998|1643822|1643826|84111|84112;2|29547|3031852|213849|72293|2353;2|544448|31969|2085|2092|2093;2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:803/5/1,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 5,Kenya,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"Egyptian, African American and European American Patients",Tumor samples of kenyans,Tumor samples of kenyan patients,54,18,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,14 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi,Joan Chuks",differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alloalcanivorax|s__Alloalcanivorax dieselolei,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|g__Denitrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Inquilinus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934|239935;2|1224|1236|135619|224372|3020832|285091;2|1224|28216|59507;2|1224|28211|204441|41295|171673;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28133;2|1239|186801|3085636|186803|100132|507843;2|74201|203494|48461|203557,Complete,Folakunmi
bsdb:803/6/1,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 6,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"Egyptian, Kenyan and European American patients",Tumor samples of African Americans,Sample of African American patients,54,18,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,14 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi",differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium succinicans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|201174|1760|85007|1653|1716;2|1224|28211|356|212791;2|1239|91061|186826|186827|66831;2|976|117743|200644|49546|237|29536;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|162289;2|1224|1236|72274|135621|286;2|1224|28211|204455|31989|1060;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|33958,Complete,Folakunmi
bsdb:803/7/1,Study 803,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W , Manne U","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 7,Egypt,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"African American, Kenya and European American patients",Tumor samples of Egyptians,sample of Egyptian patients,55,17,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,15 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi",differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter lwoffii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia acidicola,k__Bacteria|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas geniculata",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|28090;2|1224|1236|2887326|468|469|108981;2|1239|91061|1385|186817;2|1224|28211|356|41294|374;2|1224|28211|204458|76892|41275|293;2|1224|28216|80840|75682|963;2|1239|91061|1385|186817|2837504|209389;2|1224|2008785|119069|206349|70774;2|1224|1236|135614|32033|68;2|1297|188787|68933|188786|65551;2|201174|1760|85006|1268|1269;2|1239|91061|1385|186822|44249;2|1224|28211|356|69277|28100;2|1224|1236|91347|1903414|583;2|1224|1236|91347|1903411|613|615;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279;2|1224|1236|135614|32033|40323|86188,Complete,Folakunmi
bsdb:804/1/1,Study 804,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X, Wang Z, Cao J, Dong Y , Chen Y",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,SD-FMT AND SD+MEL-FMT,CON-FMT: receiving control microbiota FMT mice,FMT administered mice without sleep deprivation.,7,7,There were no antibiotic exclusions,16S,123456789,PacBio RS,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,fig 4,13 October 2023,Davvve,"Davvve,Chinelsy,Peace Sandy,Folakunmi",Difference between the gut microbiome of the CON- FNT and the SD-FMT groups by LEFse,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Deferribacterota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|s__uncultured bacterium A2_10",2|1239|186801|186802|31979|1485|1506;2|200930|68337|191393|191394;2|200930|68337|191393;2|200930|68337;2|200930;2|1239|186801|3085636|186803|877420;2|200930|68337|191393|2945020|248038;2|200930|68337|191393|2945020|248038|248039;2|1239|186801|186802|216572|1508657;2|1224|28216|80840|995019|1918598;2|1239|186801|3085636|186803|297314;2|1112285,Complete,Folakunmi
bsdb:804/2/1,Study 804,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X, Wang Z, Cao J, Dong Y , Chen Y",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CON-FMT:( receiving control microbiota FMT mice) and SD+Mel-FMT:( receiving SD+Mel (20 mg/kg) microbiota  FMT mice),SD-FMT: receiving Sleep deprivation  FMT mice,This are sleep deprived mice that are also subjected to FMT .,7,7,There were no antibiotic,16S,123456789,PacBio RS,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Fig 4C, 4F, 4D",6 November 2023,Davvve,"Davvve,Folakunmi","C Linear discriminant analysis efect 
size (LEfSe) was performed to identify the bacteria that are differentially represented between the different groups",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__uncultured Alloprevotella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__uncultured Parasutterella sp.",2|976|200643|171549|171552|1283313;2|976|200643|171549;2|976;2|1224|28216;2|1224|28216|80840|119060;2|1224|28216|80840;2|1239|526524|526525;2|1224|1236;2|1224|28216|32003|32011;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552;2|1224;2|1224|28216|80840|995019;2|1224|28216|80840|995019|1918598;2|1224|28216|80840|995019|1918598|1796652;2|976|200643;2|976|200643|171549|171552|1283313|1283315;2|1224|28216|80840|995019|577310|1263098,Complete,Folakunmi
bsdb:804/2/2,Study 804,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X, Wang Z, Cao J, Dong Y , Chen Y",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CON-FMT:( receiving control microbiota FMT mice) and SD+Mel-FMT:( receiving SD+Mel (20 mg/kg) microbiota  FMT mice),SD-FMT: receiving Sleep deprivation  FMT mice,This are sleep deprived mice that are also subjected to FMT .,7,7,There were no antibiotic,16S,123456789,PacBio RS,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 4G-J,12 February 2024,Folakunmi,Folakunmi,Linear discriminant analysis effect size (LEfSe) performed to identify the bacteria that are differentially represented between the different groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2",2|1239|186801|186802|186806|1730|39497;2|1239|186801|3085636|186803|877420;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|397290,Complete,Folakunmi
bsdb:804/3/1,Study 804,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X, Wang Z, Cao J, Dong Y , Chen Y",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CON-FMT and SD-FMT,SD+Mel-FMT:( receiving SD+Mel (20 mg/kg) microbiota FMT mice),Sleep deprived mice receiving Mel and FMT,7,7,There were no antibiotics exclusions from this study,16S,123456789,PacBio RS,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,fig 4c,6 November 2023,Davvve,Davvve,"Linear discriminant analysis efect 
size (LEfSe) was performed to identify the bacteria that are differentially represented between the different groups",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 020,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__uncultured Alistipes sp.,k__Bacteria,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas|s__uncultured Candidatus Saccharimonas sp.,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma|s__uncultured Anaeroplasma sp.,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__uncultured Gastranaerophilales bacterium,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Candidatus Melainabacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii",2|1239|186801|186802|1159215;2|544448|31969;2|544448;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|538949;2;2|95818|2093818|2093825;2|95818|2093818|2093825|2171986;2|95818|2093818|2093825|2171986|1331051|1983405;2|95818|2093818|2093825|2171986|1331051;2|95818|2093818;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|165186;2|544448|31969|186332|186333|2086;2|544448|31969|186332;2|544448|31969|186332|186333|2086|538969;2|544448|31969|186332|186333;2|1798710|1906119;2|1798710|1906119|3076055;2|1117;2|1798710;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186806|1730|39497;2|544448|31969|220137;2|976|200643|171549|171550|239759|1470347,Complete,Folakunmi
bsdb:805/1/1,Study 805,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S, Valles-Colomer M, Palomo T , Leza JC","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Psychiatric disorder,MONDO:0002025,Individuals without the comorbid state,Individuals with comorbid PTSD + depression + state + trait anxiety symptoms (Comorbidity with Psychiatric Symptoms),"This group included individuals with comorbid PTSD, depression, state and trait anxiety symptoms",190,8,6 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,inflammatory bowel disease,irritable bowel syndrome,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,20 February 2024,ChiomaBlessing,ChiomaBlessing,Relative abundance of taxa in individuals with comorbid PTSD + depression + state and trait anxiety symptoms compared to those without the comorbid state,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,2|1239|186801|3085636|186803|1407607|1150298,Complete,ChiomaBlessing
bsdb:805/2/1,Study 805,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S, Valles-Colomer M, Palomo T , Leza JC","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Psychiatric disorder,MONDO:0002025,Healthy controls (good mental health),PTSD + depression + state + trait anxiety symptoms (Comorbidity with Psychiatric Symptoms),"This group included individuals with comorbid PTSD, depression, state and trait anxiety symptoms",106,8,6 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,20 February 2024,ChiomaBlessing,ChiomaBlessing,Relative abundance of taxa in individuals with comorbid PTSD + depression + state and trait anxiety symptoms compared to healthy controls (good mental health),decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,2|1239|186801|3085636|186803|1407607|1150298,Complete,ChiomaBlessing
bsdb:805/3/1,Study 805,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S, Valles-Colomer M, Palomo T , Leza JC","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Individuals without depressive symptoms,Individuals with depressive symptoms,This group included individuals with depressive symptoms,166,32,6 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,20 February 2024,ChiomaBlessing,ChiomaBlessing,Relative abundance of taxa in individuals with depressive symptoms compared to those without depressive symptoms,increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,ChiomaBlessing
bsdb:805/3/2,Study 805,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S, Valles-Colomer M, Palomo T , Leza JC","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Individuals without depressive symptoms,Individuals with depressive symptoms,This group included individuals with depressive symptoms,166,32,6 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4D,20 February 2024,ChiomaBlessing,ChiomaBlessing,Relative abundance of taxa in individuals with depressive symptoms compared to those without depressive symptoms,decreased,k__Bacteria|p__Synergistota,2|508458,Complete,ChiomaBlessing
bsdb:805/4/1,Study 805,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S, Valles-Colomer M, Palomo T , Leza JC","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Childhood trauma measurement,EFO:0007979,Individuals who did not experience life-threatening childhood trauma,Individuals who experienced life-threatening childhood trauma,This group included individuals who experienced life-threatening childhood trauma,162,36,6 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,20 February 2024,ChiomaBlessing,ChiomaBlessing,Relative abundance of taxa in individuals who experienced life-threatening childhood trauma compared to those who did not experience life-threatening childhood trauma,increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,2|1239|526524|526525|2810281|191303|154288,Complete,ChiomaBlessing
bsdb:805/4/2,Study 805,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S, Valles-Colomer M, Palomo T , Leza JC","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Childhood trauma measurement,EFO:0007979,Individuals who did not experience life-threatening childhood trauma,Individuals who experienced life-threatening childhood trauma,This group included individuals who experienced life-threatening childhood trauma,162,36,6 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,20 February 2024,ChiomaBlessing,ChiomaBlessing,Relative abundance of taxa in individuals who experienced life-threatening childhood trauma compared to those who did not experience life-threatening childhood trauma,decreased,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,2|256845|1313211|278081|566277|256846,Complete,ChiomaBlessing
bsdb:806/1/1,Study 806,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P, Yang J, Li Y, Wu J, Liang W, Yin B, Tan X, Huang Y, Chai T, Zhang H, Duan J, Zhou J, Sun Z, Chen X, Marwari S, Lai J, Huang T, Du Y, Zhang P, Perry SW, Wong ML, Licinio J, Hu S, Xie P , Wang G",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,healthy controls (HCs),bipolar disorder (BD),Participants who suffer from depressive episodes of bipolar disorder (BD),217,217,1 month,16S,34,Illumina,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 1,Supplementary file: Figure. S4b.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,Idiaru angela",Discriminative OTUs observed in the pairwise comparisons between bipolar disorder (BD) and healthy controls (HC).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces plicatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|815|816;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301;2|201174|1760|85011|2062|1883|1922;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|1506577|2053632;2|1239|186801|186802|31979|1485,Complete,ChiomaBlessing
bsdb:806/2/1,Study 806,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P, Yang J, Li Y, Wu J, Liang W, Yin B, Tan X, Huang Y, Chai T, Zhang H, Duan J, Zhou J, Sun Z, Chen X, Marwari S, Lai J, Huang T, Du Y, Zhang P, Perry SW, Wong ML, Licinio J, Hu S, Xie P , Wang G",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,healthy controls (HCs),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Supplementary file: Figure. S4a.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing","Discriminative OTUs observed in the pairwise comparisons between major 
depressive disorder (MDD) and healthy controls (HC).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|976|200643|171549|815|816;2|1224|1236|91347|543|544;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|33039;2|1239|91061;2|1239|186801|186802|216572|1263|41978,Complete,ChiomaBlessing
bsdb:806/2/2,Study 806,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P, Yang J, Li Y, Wu J, Liang W, Yin B, Tan X, Huang Y, Chai T, Zhang H, Duan J, Zhou J, Sun Z, Chen X, Marwari S, Lai J, Huang T, Du Y, Zhang P, Perry SW, Wong ML, Licinio J, Hu S, Xie P , Wang G",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,healthy controls (HCs),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Supplementary file: Figure. S4a.,14 December 2023,ChiomaBlessing,ChiomaBlessing,Discriminative OTUs observed in the pairwise comparisons between major depressive disorder (MDD) and healthy controls (HC).,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,ChiomaBlessing
bsdb:806/3/1,Study 806,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P, Yang J, Li Y, Wu J, Liang W, Yin B, Tan X, Huang Y, Chai T, Zhang H, Duan J, Zhou J, Sun Z, Chen X, Marwari S, Lai J, Huang T, Du Y, Zhang P, Perry SW, Wong ML, Licinio J, Hu S, Xie P , Wang G",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,bipolar disorder (BD),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,LEfSe,0.05,NA,2.5,"age,body mass index",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary file: Figure. S4c.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Discriminative OTUs observed in the pairwise comparisons between major depressive disorder (MDD) and bipolar disorder (BD).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|2569097|39488;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|186804;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810280|3025755;2|976|200643|171549|171552|838|59823;2|1239|186801|3085636|186803|33042|2049024,Complete,ChiomaBlessing
bsdb:806/3/2,Study 806,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P, Yang J, Li Y, Wu J, Liang W, Yin B, Tan X, Huang Y, Chai T, Zhang H, Duan J, Zhou J, Sun Z, Chen X, Marwari S, Lai J, Huang T, Du Y, Zhang P, Perry SW, Wong ML, Licinio J, Hu S, Xie P , Wang G",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,bipolar disorder (BD),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,LEfSe,0.05,NA,2.5,"age,body mass index",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary file: Figure. S4c.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Discriminative OTUs observed in the pairwise comparisons between major depressive disorder (MDD) and bipolar disorder (BD).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|909932|1843489|31977|39948;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1506553;2|1239|909932|1843488|909930|33024;2|1224|1236|72274|135621|286;2|1239|186801|3082720|186804|1501226;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838|59823,Complete,ChiomaBlessing
bsdb:807/1/1,Study 807,time series / longitudinal observational,37525095,10.1186/s12866-023-02951-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02951-5,"Konecna E, Videnska P, Buresova L, Urik M, Smetanova S, Smatana S, Prokes R, Lanickova B, Budinska E, Klanova J , Borilova Linhartova P",Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study,BMC microbiology,2023,"16S rRNA, Bacteriome, Dust, Exposure, Hospital, Household, Indoor environment, Nasopharynx, Sequencing",Experiment 1,Czechia,Homo sapiens,Nasopharyngeal gland,UBERON:0008310,Microbiome measurement,EFO:0007882,Indoor dust samples,Nasopharyngeal swab samples from workplaces,"The workplaces in the study were commercially used buildings characterized by higher levels of human occupancy and usage of HVAC (heating, ventilation, air conditioning) systems, both contributing to the higher abundance of microorganisms and their spread in the building . The participants working at NEO, ENT, or RCX workplaces were included in the study",44,43,None.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Additional file 2,19 October 2023,Iram jamshed,"Iram jamshed,Hodan Issah,ChiomaBlessing",Comparison between indoor dust and nasopharyngeal bacteriome,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239;2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279,Complete,ChiomaBlessing
bsdb:807/2/NA,Study 807,time series / longitudinal observational,37525095,10.1186/s12866-023-02951-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02951-5,"Konecna E, Videnska P, Buresova L, Urik M, Smetanova S, Smatana S, Prokes R, Lanickova B, Budinska E, Klanova J , Borilova Linhartova P",Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study,BMC microbiology,2023,"16S rRNA, Bacteriome, Dust, Exposure, Hospital, Household, Indoor environment, Nasopharynx, Sequencing",Experiment 2,Czechia,Homo sapiens,Nasopharyngeal gland,UBERON:0008310,Microbiome measurement,EFO:0007882,"Nasopharyngeal swab samples collected in the Morning from workplaces (NEO, ENT, RCX)","Nasopharyngeal swab samples collected in the afternoon from workplaces (NEO, ENT, RCX)","Nasopharyngeal swabs collected in the afternoon (after an 8 h exposure to the workplace environment). The participants were working at NEO, ENT, or RCX workplaces.",22,21,None.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:808/1/1,Study 808,laboratory experiment,37784178,10.1186/s40168-023-01588-w,https://pubmed.ncbi.nlm.nih.gov/37784178/,"Salvador AC, Huda MN, Arends D, Elsaadi AM, Gacasan CA, Brockmann GA, Valdar W, Bennett BJ , Threadgill DW","Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets",Microbiome,2023,"diet, ketogenic, keystone species, microbiome, mouse",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,mice on American diet,mice on ketogenic diet,male and female mice placed on American diet during feeding trial,224,245,NA,16S,4,Illumina,ANOVA,0.001,TRUE,NA,NA,"diet,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 4A,18 October 2023,Winnie,"Winnie,Davvve","Precision Nutrition through the integration of genetic 
variation, microbiota, and sex affecting microbiota variation",increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|200940|3031449|213115|194924|35832;2|976|200643|171549|171550|28138;2|1239|186801|186802|216572|1508657,Complete,NA
bsdb:808/1/2,Study 808,laboratory experiment,37784178,10.1186/s40168-023-01588-w,https://pubmed.ncbi.nlm.nih.gov/37784178/,"Salvador AC, Huda MN, Arends D, Elsaadi AM, Gacasan CA, Brockmann GA, Valdar W, Bennett BJ , Threadgill DW","Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets",Microbiome,2023,"diet, ketogenic, keystone species, microbiome, mouse",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,mice on American diet,mice on ketogenic diet,male and female mice placed on American diet during feeding trial,224,245,NA,16S,4,Illumina,ANOVA,0.001,TRUE,NA,NA,"diet,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 4B,18 October 2023,Winnie,"Winnie,Iram jamshed","Precision Nutrition through the integration of genetic 
variation, microbiota, and sex affecting microbiota variation",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|2005525|375288;2|976|200643|171549|171550,Complete,NA
bsdb:809/1/1,Study 809,case-control,33816351,10.3389/fcimb.2021.646348,NA,"Huang Y, Wang Z, Ma H, Ji S, Chen Z, Cui Z, Chen J , Tang S",Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Retinopathy,EFO:0003839,healthy controls (HC),diabetes mellitus (DM),Participants who identify as diabetic patients without retinopathy (DM),25,25,1 month,16S,34,Illumina,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,decreased,NA,Signature 1,Fig.4,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Relative abundance of the bacterial community in diabetic patients without retinopathy (DM) and healthy controls (HC),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli",2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|906;2|976|200643|171549|2005525|375288;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|91061|186826|1300;2|976|200643|171549|2005525;2|1239|909932|1843489|31977|29465;2|1239|91061,Complete,ChiomaBlessing
bsdb:809/2/1,Study 809,case-control,33816351,10.3389/fcimb.2021.646348,NA,"Huang Y, Wang Z, Ma H, Ji S, Chen Z, Cui Z, Chen J , Tang S",Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Retinopathy,EFO:0003839,diabetes mellitus (DM),diabetes retinopathy (DR),Participants who identify as diabetic patients with retinopathy (DR),25,25,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental. Table S6,18 December 2023,ChiomaBlessing,ChiomaBlessing,Relative abundance between diabetes retinopathy and diabetes mellitus based on the biomarker families correlated with fasting blood sugar (FBG) and duration of type 2 diabetes (T2Dyear),decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,2|1224|1236|135625|712,Complete,ChiomaBlessing
bsdb:809/2/2,Study 809,case-control,33816351,10.3389/fcimb.2021.646348,NA,"Huang Y, Wang Z, Ma H, Ji S, Chen Z, Cui Z, Chen J , Tang S",Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Retinopathy,EFO:0003839,diabetes mellitus (DM),diabetes retinopathy (DR),Participants who identify as diabetic patients with retinopathy (DR),25,25,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental. Table S6,18 December 2023,ChiomaBlessing,ChiomaBlessing,Relative abundance between diabetes retinopathy and diabetes mellitus based on the biomarker families correlated with fasting blood sugar (FBG) and duration of type 2 diabetes (T2Dyear),increased,NA,NA,Complete,ChiomaBlessing
bsdb:809/3/1,Study 809,case-control,33816351,10.3389/fcimb.2021.646348,NA,"Huang Y, Wang Z, Ma H, Ji S, Chen Z, Cui Z, Chen J , Tang S",Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Retinopathy,EFO:0003839,healthy controls (HC),diabetes retinopathy (DR),Participants who identify as diabetic patients with retinopathy (DR),25,25,1 month,16S,34,Illumina,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,NA,NA,NA,decreased,NA,Signature 1,Fig.4,30 October 2023,Chinelsy,"Chinelsy,MyleeeA,ChiomaBlessing",Relative abundance of the bacterial community in diabetic patients with retinopathy (DR) compared to healthy controls (HC),increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",2|1239|909932|1843488|909930;2|1239|909932|1843488;2|1239|909932|1843488|909930|904;2|1239|186801|3082720|3030910;2|1239|186801|3082768|990719;2|1239|186801|3082768;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958;2|1239|186801|186802|216572;2|1224|28211|204457|41297;2|1224|28211|204457;2|1239|91061|186826|33958|46255;2|1239|186801|186802|543314|35517;2|1239|186801|186802|186807;2|1224|28211|204457|41297,Complete,ChiomaBlessing
bsdb:810/1/1,Study 810,case-control,36004326,10.3389/fcimb.2022.858732,NA,"Yan C, Hong F, Xin G, Duan S, Deng X , Xu Y",Alterations in the vaginal microbiota of patients with preterm premature rupture of membranes,Frontiers in cellular and infection microbiology,2022,"PPROM, PROM, PTB, preterm birth, vaginal microbiota",Experiment 1,China,Homo sapiens,"Uterine cervix,Anterior fornix of vagina,Lateral fornix of vagina","UBERON:0000002,UBERON:0016487,UBERON:0034963",Preterm premature rupture of the membranes,MONDO:0012511,Control(term delivery),Preterm premature rupture of membranes (PPROM),PPROM is characterized by vaginal microbial dysbiosis.,54,48,2 months,16S,34,Illumina,LEfSe,0.05,NA,3.5,"age,gestational age",NA,increased,increased,increased,increased,NA,NA,Signature 1,Fig.2C,21 October 2023,Chinelsy,Chinelsy,Differences in bacterial abundance in patients with PPROM versus controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum|s__Ochrobactrum sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171552|2974257|386414;2|1239|91061|186826|33958|1578|147802;2|1224|28211|356|118882|528|42190;2|976|200643|171549|171552|838|28125;2|544448|2790996|2790998|2129|134821,Complete,Folakunmi
bsdb:810/1/2,Study 810,case-control,36004326,10.3389/fcimb.2022.858732,NA,"Yan C, Hong F, Xin G, Duan S, Deng X , Xu Y",Alterations in the vaginal microbiota of patients with preterm premature rupture of membranes,Frontiers in cellular and infection microbiology,2022,"PPROM, PROM, PTB, preterm birth, vaginal microbiota",Experiment 1,China,Homo sapiens,"Uterine cervix,Anterior fornix of vagina,Lateral fornix of vagina","UBERON:0000002,UBERON:0016487,UBERON:0034963",Preterm premature rupture of the membranes,MONDO:0012511,Control(term delivery),Preterm premature rupture of membranes (PPROM),PPROM is characterized by vaginal microbial dysbiosis.,54,48,2 months,16S,34,Illumina,LEfSe,0.05,NA,3.5,"age,gestational age",NA,increased,increased,increased,increased,NA,NA,Signature 2,Fig.2C,11 February 2024,Folakunmi,Folakunmi,Differences in bacterial abundance in patients with PPROM versus controls.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596,Complete,Folakunmi
bsdb:811/1/1,Study 811,case-control,34897759,10.1111/lam.13630,https://academic.oup.com/lambio/article-abstract/74/4/498/6989204?redirectedFrom=fulltext&login=false,"Schade L, Mesa D, Faria AR, Santamaria JR, Xavier CA, Ribeiro D, Hajar FN , Azevedo VF",The gut microbiota profile in psoriasis: a Brazilian case-control study,Letters in applied microbiology,2022,"Akkermansia muciniphila, dysbiosis, gut microbiome, inflammatory bowel disease, psoriasis, psoriatic arthritis, skin disease",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy controls,Psoriasis patients,Psoriasis has been diagnosed by a dermatologist,24,21,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,comorbidity,sex,smoking status",NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Figure 2, within results text (Taxonomic composition, paragraph 4, lines 7-12)",28 November 2023,Andre,"Andre,Folakunmi",Taxa that showed a significant difference between the groups,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",2|1239|526524|526525|2810280|135858;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552|2974251|165179;2|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:811/1/2,Study 811,case-control,34897759,10.1111/lam.13630,https://academic.oup.com/lambio/article-abstract/74/4/498/6989204?redirectedFrom=fulltext&login=false,"Schade L, Mesa D, Faria AR, Santamaria JR, Xavier CA, Ribeiro D, Hajar FN , Azevedo VF",The gut microbiota profile in psoriasis: a Brazilian case-control study,Letters in applied microbiology,2022,"Akkermansia muciniphila, dysbiosis, gut microbiome, inflammatory bowel disease, psoriasis, psoriatic arthritis, skin disease",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy controls,Psoriasis patients,Psoriasis has been diagnosed by a dermatologist,24,21,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,comorbidity,sex,smoking status",NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Figure 2,  within results text (Taxonomic composition, paragraph 4, lines 7-12)",28 November 2023,Andre,"Andre,Folakunmi",Taxa that showed a significant difference between the groups,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|186806|264995;2|1239|186801|3085636|186803|572511;2|1239|186801|3082768|990719|990721;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:812/1/1,Study 812,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL , De Nisco NJ",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No UTI History,"rUTI History, UTI (-)","Consists of post menopausal (PM) women with a recent history of recurring urinary tract infection ( rUTI) but no active UTI at the time of urine donation (rUTI History, UTI(−))",25,25,4 weeks,WMS,NA,Sanger,Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 3D + 3E,25 October 2023,Tolulopeo,"Tolulopeo,ChiomaBlessing","Differentially abundant taxa in the rUTI History, UTI(−) group compared to the No UTI History group",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus urinae",2|1239|91061|186826|186827|1375;2|1239|1737404|1737405|1570339|165779|33032;2|1239|1737404|1737405|1570339|165779|33037;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|2742598|1633;2|1239|91061|186826|186827|1375|1376,Complete,ChiomaBlessing
bsdb:812/1/2,Study 812,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL , De Nisco NJ",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No UTI History,"rUTI History, UTI (-)","Consists of post menopausal (PM) women with a recent history of recurring urinary tract infection ( rUTI) but no active UTI at the time of urine donation (rUTI History, UTI(−))",25,25,4 weeks,WMS,NA,Sanger,Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 3D + 3E,25 October 2023,Tolulopeo,"Tolulopeo,Chinelsy,Chloe,ChiomaBlessing","Differentially abundant taxa in the rUTI History, UTI(−) group compared to the No UTI History group",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium ravenspurgense,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Gleimia|s__Gleimia europaea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",2|1239|1737404|1737405|1570339|165779|33029;2|1239|1737404|1737405|1570339|165779|33034;2|976|200643|171549|815|816;2|976|200643|171549|815|816|820;2|201174|1760|85006|85019|1696|479117;2|1239|186801|186802|543314|2137877;2|201174|1760|85007|1653|1716|38303;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350|1351;2|1224|1236|91347|543|561;2|1239|91061|186826|186827|66831|178214;2|1239|1737404|1737405|1570339|150022|1260;2|1239|91061|1385|539738|1378;2|201174|1760|2037|2049|2692113|66228;2|976|200643|171549|171552|2974257|386414;2|1224|1236|91347|543|570;2|1239|1737404|1737405|1570339|162289|33031;2|201174|1760|2037|2049|2529408|131111;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1290;2|1239|91061|186826|1300|1301;2|544448|2790996|2790998|2129;2|544448|2790996|2790998|2129|134821,Complete,ChiomaBlessing
bsdb:812/2/1,Study 812,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL , De Nisco NJ",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Hormone replacement therapy,EFO:0003961,EHT- Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who did not use estrogen hormone therapy (EHT)),EHT+ Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who used estrogen hormone therapy (EHT)),Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' with systemic and vaginal estrogen hormone therapy (EHT) who did not have UTI at the time of urine donation.,21,29,4 weeks,WMS,NA,Sanger,LEfSe,0.05,TRUE,4.5,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Fig 4C + 4H,25 October 2023,Tolulopeo,"Tolulopeo,Chinelsy,ChiomaBlessing",Urogenital microbiomes of EHT(+) (aggregated systemic and vaginal) women compared to those of EHT(−) women,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|2742598|1633,Complete,ChiomaBlessing
bsdb:812/2/2,Study 812,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL , De Nisco NJ",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Hormone replacement therapy,EFO:0003961,EHT- Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who did not use estrogen hormone therapy (EHT)),EHT+ Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who used estrogen hormone therapy (EHT)),Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' with systemic and vaginal estrogen hormone therapy (EHT) who did not have UTI at the time of urine donation.,21,29,4 weeks,WMS,NA,Sanger,LEfSe,0.05,TRUE,4.5,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Fig 4H,25 October 2023,Tolulopeo,"Tolulopeo,OdigiriGreat,ChiomaBlessing",Urogenital microbiomes of  EHT(+) women compared to those of EHT(-) women,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",2|201174|84998|84999|1643824|2767327|82135;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1313,Complete,ChiomaBlessing
bsdb:812/3/NA,Study 812,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL , De Nisco NJ",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 3,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No UTI History,"rUTI History, UTI (+)","Consists of post menopausal (PM) women with a recent history of recurring urinary tract infection ( rUTI) and an active, symptomatic UTI at the time of urine donation",25,25,4 weeks,WMS,NA,Sanger,Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:813/1/1,Study 813,laboratory experiment,33046129,10.1186/s13073-020-00784-9,NA,"Binyamin D, Werbner N, Nuriel-Ohayon M, Uzan A, Mor H, Abbas A, Ziv O, Teperino R, Gutman R , Koren O",The aging mouse microbiome has obesogenic characteristics,Genome medicine,2020,"Aging, Fecal microbiota transplantation, Metabolism, Microbiome",Experiment 1,Israel,Mus musculus,"Feces,Blood vessel","UBERON:0001988,UBERON:0001981",Body weight,EFO:0004338,Adult,Aging,Aging Mice,42,32,NIL,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,18 October 2023,Greatman,"Greatman,LGeistlinger,Peace Sandy","Genera that differed significantly between adult and aged mice. Analysis of microbiome composition (ANCOM) revealed 6 genera a Dehalobacterium, b unspecified Peptococcaceae, c Sutterella, d unspecified Desulfovibrionaceae, and e Bilophila, with significantly different relative abundance in adult versus aged mice",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|1239|186801|186802|186807|51514;2|1239|186801|186802|186807;2|1224|28216|80840|995019|40544;2|200940|3031449|213115|194924;2|200940|3031449|213115|194924|35832,Complete,LGeistlinger
bsdb:813/2/1,Study 813,laboratory experiment,33046129,10.1186/s13073-020-00784-9,NA,"Binyamin D, Werbner N, Nuriel-Ohayon M, Uzan A, Mor H, Abbas A, Ziv O, Teperino R, Gutman R , Koren O",The aging mouse microbiome has obesogenic characteristics,Genome medicine,2020,"Aging, Fecal microbiota transplantation, Metabolism, Microbiome",Experiment 2,Israel,Mus musculus,"Feces,Blood vessel","UBERON:0001988,UBERON:0001981",Body fat percentage,EFO:0007800,low body fat percentage,high body fat percentage,High body fat adult and aged mice,32,13,NIL,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5b,11 November 2023,LGeistlinger,LGeistlinger,Bacteria that are associated with fat/lean percent mass in both adult and aged mice,increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,LGeistlinger
bsdb:813/3/1,Study 813,laboratory experiment,33046129,10.1186/s13073-020-00784-9,NA,"Binyamin D, Werbner N, Nuriel-Ohayon M, Uzan A, Mor H, Abbas A, Ziv O, Teperino R, Gutman R , Koren O",The aging mouse microbiome has obesogenic characteristics,Genome medicine,2020,"Aging, Fecal microbiota transplantation, Metabolism, Microbiome",Experiment 3,Israel,Mus musculus,"Feces,Blood vessel","UBERON:0001988,UBERON:0001981",Body weight,EFO:0004338,Less weight,Higher weight,Mice with Higher Body Weight,13,32,NIL,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,20 February 2024,Peace Sandy,Peace Sandy,"Bacteria that are associated with weight and fat/lean percent mass in both adult and aged mice. Taxa abundance is represented by color scale. a Three genera Bifidobacterium, Clostridium, and Sutterella were significantly correlated with weight.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:814/1/1,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,"Adult Systemic Sclerosis patients on a low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult Systemic Sclerosis patients on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.",19,16,three weeks,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,9 October 2023,Boadiwaa,"Boadiwaa,Chloe,Tolulopeo",Differential abundance of specific genera between low versus non-low FODMAP groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|570;2|1239|909932|1843489|31977|906;2|1224|28211|204441,Complete,Folakunmi
bsdb:814/1/2,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,"Adult Systemic Sclerosis patients on a low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult Systemic Sclerosis patients on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.",19,16,three weeks,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,9 October 2023,Boadiwaa,"Boadiwaa,Chloe",Differential abundance of specific genera between low versus non-low FODMAP groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|186803|33042|2049024;2|1239|526524|526525|128827;2|1239|186801|186802|216572|216851|1946507;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|3120161|1481960;2|1239|186801|3082720|186804|1505652;2|1239|186801|3085636|186803|1506577|2053632;2|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:814/2/1,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,Not Applicable,Systemic Sclerosis patients with increased GIT 2.0 score,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting more severe Gastrointestinal Tract symptoms",NA,66,"Four weeks, no antibiotics use more than 2 times in the preceding 12 months prior to the stool collection.",16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,11 October 2023,Boadiwaa,"Boadiwaa,Chloe,Hodan Issah",Differential abundance of specific genera based on GIT 2.0 Total Score,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium",2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851|1946507;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1224|28211|204457|41297|165695,Complete,Folakunmi
bsdb:814/2/2,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,Not Applicable,Systemic Sclerosis patients with increased GIT 2.0 score,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting more severe Gastrointestinal Tract symptoms",NA,66,"Four weeks, no antibiotics use more than 2 times in the preceding 12 months prior to the stool collection.",16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,11 October 2023,Boadiwaa,"Boadiwaa,Chloe,Peace Sandy,Hodan Issah",Differential abundance of specific genera based on GIT 2.0 Total Score,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Cuneatibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Viruses|k__Orthornavirae|p__Pisuviricota|c__Pisoniviricetes|o__Picornavirales|f__Picornaviridae|s__Ensavirinae|g__Enterovirus|s__Rhinovirus A,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|s__uncultured Defluviitaleaceae bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Eukaryota|k__Viridiplantae|p__Chlorophyta|c__Chlorophyceae|o__Chlamydomonadales|s__uncultured Haematococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549;2|1239|526524|526525|2810280|135858;2|1239|186801;2|1239|186801|186802|1898207;2|1239|186801|186802|1671661;2|1239|186801|186802|31979|1485|1262798;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|2049024;2|1239|186801|3085636|186803|1918450;2|1239|526524|526525|128827|1937008;2157|28890|183925|2158|2159|2172;2|544448|31969;2|976|200643|171549|171552|838;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|292632|2053618;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803|1506577;10239|2732396|2732408|2732506|464095|12058|2946630|12059|147711;2|1239|186801|3085636|1185407|2065077;2|1239|526524|526525|128827|331630;2759|33090|3041|3166|3042|404784;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:814/3/1,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with more severe diarrhoea,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, reporting more severe diarrhea based on the diarrhea score.",NA,66,"Four weeks, no antibiotics use more than 2 times in the preceding 12 months prior to the stool collection.",16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplemental Figure 1,30 October 2023,Boadiwaa,Boadiwaa,Differential abundance of specific genera based on symptom score for the diarrhea domain.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium",2|1239|91061|186826|81852|1350;2|1239|186801|186802|1671661;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|1578;2|1224|28211|204457|41297|165695,Complete,Folakunmi
bsdb:814/3/2,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with more severe diarrhoea,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, reporting more severe diarrhea based on the diarrhea score.",NA,66,"Four weeks, no antibiotics use more than 2 times in the preceding 12 months prior to the stool collection.",16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplemental Figure 1,30 October 2023,Boadiwaa,"Boadiwaa,Idiaru angela",Differential abundance of specific genera based on symptom score for the diarrhea domain.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|s__uncultured Defluviitaleaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|216572|244127;2|201174|1760|85004|31953|1678;2|1239|186801|3082768|990719|990721|1935934;2|1239|186801|3082768|990719;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803|33042;2|201174|84998|84999;2|1239|526524|526525|128827|61170;2|1239|186801|3082720|186804|1505657;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|2485925;2|976|200643|171549|171552|838;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263;2|1239|186801|186802|1470353;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803|1506577;2|1239|186801|3085636|1185407|2065077;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003;2|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:814/4/1,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with  worsened social functioning,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting worsened social functioning",NA,66,four weeks,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Figure 2,30 October 2023,Boadiwaa,"Boadiwaa,Folakunmi",Differential abundance of specific genera based on symptom score for the social functioning domain.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851|1946507;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|909932|1843489|31977|906;2|1224|28211|204457|41297|165695;2|1224|1236|91347|543|1940338,Complete,Folakunmi
bsdb:814/4/2,Study 814,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP , Volkmann ER",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with  worsened social functioning,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting worsened social functioning",NA,66,four weeks,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Figure 2,30 October 2023,Boadiwaa,"Boadiwaa,Welile",Differential abundance of specific genera based on symptom score for the social functioning domain.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium Phil7",2|1239|186801|3085636|186803|33042;2|1239|1263031;2157|28890|183925|2158|2159|2172;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|128827|331630;2|1239|186801|186802|216572|707003;2|1239|186801|3082768|990719|1930013,Complete,Folakunmi
bsdb:815/1/1,Study 815,time series / longitudinal observational,36138438,https://doi.org/10.1186/s40168-022-01322-y,https://pubmed.ncbi.nlm.nih.gov/36138438/,"Martin VM, Virkud YV, Dahan E, Seay HL, Itzkovits D, Vlamakis H, Xavier R, Shreffler WG, Yuan Q , Yassour M",Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis,Microbiome,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative proctosigmoiditis,EFO:1001223,Infants diagnosed without food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP) who had a minimum of 4 longitudinal stool samples in the first year.  FPIAP was diagnosed by the treating physician and confirmed by comprehensive study staff chart review.,81,79,NIL,16S,4,Illumina,MaAsLin2,0.2,TRUE,NA,age,"age,diet,mode of birth",NA,NA,NA,NA,NA,unchanged,Signature 1,Fig 3 (A) and 3 (B),10 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy","Summary of key differential taxa between infants with FPIAP and healthy controls. A Significantly different taxa comparing infants with FPIAP to healthy controls (q < 0.20; absolute coefficient > = 0.05) when looking at sample subsets: 0–2 months, last pre-symptomatic, first symptomatic, and first resolved. Bars to the right are enriched in infants with FPIAP, while bars to the left are enriched in the controls. Number of samples in each group is shown under the name of the subset analyzed in that model (FPIAP, control). B Significantly different taxa (q < 0.20) when comparing infants with FPIAP to matched controls before their symptom onset (top section) and then during the symptomatic period (lower section) over the first 2 months of age. Association directionality and numbers are as in (A).",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3085636|186803|572511;2|1239|186801|186802,Complete,Peace Sandy
bsdb:815/1/2,Study 815,time series / longitudinal observational,36138438,https://doi.org/10.1186/s40168-022-01322-y,https://pubmed.ncbi.nlm.nih.gov/36138438/,"Martin VM, Virkud YV, Dahan E, Seay HL, Itzkovits D, Vlamakis H, Xavier R, Shreffler WG, Yuan Q , Yassour M",Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis,Microbiome,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative proctosigmoiditis,EFO:1001223,Infants diagnosed without food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP) who had a minimum of 4 longitudinal stool samples in the first year.  FPIAP was diagnosed by the treating physician and confirmed by comprehensive study staff chart review.,81,79,NIL,16S,4,Illumina,MaAsLin2,0.2,TRUE,NA,age,"age,diet,mode of birth",NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 3 (A) and (B),22 February 2024,Peace Sandy,Peace Sandy,"Summary of key differential taxa between infants with FPIAP and healthy controls. A Significantly different taxa comparing infants with FPIAP to healthy controls (q < 0.20; absolute coefficient > = 0.05) when looking at sample subsets: 0–2 months, last pre-symptomatic, first symptomatic, and first resolved. Bars to the right are enriched in infants with FPIAP, while bars to the left are enriched in the controls. Number of samples in each group is shown under the name of the subset analyzed in that model (FPIAP, control). B Significantly different taxa (q < 0.20) when comparing infants with FPIAP to matched controls before their symptom onset (top section) and then during the symptomatic period (lower section) over the first 2 months of age. Association directionality and numbers are as in (A).",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1224|1236|91347|543;2|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:816/1/1,Study 816,"cross-sectional observational, not case-control",33584071,10.3748/wjg.v27.i5.391,https://www.wjgnet.com/1007-9327/full/v27/i5/391.htm,"Li YD, Liu BN, Zhao SH, Zhou YL, Bai L , Liu EQ",Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea,World journal of gastroenterology,2021,"16S rRNA, Bifidobacterium, Cholecystectomy, Diarrhea, Microbiota, Post-cholecystectomy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postcholecystectomy syndrome,EFO:1001117,healthy control (HC),post-cholecystectomy (PC),Participants who have post-cholecystectomy (PC) syndrome are difficult to treat.,20,31,3 months,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1D,30 October 2023,Chinelsy,Chinelsy,Comparison of gut microbiota structure and abundance between post-cholecystectomy (PC) and healthy control (HC) groups. Logarithmic linear discriminant analysis scores identify the taxa with the greatest differences in abundance between the healthy control and post-cholecystectomy groups.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174;2|1239|909932|1843489|31977;2|1239|909932|909929;2|1239|909932,Complete,Folakunmi
bsdb:816/2/1,Study 816,"cross-sectional observational, not case-control",33584071,10.3748/wjg.v27.i5.391,https://www.wjgnet.com/1007-9327/full/v27/i5/391.htm,"Li YD, Liu BN, Zhao SH, Zhou YL, Bai L , Liu EQ",Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea,World journal of gastroenterology,2021,"16S rRNA, Bifidobacterium, Cholecystectomy, Diarrhea, Microbiota, Post-cholecystectomy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,post-cholecystectomy non-diarrhea (PCND),post-cholecystectomy diarrhea (PCD),This group included patients who experienced post-cholecystectomy diarrhea (PCD). These individuals had diarrhea as a clinical symptom following gallbladder removal.,15,16,3 months,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig.2C,30 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing",Comparison of gut microbiota structure and abundance between the post-cholecystectomy non-diarrhea (PCND) and post-cholecystectomy diarrhea (PCD) groups. Linear discriminant analysis and effect size analysis show the taxa with the greatest differences in abundance between the PCND and PCD groups. Yellow bars: PCND group-enriched taxa; Green bars: PCD group-enriched taxa.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|91061|186826|1300|1357;2|1239|186801|186802|31979|1266;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|1236|91347|543|160674;2|1224|1236|91347|543|544;2|1239|186801|186802,Complete,Folakunmi
bsdb:816/2/2,Study 816,"cross-sectional observational, not case-control",33584071,10.3748/wjg.v27.i5.391,https://www.wjgnet.com/1007-9327/full/v27/i5/391.htm,"Li YD, Liu BN, Zhao SH, Zhou YL, Bai L , Liu EQ",Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea,World journal of gastroenterology,2021,"16S rRNA, Bifidobacterium, Cholecystectomy, Diarrhea, Microbiota, Post-cholecystectomy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,post-cholecystectomy non-diarrhea (PCND),post-cholecystectomy diarrhea (PCD),This group included patients who experienced post-cholecystectomy diarrhea (PCD). These individuals had diarrhea as a clinical symptom following gallbladder removal.,15,16,3 months,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig.2C,30 October 2023,Chinelsy,"Chinelsy,MyleeeA,ChiomaBlessing",Comparison of gut microbiota structure and abundance between the post-cholecystectomy non-diarrhea (PCND) and post-cholecystectomy diarrhea (PCD) groups. Linear discriminant analysis and effect size analysis show the taxa with the greatest differences in abundance between the PCND and PCD groups. Yellow bars: PCND group-enriched taxa; Green bars: PCD group-enriched taxa.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549;2|976|200643;2|1224|28216;2|1224|28216|80840;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:817/1/1,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 1,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Kidneys with calcification,Meagre fishes with tissue calcification in their kidneys,7,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Table 2",9 March 2024,Barrakat,Barrakat,The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and kidney with calcification),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Candidatus Actinomarinales|f__Candidatus Actinomarinaceae|g__Candidatus Actinomarina|s__Candidatus Actinomarina sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",2|201174|1760|1389450|1389452|1389453|2578121;2|976|117743|200644|49546,Complete,Svetlana up
bsdb:817/1/2,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 1,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Kidneys with calcification,Meagre fishes with tissue calcification in their kidneys,7,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Figure 6",10 March 2024,Barrakat,"Barrakat,Svetlana up",The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and kidney with calcification),decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus",2|1239|91061|1385|186817|150247;2|201174|1760|85006|145357|57495;2|201174|1760|85006|1268|1269;2|1224|28211|204455|31989|265,Complete,Svetlana up
bsdb:817/2/1,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 2,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Systemic Granulomatosis (SG)-affected,Sick with Kidney calcification,Meagre fishes with tissue calcifications in their kidneys,10,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Table 2",9 March 2024,Barrakat,Barrakat,"The differential abundance of microbial taxa as identified by LefSe in two health groups:
Systemic granulomatosis (SG)-affected and kidney with calcification.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Candidatus Actinomarinales|f__Candidatus Actinomarinaceae|g__Candidatus Actinomarina|s__Candidatus Actinomarina sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",2|201174|1760|1389450|1389452|1389453|2578121;2|976|117743|200644|49546,Complete,Svetlana up
bsdb:817/2/2,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 2,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Systemic Granulomatosis (SG)-affected,Sick with Kidney calcification,Meagre fishes with tissue calcifications in their kidneys,10,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 Fig 6,10 March 2024,Barrakat,Barrakat,"The differential abundance of microbial taxa as identified by LefSe in two health groups:
Systemic granulomatosis (SG)-affected and kidney with calcification.",decreased,"k__Bacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales|f__Pyrinomonadaceae|g__Pyrinomonas,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae",2;2|1224|28216|80840|119060;2|1224|28211|204455|31989|265;2|57723|1562566|1748771|2048906|1562565;2|976|117747|200666;2|1224|28211|356|45404,Complete,Svetlana up
bsdb:817/3/1,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 3,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Sick,Meagre fishes with SG-affected kidneys and tissue calcification in their kidneys,7,20,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Figure 2, Supplementary Figure 3",9 March 2024,Barrakat,"Barrakat,Svetlana up","The differential abundance of microbial taxa as identified by LefSe in two health groups
(healthy and sick)",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales",2|1224|28216|80840|119060;2|1224|28216|32003|90627;2|1224|28211|204455,Complete,Svetlana up
bsdb:817/3/2,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 3,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Sick,Meagre fishes with SG-affected kidneys and tissue calcification in their kidneys,7,20,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Supplementary Figure 2, Supplementary Figure 3",10 March 2024,Barrakat,"Barrakat,Svetlana up","The differential abundance of microbial taxa as identified by LefSe in two health groups
(healthy and sick)",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|1385;2|1239|91061|1385|186817|1386;2|74201|414999|415001|3056371|442430;2|1297|188787|68933|188786|65551;2|1224|28211|204455|31989|265;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:818/1/1,Study 818,"prospective cohort,time series / longitudinal observational",37644001,10.1038/s41467-023-40336-4,NA,"Hoskinson C, Dai DLY, Del Bel KL, Becker AB, Moraes TJ, Mandhane PJ, Finlay BB, Simons E, Kozyrskyj AL, Azad MB, Subbarao P, Petersen C , Turvey SE",Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease,Nature communications,2023,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,"Asthma,Allergic rhinitis,Dermatitis,Food allergy","MONDO:0002406,MONDO:0004979,EFO:1001890,EFO:0005854",Healthy controls,Allergic Children,Children diagnosed by an expert physician at the 5-year scheduled visit with one or more allergic disorders.,523,592,No Antibiotics exclusion was mentioned,WMS,NA,Illumina,Random Forest Analysis,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,figure 4C,11 October 2023,Nwajei Edgar,"Nwajei Edgar,Peace Sandy,Folakunmi",Comparing species abundance within the 1-year microbiota between children who did or did not receive an allergic diagnosis at 5 years,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|1407607|1150298,Complete,Folakunmi
bsdb:818/1/2,Study 818,"prospective cohort,time series / longitudinal observational",37644001,10.1038/s41467-023-40336-4,NA,"Hoskinson C, Dai DLY, Del Bel KL, Becker AB, Moraes TJ, Mandhane PJ, Finlay BB, Simons E, Kozyrskyj AL, Azad MB, Subbarao P, Petersen C , Turvey SE",Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease,Nature communications,2023,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,"Asthma,Allergic rhinitis,Dermatitis,Food allergy","MONDO:0002406,MONDO:0004979,EFO:1001890,EFO:0005854",Healthy controls,Allergic Children,Children diagnosed by an expert physician at the 5-year scheduled visit with one or more allergic disorders.,523,592,No Antibiotics exclusion was mentioned,WMS,NA,Illumina,Random Forest Analysis,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,figure 4C,11 October 2023,Nwajei Edgar,"Nwajei Edgar,Peace Sandy,Folakunmi",Comparing species abundance within the 1-year microbiota between children who did or did not receive an allergic diagnosis at 5 years,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile",2|201174|84998|1643822|1643826|84111|84112;2|1239|91061|186826|81852|1350|1351;2|1224|1236|91347|543|561|562;2|1239|526524|526525|128827|1522;2|1239|186801|3085636|186803|1506577|29361,Complete,Folakunmi
bsdb:819/1/NA,Study 819,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti RM, Handley SA, Droit L, Ghannoum M, Jacobson M, Shiboski CH, Webster-Cyriaque J, Brown T, Yin MT , Overton ET",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Viral load,EFO:0010125,High viral load at baseline,Low viral load at baseline,Participants with viral load less than 100 000 copies/ml at baseline,9,26,N/A,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:819/2/1,Study 819,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti RM, Handley SA, Droit L, Ghannoum M, Jacobson M, Shiboski CH, Webster-Cyriaque J, Brown T, Yin MT , Overton ET",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to antiviral drug,EFO:0010123,Baseline samples,Week 24 samples,Saliva samples after 24 weeks of antiretroviral therapy,35,35,N/A,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2 :Table S1,16 October 2023,MyleeeA,MyleeeA,Bacterial taxa differentially abundant in saliva prior to and following 24 weeks of antiretroviral therapy,increased,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,2|203691|203692|136|2845253|157|53418,Complete,Folakunmi
bsdb:819/2/2,Study 819,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti RM, Handley SA, Droit L, Ghannoum M, Jacobson M, Shiboski CH, Webster-Cyriaque J, Brown T, Yin MT , Overton ET",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to antiviral drug,EFO:0010123,Baseline samples,Week 24 samples,Saliva samples after 24 weeks of antiretroviral therapy,35,35,N/A,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2, Table S1",16 October 2023,MyleeeA,"MyleeeA,Folakunmi",Bacterial taxa differentially abundant in saliva prior to and following 24 weeks of antiretroviral therapy,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,2|976|200643|171549|2005473|1918540|1796646,Complete,Folakunmi
bsdb:819/3/1,Study 819,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti RM, Handley SA, Droit L, Ghannoum M, Jacobson M, Shiboski CH, Webster-Cyriaque J, Brown T, Yin MT , Overton ET",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,CD4-positive T-lymphocyte count,EFO:0010105,Baseline CD4+ low samples,Baseline CD4+ high samples,Baseline CD4+ high samples before administering Anti Retroviral Therapy,35,35,N/A,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Table S2",16 October 2023,MyleeeA,"MyleeeA,Folakunmi",The effect of CD4+ T-cell counts on the salivary bacterial microbiome: Differential abundance of bacterial taxa in CD4+ low vs. CD4+ high patient saliva.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,2|1224|1236|135625|712|724|729,Complete,Folakunmi
bsdb:819/4/1,Study 819,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti RM, Handley SA, Droit L, Ghannoum M, Jacobson M, Shiboski CH, Webster-Cyriaque J, Brown T, Yin MT , Overton ET",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,CD4-positive T-lymphocyte count,EFO:0010105,week 24 CD4+ low samples,week 24 CD4+ high samples,samples with high CD4+ at Week 24 following Anti Retroviral Therapy,35,35,N/A,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3, Table S2",16 October 2023,MyleeeA,"MyleeeA,Folakunmi",The effect of CD4+ T-cell counts on the salivary bacterial microbiome: Differential abundance of bacterial taxa in CD4+ low vs. CD4+ high patient saliva.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,2|1224|1236|135625|712|724|729,Complete,Folakunmi
bsdb:820/1/2,Study 820,time series / longitudinal observational,37032359,10.1186/s40168-023-01516-y,NA,"Spatz M, Da Costa G, Ventin-Holmberg R, Planchais J, Michaudel C, Wang Y, Danne C, Lapiere A, Michel ML, Kolho KL, Langella P, Sokol H , Richard ML",Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem,Microbiome,2023,"Antibiotics, Enterobacteriaceae, Microbiota, Mycobiota",Experiment 1,France,Mus musculus,Feces,UBERON:0001988,"Antimicrobial agent,Amoxicillin","CHEBI:33281,CHEBI:2676",mouse before antibiotic treatment,mouse  after antibiotic treatment,Mouse sample fungal results post-antibiotic treatment using Amoxicillin/clavulanate acid,7,12,NA,ITS / ITS2,NA,NA,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,figure 2D,13 October 2023,Hodan Issah,Hodan Issah,Amoxicillin/clavulanate acid treatment alters the fungal microbiota,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Valsaceae|g__Valsa",2759|4751|4890|147545|5042|1131492|5052;2759|4751|4890|147541|2726946|452563|5498;2759|4751|4890|147550|5114|5117|83174,Complete,Folakunmi
bsdb:820/2/2,Study 820,time series / longitudinal observational,37032359,10.1186/s40168-023-01516-y,NA,"Spatz M, Da Costa G, Ventin-Holmberg R, Planchais J, Michaudel C, Wang Y, Danne C, Lapiere A, Michel ML, Kolho KL, Langella P, Sokol H , Richard ML",Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem,Microbiome,2023,"Antibiotics, Enterobacteriaceae, Microbiota, Mycobiota",Experiment 2,France,Mus musculus,Feces,UBERON:0001988,"Antimicrobial agent,Amoxicillin","CHEBI:33281,CHEBI:2676",Mouse before antibiotic  treatment,Mouse after antibiotic treatment,Mouse sample bacterial results post-antibiotic treatment using amoxicillin-acid clavulanic,7,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,figure 3D,13 October 2023,Hodan Issah,"Hodan Issah,Folakunmi",Amoxicillin/clavulanate acid treatment alters the bacterial microbiota,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:821/1/1,Study 821,laboratory experiment,31686318,10.1007/s11427-019-9540-y,NA,"Li J, Rui J, Li Y, Tang N, Zhan S, Jiang J , Li X",Ambient temperature alters body size and gut microbiota of Xenopus tropicalis,Science China. Life sciences,2020,"Xenopus tropicalis, body size, gut microbiota, temperature, thermal adaptation",Experiment 1,China,Xenopus tropicalis,Midgut,UBERON:0001045,Temperature,EFO:0001702,Cool Gut,Warm Gut,Xenopus tropicalis gut microbiota response to warm environmental conditions,23,28,None,16S,45,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S4 (Genus level),12 October 2023,Chikamso,"Chikamso,Peace Sandy,Folakunmi",Different abundance of gut microbiota between warm (group 1) and cool (group 0) environment (Warm Gut vs. Cool Gut),increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572|244127;2|1239|526524|526525|2810280|100883;2|976|200643|171549|2005525|375288;2|1224|28211|204441|2844866|168934,Complete,Folakunmi
bsdb:821/1/2,Study 821,laboratory experiment,31686318,10.1007/s11427-019-9540-y,NA,"Li J, Rui J, Li Y, Tang N, Zhan S, Jiang J , Li X",Ambient temperature alters body size and gut microbiota of Xenopus tropicalis,Science China. Life sciences,2020,"Xenopus tropicalis, body size, gut microbiota, temperature, thermal adaptation",Experiment 1,China,Xenopus tropicalis,Midgut,UBERON:0001045,Temperature,EFO:0001702,Cool Gut,Warm Gut,Xenopus tropicalis gut microbiota response to warm environmental conditions,23,28,None,16S,45,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table S4 (Genus level),12 October 2023,Chikamso,"Chikamso,OdigiriGreat,Chinelsy,Peace Sandy,Folakunmi",Different abundance of gut microbiota between warm (group 1) and cool (group 0) environment (Warm Gut vs. Cool Gut),decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium",2|1224|1236|91347|543|544;2|1239|91061|1385|186817|150247;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803|653683;2|1239|186801|3082720|186804|1501226;2|1224|1236|2887326|468|469;2|1224|28216|80840|75682|29580,Complete,Folakunmi
bsdb:822/1/1,Study 822,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA , Nicol MP",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 1,"Zimbabwe,Malawi",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,Placebo at 48 Weeks,Azithromycin(AZM) at 48 weeks,Participants with HIV-associated Chronic Lung Disease (HCLD) who received  azithromycin (AZM),150,154,NIL,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S 24,11 October 2023,Chinelsy,"Chinelsy,Peace Sandy,ChiomaBlessing","Heatmap displaying the q values of the genera detected as differentially abundant between AZM and placebo arms at 48 weeks by 10 statistical methods. For ANCOM2, taxa with w 0.6, 0.7, 0.8 and 0.9 were assigned q value of 0.01, 0.001, 0.0001 and 0.00001 respectively. Five genera were detected as differentially abundant by all methods (Lautropia, Moraxella, Rothia, Treponema and Veilonella).",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1224|28216|80840|119060|47670;2|1224|1236|2887326|468|475;2|201174|1760|85006|1268|32207;2|203691|203692|136|2845253|157,Complete,Peace Sandy
bsdb:822/2/1,Study 822,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA , Nicol MP",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 2,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,Placebo at 72 weeks,AZM at 72 weeks,Participants with HIV-associated Chronic Lung Disease (HCLD) who received  azithromycin (AZM),117,123,NIL,16S,4,Illumina,"DESeq2,ANCOM",0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Tables S6 and S7,12 October 2023,Chinelsy,"Chinelsy,Peace Sandy,Davvve,Chloe","Table S 6. Results of differential abundance testing of bacterial taxa from AZM and Placebo samples from 72 weeks using DESeq2.

Table S 7. Results of differential abundance testing of bacterial taxa from AZM and Placebo samples from 72 weeks using Ancom-II",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1224|28216|80840|119060|47670;2|203691|203692|136|2845253|157,Complete,Chloe
bsdb:822/3/1,Study 822,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA , Nicol MP",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 3,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,AZM at baseline - Azithromycin arm only,AZM at 48 weeks - Azithromycin arm only,Participants with HIV-associated Chronic Lung Disease (HCLD) who received  azithromycin (AZM) at 48weeks,173,154,NIL,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Table S 8.,12 October 2023,Chinelsy,"Chinelsy,Peace Sandy",Results of differential abundance testing of bacterial taxa from samples from the AZM arm at baseline and 48 72 weeks using 10 methods.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",2|1224|28216|80840|119060|47670;2|1224|1236|2887326|468|475;2|203691|203692|136|2845253|157;2|1239|186801|3085636|186803|265975,Complete,Peace Sandy
bsdb:822/4/1,Study 822,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA , Nicol MP",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 4,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,Placebo at 48 Weeks - Arm Only,Placebo at 72 Weeks - Arm Only,Placebo treatment at 72 Weeks (arm only),174,174,NIL,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Table S 10.,24 February 2024,Peace Sandy,Peace Sandy,Results of differential abundance testing of bacterial taxa from Placebo samples from 48 and 72 weeks using DESeq2.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,2|1224|1236|2887326|468|475,Complete,Peace Sandy
bsdb:822/5/1,Study 822,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA , Nicol MP",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 5,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,Placebo at baseline,Placebo at 72 weeks,Placebo at 72 weeks,174,117,NIL,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Table S 11,24 February 2024,Peace Sandy,Peace Sandy,Results of differential abundance testing of bacterial taxa from Placebo samples from baseline and 72 weeks using DESeq2.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,2|1224|1236|2887326|468|475,Complete,Peace Sandy
bsdb:823/1/1,Study 823,case-control,31738825,10.1167/iovs.19-27719,NA,"Dong X, Wang Y, Wang W, Lin P , Huang Y",Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2019,NA,Experiment 1,China,Homo sapiens,"Margin of eyelid,Conjunctival sac","UBERON:0034772,UBERON:0005908",Dry eye syndrome,EFO:1000906,Healthy controls,Meibomian Gland Dysfunction (MGD) Groups,Patients with diagnosis of  Meibomian Gland Dysfunction MGD,42,47,No participant used oral antibiotics within 2 weeks,16S,34,Illumina,LEfSe,0.05,NA,4,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig 3,16 October 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","LEfSe analysis of the normal control group and the MGD groups. (B) Linear discriminant analysis scoring of biomarkers corresponding to (A), computed by the LEfSe tool. When the score of a taxon was >4.0 with P < 0.01, it was listed in the histogram, which showed all the biomarkers found from the domain to species level. “p”, “c”, “o”, “f”, “g”, and “s” referred to phylum, class, order, family, genus, and species, respectively. At the genus level, the biomarkers were Staphylococcus and Sphingomonas in the patients with MGD, and Corynebacterium in the controls. The length of the histogram represented the linear discriminate analysis values of the different taxa.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas melonis",2|1239|91061|1385;2|1239|91061;2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964;2|1239;2|1239|91061|1385|90964|1279|1282;2|1224|28211|204457|41297|13687;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687|152682,Complete,Peace Sandy
bsdb:823/1/2,Study 823,case-control,31738825,10.1167/iovs.19-27719,NA,"Dong X, Wang Y, Wang W, Lin P , Huang Y",Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2019,NA,Experiment 1,China,Homo sapiens,"Margin of eyelid,Conjunctival sac","UBERON:0034772,UBERON:0005908",Dry eye syndrome,EFO:1000906,Healthy controls,Meibomian Gland Dysfunction (MGD) Groups,Patients with diagnosis of  Meibomian Gland Dysfunction MGD,42,47,No participant used oral antibiotics within 2 weeks,16S,34,Illumina,LEfSe,0.05,NA,4,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig 3,16 October 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","LEfSe analysis of the normal control group and the MGD groups. (B) Linear discriminant analysis scoring of biomarkers corresponding to (A), computed by the LEfSe tool. When the score of a taxon was >4.0 with P < 0.01, it was listed in the histogram, which showed all the biomarkers found from the domain to species level. “p”, “c”, “o”, “f”, “g”, and “s” referred to phylum, class, order, family, genus, and species, respectively. At the genus level, the biomarkers were Staphylococcus and Sphingomonas in the patients with MGD, and Corynebacterium in the controls. The length of the histogram represented the linear discriminate analysis values of the different taxa.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|201174|1760|85007|1653|1716;2|201174|1760|2037;2|201174;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716,Complete,Peace Sandy
bsdb:824/1/1,Study 824,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E, Kato-Kogoe N, Imai Y, Sakaguchi S, Taniguchi K, Omori M, Ohmichi M, Nakamura S, Nakano T, Lee SW , Ueno T",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,Patients who were on antibiotics three months preceding the sample collection were excluded from the study,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 3a,19 October 2023,Aleru002,Aleru002,The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the saliva sample identified by linear discriminant analysis effect size (LEfSe).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|s__uncultured bacterium",2|1239|186801|186802|404402;2|1239|91061|186826|33958|1578;2|77133,Complete,Chloe
bsdb:824/1/2,Study 824,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E, Kato-Kogoe N, Imai Y, Sakaguchi S, Taniguchi K, Omori M, Ohmichi M, Nakamura S, Nakano T, Lee SW , Ueno T",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,Patients who were on antibiotics three months preceding the sample collection were excluded from the study,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3a,19 October 2023,Aleru002,Aleru002,The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the saliva sample identified by linear discriminant analysis effect size (LEfSe).,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral clone CW040,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171550|239759;2|1239|186801|3082720|3030910|2060094;2|1239|186801|3085636|186803|207244;2|201174|1760|85009|31957|2801844;2|1239|186801|3085636|186803|830;2|95818|2093818|2093825|2171986|1331051;2|32066|203490|203491|203492|848;2|976|200643|171549|2005473;2|1239|186801|186802|186807|2740;2|1224|28216|80840|995019|40544;2|95818|163601;2|1239|186801|3082720|3118655|1913599|39498,Complete,Chloe
bsdb:824/2/1,Study 824,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E, Kato-Kogoe N, Imai Y, Sakaguchi S, Taniguchi K, Omori M, Ohmichi M, Nakamura S, Nakano T, Lee SW , Ueno T",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 2,Japan,Homo sapiens,Gastric juice,UBERON:0001971,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,Patients who were on antibiotics three months preceding the sample collection were excluded from the study,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3b,19 October 2023,Aleru002,Aleru002,The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the gastric fluid sample identified by linear discriminant analysis effect size (LEfSe).,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium",2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|3120161|1481960,Complete,Chloe
bsdb:824/2/2,Study 824,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E, Kato-Kogoe N, Imai Y, Sakaguchi S, Taniguchi K, Omori M, Ohmichi M, Nakamura S, Nakano T, Lee SW , Ueno T",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 2,Japan,Homo sapiens,Gastric juice,UBERON:0001971,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,Patients who were on antibiotics three months preceding the sample collection were excluded from the study,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3b,19 October 2023,Aleru002,Aleru002,The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the gastric fluid sample identified by linear discriminant analysis effect size (LEfSe).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral clone CW040,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum,k__Bacteria|s__uncultured bacterium",2|976|200643|171549|171552|1283313;2|1239|186801|3085636|186803|830;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|3085636|186803|43996;2|1239|186801|186802|31979|1485|1262798;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827|1573534;2|32066|203490|203491|203492|848;2|29547|3031852|213849|72293|209;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803;2|201174|1760|85009|85015|86795;2|1224|28216|206351|481|482;2|1224|28216|80840|995019|577310;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|201174|1760|85004|31953|196081;2|95818|163601;2|1239|186801|186802|543314|35518;2|77133,Complete,Chloe
bsdb:825/1/1,Study 825,meta-analysis,37602324,https://doi.org/10.3389/fmolb.2023.1210225,NA,"Suryavanshi M, Agudelo J , Miller A","Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease",Frontiers in molecular biosciences,2023,"human microbiome, kidney stones, rare phylotype, reference database, urinary stone disease, urobiome, urology",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Urolithiasis,MONDO:0024647,healthy controls,urinary stone disease patients,patients with urinary stone disease,136,201,NA,NA,NA,NA,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,21 October 2023,Joju,"Joju,Iram jamshed,MyleeeA",Bubble plot showing the fold change of differentially abundant common rare (B) taxa associated with health disparities (control and USD phenotypes) in stool samples. Selection of taxa is defined using DESeq2 differential abundance analysis with a false discovery rate-corrected p-value <0.05. Taxa are listed as the number of ASVs within the lowest assigned taxonomy as a means to elucidate the most important taxa associated with USD.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174|1760|2037|2049|1654;2|976|200643|171549|171550|239759;2|1239|909932|1843489|31977|209879;2|976|200643|171549|171552|1283313;2|1239|186801|186802|216572|244127;2|1239;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|135858;2|1239|186801;2|1239|186801|186802|1898207;2|1239|186801|186802|1980681;2|201174|84998|84999|84107|102106;2|976|200643|171549|2005519|1348911;2|201174|84998|84999;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924|872;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827;2|32066|203490|203491|203492|848;2|1239|186801|186802|216572|596767;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|248744;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085656|3085657|2039302;2|976|200643|171549|2005473;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1224|28216|80840|995019|40544;2|203691|203692|136|2845253|157;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977|29465;2|1239|186801|3082768|990719;2|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:825/2/1,Study 825,meta-analysis,37602324,https://doi.org/10.3389/fmolb.2023.1210225,NA,"Suryavanshi M, Agudelo J , Miller A","Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease",Frontiers in molecular biosciences,2023,"human microbiome, kidney stones, rare phylotype, reference database, urinary stone disease, urobiome, urology",Experiment 2,NA,Homo sapiens,Urine,UBERON:0001088,Urolithiasis,MONDO:0024647,healthy controls,urinary stone disease patients,patients with urinary stone disease,136,201,TEST,NA,NA,NA,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,30 October 2023,Joju,Joju,Bubble plot showing the fold change of differentially abundant rare (B) taxa associated with health disparities (control and USD phenotypes) in urine samples.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Undibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Chujaibacter,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|1224|1236|2887326|468|469;2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|165779;2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1224|28211|356|41294|374;2|201174|1760|85006|85019|1696;2|976|117743|200644|2762318|59732;2|1239|186801;2|1224|28216|80840|80864;2|201174|1760|85007|1653|1716;2|976|117743|200644|2762318|308865;2|1239|91061|186826|186827|66831;2|1239|186801|186802|216572|236752;2|976|117743|200644|49546|237;2|1239|186801|3085636|186803|1407607;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|162290;2|1239|1737404|1737405|1570339|31983;2|201174|1760|85006|1268|57493;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|1578;2|201174|1760|85007|2805586|1847725;2|1224|28211|356|119045|407;2|1239|1737404|1737405|1570339|1161127;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186807|2740;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297|13687;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|1239|909932|1843489|31977|29465;2|1224|1236|135624|84642|43947;2|1224|28216|80840|75682|401469;2|976|117743|200644|1853230|332102;2|1224|28216|80840|75682|149698;2|1224|1236|135614|32033|1931224;2759|33090|35493|3398|72025|3803|3814|508215,Complete,Peace Sandy
bsdb:826/1/1,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,16S,34,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,19 October 2023,Yjung24,"Yjung24,Davvve,Folakunmi","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. 47_25,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota",2|1224|28211|204441|2829815|191|1896971;2|1224|1236|91347|543|1940338;2|1224,Complete,Folakunmi
bsdb:826/1/2,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,16S,34,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,19 October 2023,Yjung24,"Yjung24,Folakunmi","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,k__Bacteria|p__Bacillota,2|1239,Complete,Folakunmi
bsdb:826/2/1,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC (participants diagnosed with colorectal cancer),participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.,53,28,NA,16S,34,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,"Yjung24,Folakunmi","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1239;2|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:826/3/1,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,"Colorectal adenoma,Colorectal cancer","EFO:0005406,EFO:0005842",Healthy controls,HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group,"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity. Combined with individuals selected from available archive of fresh-frozen stool samples diagnosed with colorectal cancer at screening or by registry follow-up.",53,91,NA,16S,34,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,Yjung24,"Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,k__Bacteria|p__Bacillota,2|1239,Complete,Folakunmi
bsdb:826/4/1,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,WMS,NA,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,"Yjung24,Folakunmi",Differential abundance analyses of taxa and pathways between HRA and healthy controls.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,2|1239|186801|3085636|186803|2719231|84030,Complete,Folakunmi
bsdb:826/4/2,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,WMS,NA,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,22 October 2023,Yjung24,"Yjung24,Folakunmi",Differential abundance analyses of taxa and pathways between HRA and healthy controls.,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,2|1224|28216|80840|995019|577310,Complete,Folakunmi
bsdb:826/5/1,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC (participants diagnosed with colorectal cancer),participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.,22,7,NA,WMS,NA,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,Yjung24,"Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens",2|1239|909932|1843488|909930|904;2|1239|909932|1843488|909930|904|187327;2|1239|186801|3085636|186803|33042|33043;2|1239|1262988;2|1239|186801|3085636|186803|28050|706562;2|1239|909932|1843488|909930|33024|626940,Complete,Folakunmi
bsdb:826/5/2,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC (participants diagnosed with colorectal cancer),participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.,22,7,NA,WMS,NA,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,22 October 2023,Yjung24,Yjung24,"Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:303,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",2|976|200643|171549|815|816|338188;2|1239|186801|3085656|3085657|2039302|1981510;2|1239|186801|3085636|186803|841|1262944;2|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:826/6/1,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 6,Norway,Homo sapiens,Feces,UBERON:0001988,"Colorectal adenoma,Colorectal cancer","EFO:0005406,EFO:0005842",Healthy controls,HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group,"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity. Combined with individuals selected from available archive of fresh-frozen stool samples diagnosed with colorectal cancer at screening or by registry follow-up.",22,25,NA,WMS,NA,Illumina,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,Yjung24,"Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,2|1239|186801|3085636|186803|2719231|84030,Complete,Folakunmi
bsdb:826/7/1,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 7,Norway,Homo sapiens,Feces,UBERON:0001988,Time,EFO:0000721,Colorectal cancer diagnosed at time of screening,Colorectal cancer diagnosed during 17-year follow-up/post screening,Diagnosed with colorectal cancer at screening in the beginning of the Norwegian Colorectal Cancer Prevention Trial,5,23,NA,16S,34,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,26 October 2023,Yjung24,Yjung24,"Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:826/7/2,Study 826,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P , Rounge TB",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 7,Norway,Homo sapiens,Feces,UBERON:0001988,Time,EFO:0000721,Colorectal cancer diagnosed at time of screening,Colorectal cancer diagnosed during 17-year follow-up/post screening,Diagnosed with colorectal cancer at screening in the beginning of the Norwegian Colorectal Cancer Prevention Trial,5,23,NA,16S,34,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,"geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,26 October 2023,Yjung24,Yjung24,"Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:827/1/1,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 1,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,Early cholangiocarcinoma,Advanced cholangiocarcinoma,"Patients with lymph node metastasis in cholangiocarcinoma, where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",NA,NA,none,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,30 October 2023,Folakunmi,Folakunmi,"Patients with lymph node metastasis in cholangiocarcinoma, where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|29547|3031852|213849|72294|194;2|1224|1236|91347|543|544;2|32066|203490|203491|1129771|32067,Complete,ChiomaBlessing
bsdb:827/2/1,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 2,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,Early pancreatic ductal adenocarcinoma,Advanced pancreatic ductal adenocarcinoma,"Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",NA,NA,none,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,30 October 2023,Folakunmi,Folakunmi,"Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|28211|356|69277|28100;2|1224|28211|204457|41297|13687,Complete,ChiomaBlessing
bsdb:827/2/2,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 2,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,Early pancreatic ductal adenocarcinoma,Advanced pancreatic ductal adenocarcinoma,"Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",NA,NA,none,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Table 2,30 October 2023,Folakunmi,Folakunmi,"Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",2|1224|1236|91347|543|547;2|1239|186801|3085636|186803|1649459;2|201174|1760|85007|1762|1763,Complete,ChiomaBlessing
bsdb:827/3/1,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 3,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,intraductal papillary mucinous neoplasm (IPMN),Intraductal papillary mucinous carcinoma (IPMC),Patients with Intraductal papillary mucinous carcinoma (IPMC) in pancreas cystic lesions.,20,10,none,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,30 October 2023,Folakunmi,Folakunmi,Abundant taxa in Intraductal papillary mucinous carcinoma (IPMC) when compared to intraductal papillary mucinous neoplasm.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|1283313;2|200940|3031449|213115|194924|35832;2|1239|909932|1843489|31977|39948;2|201174|84998|1643822|1643826|84111;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:827/4/1,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 4,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in bile duct lesion cases,Good prognosis in bile duct lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in bile duct lesion cases. These clinical conditions were found to be non-confounding.",101,101,none,16S,34,Illumina,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 1,"Table 4 + Results within text (Page 4, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa between poor prognosis and good prognosis in bile duct lesion cases using Cox proportional hazards model analysis.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|32066|203490|203491|203492|848;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:827/4/2,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 4,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in bile duct lesion cases,Good prognosis in bile duct lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in bile duct lesion cases. These clinical conditions were found to be non-confounding.",101,101,none,16S,34,Illumina,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 2,"Table 4 + Results within text (Page 4, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa between poor prognosis and good prognosis in bile duct lesion cases using Cox proportional hazards model analysis.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|976|200643|171549|815|816;2|201174|1760|85007|1653|1716;2|1239|91061|186826|81852|1350;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1649459;2|201174|1760|85007|2805586|1847725;2|1224|1236|2887326|468|475;2|1239|91061|1385|90964|1279,Complete,ChiomaBlessing
bsdb:827/5/1,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 5,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in pancreatic lesion cases,Good prognosis in pancreatic lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in pancreatic lesion cases. These clinicopathologic variables were found to be non-confounding.",112,112,none,16S,34,Illumina,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 1,"Table 4 + Results within text (Page 5, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|815|816;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|160674;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:827/5/2,Study 827,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M, Yokoyama S, Matsuo K, Hamada T, Shimokawa M, Akahane T, Sugimoto T, Tsurumaru H, Ishibashi M, Mataki Y, Ootsuka T, Nomoto M, Hayashi C, Horiguchi A, Higashi M , Tanimoto A",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 5,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in pancreatic lesion cases,Good prognosis in pancreatic lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in pancreatic lesion cases. These clinicopathologic variables were found to be non-confounding.",112,112,none,16S,34,Illumina,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 2,"Table 4 + Results within text (Page 5, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|2887326|468|469;2|1224|1236|91347|543|570;2|1224|28211|204455|31989|265;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:828/1/NA,Study 828,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I , Di Camillo B",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 1,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,COVID-19,MONDO:0100096,Asymptomatic patients,Symptomatic patients,Symptomatic patients with signs of COVID-19,36,156,Patients were excluded from the study if they had received antibiotics within 4 weeks of enrollment.,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:828/2/1,Study 828,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I , Di Camillo B",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 2,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,"COVID-19,Pneumonia","EFO:0003106,MONDO:0100096",COVID-19 patients with mild pneumonia,COVID-19 patients with severe pneumonia,"COVID-19 patients with severe pneumonia. Severe pneumonia is a type of pneumonia that is characterized by inflammation of the lungs, difficulty breathing, and low oxygen levels in the blood. It can be a life-threatening condition. 

This was the most exposed group in the study",17,89,4 weeks,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,Signature 1,Table 3,24 October 2023,Fortunehechi,"Fortunehechi,Folakunmi",MaAsLin2 differentially abundant taxa analysis in COVID patients with pneumonia,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium,2|201174|1760|85006|2805590|125287,Complete,Folakunmi
bsdb:828/3/1,Study 828,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I , Di Camillo B",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 3,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,"COVID-19,Respiratory failure requiring assisted ventilation","MONDO:0100096,HP:0004887",Non-intubated,Intubated,Patients unable to provide enough oxygen to their body.,0,18,4 weeks,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,Signature 1,Table 3,17 February 2024,Folakunmi,Folakunmi,MaAsLin2 differentially abundant taxa analysis in COVID patients with and without intubation,increased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella|s__Jonquetella anthropi,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium|s__Ornithinimicrobium pekingense,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium",2|508458|649775|649776|3029088|428711|428712;2|201174|1760|85006|2805590|125287|384677;2|1239|91061|186826|81852|1350;2|201174|1760|85006|2805590|125287,Complete,Folakunmi
bsdb:828/4/NA,Study 828,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I , Di Camillo B",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 4,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,Response to supplemental oxygen,EFO:0009796,No Supplemental O2,Supplemental O2 (High/Low),Patients in need of supply of oxygen to help them breathe better and keep their blood oxygen levels up.,0,72,4 weeks,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:829/1/1,Study 829,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth EA, Williams JE, Pace RM, Lane AA, Gartstein M, McGuire MA, McGuire MK , Meehan CL","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 1,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Total Time Breastfeeding,Low Total Time Breastfeeding,Breastfeeding pattern,28,10,Any antibiotics consumed by or administered to the mother or infant in the past 30 days,16S,123,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3A,12 October 2023,Peace Sandy,Peace Sandy,"Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Rugamonas",2|201174|1760|85006|85023|110934;2|201174|1760|85004|31953|1678;2|976|117747|200666|84566|84567;2|1224|1236|135614|32033|40323;2|1224|28216|80840|75682|212744,Complete,Chloe
bsdb:829/2/1,Study 829,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth EA, Williams JE, Pace RM, Lane AA, Gartstein M, McGuire MA, McGuire MK , Meehan CL","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 2,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Total Time Breastfeeding,High Total Time Breastfeeding,Breastfeeding pattern,28,8,Any antibiotics consumed by or administered to the mother or infant in the past 30 days,16S,123,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3A,12 October 2023,Peace Sandy,Peace Sandy,"Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Rugamonas",2|201174|1760|85006|85023|110934;2|201174|1760|85004|31953|1678;2|976|117747|200666|84566|84567;2|1224|1236|135614|32033|40323;2|1224|28216|80840|75682|212744,Complete,Chloe
bsdb:829/3/1,Study 829,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth EA, Williams JE, Pace RM, Lane AA, Gartstein M, McGuire MA, McGuire MK , Meehan CL","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 3,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,Low Breastfeeding Bouts,Breastfeeding pattern,30,10,Any antibiotics consumed by or administered to the mother or infant in the past 30 days,16S,123,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3B,12 October 2023,Peace Sandy,Peace Sandy,"Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus",2|201174|1760|85004|31953|1678;2|201174|1760|85006|1268|1269,Complete,Chloe
bsdb:829/3/2,Study 829,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth EA, Williams JE, Pace RM, Lane AA, Gartstein M, McGuire MA, McGuire MK , Meehan CL","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 3,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,Low Breastfeeding Bouts,Breastfeeding pattern,30,10,Any antibiotics consumed by or administered to the mother or infant in the past 30 days,16S,123,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3B,12 October 2023,Peace Sandy,Peace Sandy,"Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acidocella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",2|976|117747|200666|84566|84567;2|1224|28211|204441|433|50709;2|1224|28216|80840|506|222,Complete,Chloe
bsdb:829/4/1,Study 829,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth EA, Williams JE, Pace RM, Lane AA, Gartstein M, McGuire MA, McGuire MK , Meehan CL","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 4,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,High Breastfeeding Bouts,Breastfeeding pattern,30,6,Any antibiotics consumed by or administered to the mother or infant in the past 30 days,16S,123,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3B,12 October 2023,Peace Sandy,Peace Sandy,"Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Chloe
bsdb:829/4/2,Study 829,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth EA, Williams JE, Pace RM, Lane AA, Gartstein M, McGuire MA, McGuire MK , Meehan CL","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 4,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,High Breastfeeding Bouts,Breastfeeding pattern,30,6,Any antibiotics consumed by or administered to the mother or infant in the past 30 days,16S,123,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3B,12 October 2023,Peace Sandy,Peace Sandy,"Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acidocella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",2|201174|1760|85006|1268|1269;2|976|117747|200666|84566|84567;2|1224|28211|204441|433|50709;2|1224|28216|80840|506|222,Complete,Chloe
bsdb:830/1/2,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,female patients with dry eye disease,male patients with dry eye disease,male patients with dry eye disease,22,25,90 days prior to enrollment,WMS,NA,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 2,Supp fig 2c and 2d,14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Sex-related differences of the conjunctival microbiota in patients with dry eye.,decreased,"k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus sp. NW-56,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1297|188787|118964|183710|1298|2080419;2|1224|1236|72274|135621|286|287,Complete,ChiomaBlessing
bsdb:830/2/1,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 2,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,Healthy female,Healthy male,Healthy male without dry eye disease,22,25,90 days prior to enrollment,WMS,NA,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,increased,NA,NA,NA,NA,Signature 1,"Supp fig 2c and 2d, Figure 3D",14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Sex-related differences of the conjunctival microbiota in healthy individuals.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",2|1224|1236|72274|135621|286|287;2759|4751|5204|1538075|162474|742845|55193|76773,Complete,ChiomaBlessing
bsdb:830/3/1,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 3,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Aqueous tear deficient (ATD) DED,Meibomian Gland Dysfunction (MGD) DED,Patients with MGD DED,14,19,90 days prior to study enrollment,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Supp. fig 5,14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and meibomian gland dysfunction (MGD),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis",2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|29388,Complete,ChiomaBlessing
bsdb:830/3/2,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 3,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Aqueous tear deficient (ATD) DED,Meibomian Gland Dysfunction (MGD) DED,Patients with MGD DED,14,19,90 days prior to study enrollment,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Supp. fig 5,14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and meibomian gland dysfunction (MGD),decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,2|1239|91061|1385|90964|1279|1290,Complete,ChiomaBlessing
bsdb:830/4/1,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 4,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Aqueous tear deficient (ATD) DED,Mixed DED,Patients with mixed type diagnosis of DED (more closely related to MGD than ATD),14,35,90 days prior to study enrollment,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,"age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Supp fig 5,15 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and mixed dry eye,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii",2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|29388;2|1239|91061|1385|90964|1279|29382,Complete,ChiomaBlessing
bsdb:830/5/NA,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 5,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction (MGD) DED,Mixed DED,Patients with mixed type diagnosis of DED (more closely related to MGD than ATD),19,35,90 days prior to study enrollment,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:830/6/1,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 6,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,Patients with Dry eye disease,48,47,90 days prior to study enrollment,WMS,NA,Illumina,MaAsLin2,0.05,NA,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Supp table 4,3 December 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Comparison between dry eye group and healthy group showing species with polarized abundance (decreased abundance) in dry eye samples,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. WCHA45,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium taklimakanense,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus ficus,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus sp. NW-56,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter|s__Janibacter melonis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Micropruina|s__Micropruina glycogenica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus yeei,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|1224|1236|2887326|468|469|40216;2|1224|1236|2887326|468|469|2004644;2|1224|1236|135625|712|416916|739;2|976|117743|200644|2762318|59732|1871047;2|976|117743|200644|2762318|59732|536441;2|201174|1760|85007|1653|1716|43768;2|1297|188787|118964|183710|1298|317577;2|1297|188787|118964|183710|1298|2080419;2|32066|203490|203491|203492|848|851;2|201174|1760|85006|85021|53457|262209;2|1239|91061|186826|33958|1578|147802;2759|4751|5204|1538075|162474|742845|55193|76773;2|201174|1760|85009|85015|116071|75385;2|1224|28216|206351|481|482|28449;2|1224|28211|204455|31989|265|147645;2|1239|1737404|1737405|1570339|543311|33033;2|201174|1760|85006|1268|32207|43675;2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|1290;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|712633;2|1239|909932|1843489|31977|29465|29466;2|201174|1760|85007|1653|1716,Complete,ChiomaBlessing
bsdb:830/7/1,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 7,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonATD,Dry Eye- ATD,Patients with Dry eye disease characterized as aqueous tear deficient,54,14,90 days prior to study enrollment,WMS,NA,Illumina,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4b,29 December 2023,Mary Bearkland,Mary Bearkland,"B) Model coefficients of top-ranked species associated with either ATD or non-ATD dry eye (p < 0.1, coefficient >0.2)",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter|s__Janibacter melonis,2|201174|1760|85006|85021|53457|262209,Complete,Folakunmi
bsdb:830/7/2,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 7,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonATD,Dry Eye- ATD,Patients with Dry eye disease characterized as aqueous tear deficient,54,14,90 days prior to study enrollment,WMS,NA,Illumina,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4b,29 December 2023,Mary Bearkland,Mary Bearkland,"Figure 4b) Model coefficients of top-ranked species associated with either ATD or non-ATD dry eye (p < 0.1, coefficient >0.2) (",decreased,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,2|976|117743|200644|49546|1016|1017,Complete,Folakunmi
bsdb:830/8/1,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 8,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonMGD,Dry Eye- MGD,Patients with Dry eye disease characterized as meibomian gland disorder,49,19,90 days prior to study enrollment,WMS,NA,Illumina,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,29 December 2023,Mary Bearkland,Mary Bearkland,"Model coefficients of
top-ranked species associated with either MGD or non-MGD dry eye (p < 0.1, coefficient >0.2)",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. WCHA45,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus sp. NW-56,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii",2|1224|1236|2887326|468|469|2004644;2|1297|188787|118964|183710|1298|2080419;2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|29388;2|1239|91061|1385|90964|1279|29382,Complete,Folakunmi
bsdb:830/8/2,Study 830,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L , Wen X",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 8,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonMGD,Dry Eye- MGD,Patients with Dry eye disease characterized as meibomian gland disorder,49,19,90 days prior to study enrollment,WMS,NA,Illumina,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4c,29 December 2023,Mary Bearkland,Mary Bearkland,"Model coefficients of
top-ranked species associated with either MGD or non-MGD dry eye (p < 0.1, coefficient >0.2)",decreased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,2|201174|84998|84999|84107|102106|74426,Complete,Folakunmi
bsdb:831/1/1,Study 831,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T, Choi Y, Pagani JL, Kritikos A, Papadimitriou-Olivgeris M, Méan M, Scherz V, Opota O, Greub G, Guery B , Bertelli C",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-Covid 19 Patients - pneumonia patients,COVID-19 Patients,Patients admitted for COVID-19,19,57,3 Months,16S,34,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Fig. 1C,15 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy","C, D Differential abundance analysis and distance-based redundancy analysis (db-RDA) in COVID-19 and non-COVID-19 patients. COVID-19 and non-COVID-19 pneumonia patients were compared to evaluate the COVID-19 effect. C Differentially abundant taxa identified by linear discriminant analysis effect size (LEfSe) at genus level. The results with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented as a bar plot (**p < 0.01, ***p < 0.001).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium",2|976|200643|171549|815|816;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1905344,Complete,Peace Sandy
bsdb:831/1/2,Study 831,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T, Choi Y, Pagani JL, Kritikos A, Papadimitriou-Olivgeris M, Méan M, Scherz V, Opota O, Greub G, Guery B , Bertelli C",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-Covid 19 Patients - pneumonia patients,COVID-19 Patients,Patients admitted for COVID-19,19,57,3 Months,16S,34,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Fig. 1c,15 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy","C, D Differential abundance analysis and distance-based redundancy analysis (db-RDA) in COVID-19 and non-COVID-19 patients. COVID-19 and non-COVID-19 pneumonia patients were compared to evaluate the COVID-19 effect. C Differentially abundant taxa identified by linear discriminant analysis effect size (LEfSe) at genus level. The results with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented as a bar plot (**p < 0.01, ***p < 0.001).",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus",2|1239|186801|186802|1686313;2|1239|1737404|1737405|1570339|150022;2|976|200643|171549|171551|836;2|201174|1760|85007|1653|1716;2|1224|28216|80840|995019|40544;2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|909928,Complete,Peace Sandy
bsdb:831/2/1,Study 831,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T, Choi Y, Pagani JL, Kritikos A, Papadimitriou-Olivgeris M, Méan M, Scherz V, Opota O, Greub G, Guery B , Bertelli C",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients - Non-Ventilated,COVID-19 patients - Ventilated,COVID-19 patients in Intensive Care Unit [ICU] - Ventilated,43,14,3 Months,16S,34,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 2 A,16 October 2023,Tolulopeo,"Tolulopeo,Davvve,Peace Sandy","Impact of COVID-19 severity on the taxa composition and longitudinal changes of the gut microbiota. A, B Differential abundance analysis and db-RDA analysis in ventilated and non-ventilated COVID-19 patients. A Genera differentially abundant among the two groups were identified by a complex model including ventilation, antibiotics and timepoint with longitudinal sampling correction using negative binomial and zero-inflated mixed model (NBZIMM). The taxa with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented in the bar plot (**p < 0.01, ***p < 0.001).",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|29547|3031852|213849|72294|194;2|1239|186801|186802|216572|1263;2|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:831/2/2,Study 831,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T, Choi Y, Pagani JL, Kritikos A, Papadimitriou-Olivgeris M, Méan M, Scherz V, Opota O, Greub G, Guery B , Bertelli C",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients - Non-Ventilated,COVID-19 patients - Ventilated,COVID-19 patients in Intensive Care Unit [ICU] - Ventilated,43,14,3 Months,16S,34,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 2 A,16 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy","Impact of COVID-19 severity on the taxa composition and longitudinal changes of the gut microbiota. A, B Differential abundance analysis and db-RDA analysis in ventilated and non-ventilated COVID-19 patients. A Genera differentially abundant among the two groups were identified by a complex model including ventilation, antibiotics and timepoint with longitudinal sampling correction using negative binomial and zero-inflated mixed model (NBZIMM). The taxa with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented in the bar plot (**p < 0.01, ***p < 0.001).",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,Peace Sandy
bsdb:832/1/1,Study 832,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J, Börschel CS, Ortega-Alonso A, Markó L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna AS, Forslund SK, Knight R, Lahti L, Niiranen T , Schnabel RB",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Prevalent Atrial Fibrillation (AF),Individuals with Prevalent Atrial Fibrillation (AF),Participants with prevalent atrial fibrillation. Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations,6647,116,None.,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,physical activity,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Table 2",15 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing",Abundant genera in individuals with Prevalent Atrial Fibrillation (AF) compared to individuals without Prevalent AF,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera",2|1239|186801|3085636|186803|1432051;2|201174|84998|84999|84107|1472762;2|1224|1236|91347|543|547;2|1224|1236|91347|543|579,Complete,ChiomaBlessing
bsdb:832/1/2,Study 832,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J, Börschel CS, Ortega-Alonso A, Markó L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna AS, Forslund SK, Knight R, Lahti L, Niiranen T , Schnabel RB",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Prevalent Atrial Fibrillation (AF),Individuals with Prevalent Atrial Fibrillation (AF),Participants with prevalent atrial fibrillation. Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations,6647,116,None.,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,physical activity,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Table 2",15 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing",Abundant genera in individuals with Prevalent Atrial Fibrillation (AF) compared to individuals without Prevalent AF,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|1573535;2|976|200643|171549|2005525|375288;2|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:832/2/1,Study 832,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J, Börschel CS, Ortega-Alonso A, Markó L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna AS, Forslund SK, Knight R, Lahti L, Niiranen T , Schnabel RB",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Incident Atrial Fibrillation (AF),Individuals with Incident Atrial Fibrillation (AF),"Incident AF refers to new cases of atrial fibrillation that occurred during the follow-up period of the study, among individuals who did not have a history of atrial fibrillation at baseline.",6647,539,None.,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Table 3",17 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing",Abundant genera in individuals with Incident Atrial Fibrillation (AF) compared to individuals without Incident AF,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|1472762;2|1239|91061|186826|1300|1357;2|1239|909932|909929|1843491|52225;2|1239|186801|3085636|186803|1769710,Complete,ChiomaBlessing
bsdb:832/2/2,Study 832,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J, Börschel CS, Ortega-Alonso A, Markó L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna AS, Forslund SK, Knight R, Lahti L, Niiranen T , Schnabel RB",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Incident Atrial Fibrillation (AF),Individuals with Incident Atrial Fibrillation (AF),"Incident AF refers to new cases of atrial fibrillation that occurred during the follow-up period of the study, among individuals who did not have a history of atrial fibrillation at baseline.",6647,539,None.,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Table 3",17 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing",Abundant genera in individuals with Incident Atrial Fibrillation (AF) compared to individuals without Incident AF,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides",2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506577;2|976|200643|171549|171551|1635148,Complete,ChiomaBlessing
bsdb:832/3/1,Study 832,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J, Börschel CS, Ortega-Alonso A, Markó L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna AS, Forslund SK, Knight R, Lahti L, Niiranen T , Schnabel RB",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,NA,Individuals with Incident Atrial Fibrillation (AF),"Incident AF refers to new cases of atrial fibrillation that occurred during the follow-up period of the study, among individuals who did not have a history of atrial fibrillation at baseline.",NA,6923,NA,WMS,NA,Illumina,Cox Proportional-Hazards Regression,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,diabetes mellitus,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,29 October 2023,Iram jamshed,Iram jamshed,Differential abundance of microorganism in incident atrial fibrillation in Cox regression analyses considering the hazard ratio.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Sanguibacteraceae|g__Sanguibacter",2|976|200643|171549|171550|239759;2|976|200643|171549|2005519|397864;2|1239|91061|186826|81852|1350;2|976|200643|171549|1853231|283168;2|976|200643|171549|171552|577309;2|201174|1760|85006|145360|60919,Complete,NA
bsdb:832/3/2,Study 832,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J, Börschel CS, Ortega-Alonso A, Markó L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna AS, Forslund SK, Knight R, Lahti L, Niiranen T , Schnabel RB",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,NA,Individuals with Incident Atrial Fibrillation (AF),"Incident AF refers to new cases of atrial fibrillation that occurred during the follow-up period of the study, among individuals who did not have a history of atrial fibrillation at baseline.",NA,6923,NA,WMS,NA,Illumina,Cox Proportional-Hazards Regression,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,diabetes mellitus,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,29 October 2023,Iram jamshed,Iram jamshed,Differential abundance of microorganism in incident atrial fibrillation in Cox regression analyses considering the hazard ratio.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|1472762;2|1239|526524|526525|128827|123375,Complete,NA
bsdb:833/1/1,Study 833,case-control,36624530,10.1186/s40168-022-01450-5,NA,"Jacobs JP, Lagishetty V, Hauer MC, Labus JS, Dong TS, Toma R, Vuyisich M, Naliboff BD, Lackner JM, Gupta A, Tillisch K , Mayer EA",Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes,Microbiome,2023,"Biomarkers, Bowel habit subtypes, Irritable bowel syndrome, Metabolomics, Metatranscriptomics, Microbiome, Multi-omics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,Irritable Bowel Syndrome,Patients diagnosed with Irritable Bowel Syndrome via Rome III criteria,177,318,12 weeks,16S,4,Illumina,Random Forest Analysis,0.05,TRUE,NA,NA,"age,anxiety disorder,body mass index,diet,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2B,15 October 2023,Chisom,Chisom,"Differentially abundant bacterial taxa (q < 0.25) between IBS subjects and HC were identified in multivariate models adjusting for batch, age, sex, race/ethnicity, BMI, dietary category, and HAD-A. The result of assessing the taxonomic profiles of the metatranscriptome.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae",2|201174|1760|2037|2049|1654;2|976|200643|171549|815|816|626930;2|1239|186801|3085636|186803|572511|53443;2|1239|186801|3085636|186803|43996|43997;2|201174|84998|1643822|1643826|84111|84112;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|815|909656|357276;2|976|200643|171549|171552|2974257|386414;2|1239|186801|3085636|186803|1506553|89153,Complete,Peace Sandy
bsdb:833/1/2,Study 833,case-control,36624530,10.1186/s40168-022-01450-5,NA,"Jacobs JP, Lagishetty V, Hauer MC, Labus JS, Dong TS, Toma R, Vuyisich M, Naliboff BD, Lackner JM, Gupta A, Tillisch K , Mayer EA",Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes,Microbiome,2023,"Biomarkers, Bowel habit subtypes, Irritable bowel syndrome, Metabolomics, Metatranscriptomics, Microbiome, Multi-omics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,Irritable Bowel Syndrome,Patients diagnosed with Irritable Bowel Syndrome via Rome III criteria,177,318,12 weeks,16S,4,Illumina,Random Forest Analysis,0.05,TRUE,NA,NA,"age,anxiety disorder,body mass index,diet,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2B,15 October 2023,Chisom,Chisom,"Differentially abundant bacterial taxa (q < 0.25) between IBS subjects and HC were identified in multivariate models adjusting for batch, age, sex, race/ethnicity, BMI, dietary category, and HAD-A. The result of assessing the taxonomic profiles of the metatranscriptome.",decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae",2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|841|360807;2|201174|1760|85004|31953|1678|28025;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|376804,Complete,Peace Sandy
bsdb:834/1/1,Study 834,case-control,37737154,10.1186/s12866-023-03020-7,NA,"Luan M, Niu M, Yang P, Han D, Zhang Y, Li W, He Q, Zhao Y, Mao B, Chen J, Mou K , Li P",Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo,BMC microbiology,2023,"Gut microbiota, Metagenomic sequencing, Vitiligo",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Vitiligo,EFO:0004208,Healthy controls,Non-segmental Vitiligo patients,"Individuals characterized by the progressive loss of skin pigmentation in various areas of the body, resulting in depigmented white patches that is mostly widespread in distribution.",25,25,3 months,WMS,NA,BGISEQ-500 Sequencing,"Mann-Whitney (Wilcoxon),LEfSe",0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Figure 2b, 3",16 October 2023,Deacme,Deacme,Increased abundant species in Non-segmental Vitiligo patients,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OF09-6,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium|s__Massilioclostridium coli,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 348,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis",2|1239|186801|3085636|186803|1766253|39491;2|976|200643|171549|171550|239759|28117;2|1239|526524|526525|128827|2749846|31971;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|820;2|976|200643|171549|2005519|397864|487174;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|418240;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|3085636|186803|2293831;2|1239|186801|186802|31979|1935927|1870991;2|1239|909932|909929|1843491|158846|437897;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|841|301302;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40518;2|95818|671231;2|1239|186801|3085636|186803|2316020|33039;2|1239|909932|1843489|31977|39948|2582419,Complete,Chloe
bsdb:834/1/2,Study 834,case-control,37737154,10.1186/s12866-023-03020-7,NA,"Luan M, Niu M, Yang P, Han D, Zhang Y, Li W, He Q, Zhao Y, Mao B, Chen J, Mou K , Li P",Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo,BMC microbiology,2023,"Gut microbiota, Metagenomic sequencing, Vitiligo",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Vitiligo,EFO:0004208,Healthy controls,Non-segmental Vitiligo patients,"Individuals characterized by the progressive loss of skin pigmentation in various areas of the body, resulting in depigmented white patches that is mostly widespread in distribution.",25,25,3 months,WMS,NA,BGISEQ-500 Sequencing,"Mann-Whitney (Wilcoxon),LEfSe",0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Figure 2d, 3",16 October 2023,Deacme,Deacme,Decreased abundant species in non-segmental Vitiligo patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM58,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella|s__Allisonella histaminiformans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides bouchesdurhonensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF20-17LB,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__Eggerthellaceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Isoptericola|s__Isoptericola variabilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella|s__Trueperella pyogenes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neobittarella|s__Neobittarella massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",2|201174|1760|2037|2049|1654|1105030;2|1239|909932|1843489|31977|209879|209880;2|976|200643|171549|815|816|1841855;2|976|200643|171549|815|816|28111;2|1239|186801|2044939;2|1239|186801|186802|31979|1485|2292205;2|976|200643|171549|2005519|1348911|1501392;2|1239|186801|3085636|186803|33042|410072;2|200940|3031449|213115|194924|872|876;2|1239|186801|3085636|186803|189330|88431;2|201174|84998|1643822|1643826|1972561;2|201174|1760|85006|85017|254250|139208;2|1239|186801|186802|216572|2485925;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|171550|2049048;2|1239|186801|3085636|186803|1769710|1653434;2|201174|1760|2037|2049|1069494|1661;2|1239|909932|1843489|31977|29465|423477;2|1239|91061|186826|1300|1301|1308;2|1239|186801|3085636|186803|2005359|290055;2|1239|186801|3085636|186803|2005355|1912855;2|976|200643|171549|171550|239759|1288121;2|976|200643|171549|1853231|574697|2093856;2|1239|186801|186802|216572|2126544|2041842;2|976|200643|171549|171550|239759|1470347;2|1239|526524|526525|128827|1573535|1735,Complete,Chloe
bsdb:835/1/1,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 1,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913","Response to vaccine,Timepoint","EFO:0004645,EFO:0000724",Mothers at pre-vaccination timepoint,Mothers at post vaccination timepoints,"Breastfeeding mothers at post vaccination timepoints; one week post-first dose, one week post second-dose, one month post-second dose.",44,44,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1g,22 October 2023,Folakunmi,Folakunmi,"The most differentially abundant taxa in mothers throughout all post-vaccination timepoints; at one week post-first dose, one week post-second dose and one month post-second dose.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas|s__Roseomonas gilardii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae",2|1224|1236|2887326|468|469|108980;2|1224|28211|204441|433|125216|257708;2|1224|28211|204458|76892|41275;2|201174|1760|85007|85026|2053;2|1224|28211|204455|31989,Complete,ChiomaBlessing
bsdb:835/1/2,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 1,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913","Response to vaccine,Timepoint","EFO:0004645,EFO:0000724",Mothers at pre-vaccination timepoint,Mothers at post vaccination timepoints,"Breastfeeding mothers at post vaccination timepoints; one week post-first dose, one week post second-dose, one month post-second dose.",44,44,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 1g,22 October 2023,Folakunmi,Folakunmi,"The most differentially abundant taxa in mothers throughout all post-vaccination timepoints; at one week post-first dose, one week post-second dose and one month post-second dose.",decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|29547|3031852|213849|72293|209|59617;2|1239|526524|526525|128827|174708;2|976|200643|171549|2005473;2|1224|28216|80840|119060|48736;2|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:835/2/1,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 2,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at Baseline,High IgA mothers at Baseline,Breastfeeding mothers with high IgA at baseline,25,18,None,16S,34,Illumina,LEfSe,0.004,FALSE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure 2d,22 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Taxonomic differences in baseline microbiota between high- and low-IgA subjects.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Endobacter|s__Endobacter medicaginis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas balearica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",2|201174|1760|2037|2049|1654|461393;2|1239;2|201174|1760|85009|31957|1912216|33011;2|1224|28211|204441|433|1649268|1181271;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482|495;2|976|200643|171549|171552|838|470565;2|1239|186801|186802|216572|1263|40519;2|1224|1236|72274|135621|2901164|74829;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|1236|135622|72275|111142;2|201174|1760|85009|31957|2801844;2|1224|28216|80840|506|359336;2|1239|186801|3085656|3085657|2039302;2|1224|28216|206351|481|482;2|1239|186801|186802|216572;2|1239|186801|3085636|186803|1213720;2|1224|28216|80840|995019|40544;2|1239|186801|3082720|186804|1505652,Complete,ChiomaBlessing
bsdb:835/2/2,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 2,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at Baseline,High IgA mothers at Baseline,Breastfeeding mothers with high IgA at baseline,25,18,None,16S,34,Illumina,LEfSe,0.004,FALSE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure 2d,15 February 2024,ChiomaBlessing,ChiomaBlessing,Taxonomic differences in baseline microbiota between high- and low-IgA subjects.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas",2|201174|1760|85007|1653|1716|161879;2|1224|1236|2887326|468|469;2|1224|28211|204458|76892|41275,Complete,ChiomaBlessing
bsdb:835/3/1,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 3,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at one week post-second dose,High IgA mothers at one week post-second dose,Breastfeeding mothers with high IgA at one week after receiving the second dose of the SARS-CoV-2 mRNA vaccine (BNT162b2).,25,18,None,16S,34,Illumina,LEfSe,0.004,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3d,22 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Taxonomic differences in microbiota one week post-second dose between high- and low-IgA subjects,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Candidatus Marinarcus|s__Candidatus Marinarcus aquaticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasuis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Gemmobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Neptunomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",2|201174|1760|85004|31953|1678|1681;2|29547|3031852|213849|2808963|2321204|2044504;2|1239|91061|186826|1300|1301|1501662;2|1239|909932|1843488|909930|904;2|201174|1760|85004|31953|1678;2|201174|1760|85007|1653|1716;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730;2|1224|28211|204455|31989|204456;2|1239|526524|526525|128827|1573535;2|201174|1760|85006|85023|55968;2|1224|1236|135619|135620|75687;2|1224|28211|204455|31989|1060;2|1239|186801|186802|216572|292632;2|1224|1236|135623|641|662,Complete,ChiomaBlessing
bsdb:835/3/2,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 3,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at one week post-second dose,High IgA mothers at one week post-second dose,Breastfeeding mothers with high IgA at one week after receiving the second dose of the SARS-CoV-2 mRNA vaccine (BNT162b2).,25,18,None,16S,34,Illumina,LEfSe,0.004,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3d,15 February 2024,ChiomaBlessing,ChiomaBlessing,Taxonomic differences in microbiota one week post-second dose between high- and low-IgA subjects,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas",2|1224|1236|2887326|468|469|487316;2|1224|28211|204458|76892|41275,Complete,ChiomaBlessing
bsdb:835/4/1,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 4,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-first dose,Breastfeeding mothers at one week after receiving the first dose of BNT162b2 vaccine.,44,44,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,supplementary table 3,24 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",differential abundance of mothers one week after first dose of BNT162b2 when compared to baseline.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus|s__Caldibacillus thermoamylovorans,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter|s__Empedobacter brevis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas|s__Roseomonas gilardii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI001,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",2|1224|1236|2887326|468|469|40216;2|1224|1236|2887326|468|469|487316;2|1224|1236|2887326|468|469|108980;2|1239|91061|1385|186817|1276290|35841;2|976|117743|200644|2762318|59734|247;2|1239|186801|186802|186806|1730|39496;2|1224|1236|135625|712|724|726;2|1224|1236|135625|712|724|735;2|1224|28211|204441|433|125216|257708;2|1224|1236|135625|712|713;2|1239|91061|1385|186817|150247;2|1239|91061|1385|186817|1386;2|976|117743|200644|2762318|59735;2|1224|28211|204458|76892|41275;2|1224|28216|80840|75682|75654;2|976|117743|200644|2762318|59734;2|1224|28211|356|212791;2|976|117743|200644|49546|237;2|1224|28216|80840|75682|29580;2|201174|1760|85006|85023|33882;2|1224|28211|204455|31989;2|1224|1236|91347|1903414|586;2|201174|1760|85006|1268|1742993;2|1224|1236|135622|267890|22;2|1224|28211|204457|41297;2|1224|28211|204457|41297|13687;2|1239|186801|186802|1780378;2|201174|1760|85007|85026|2053;2|976|117747|200666|84566|28453,Complete,ChiomaBlessing
bsdb:835/4/2,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 4,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-first dose,Breastfeeding mothers at one week after receiving the first dose of BNT162b2 vaccine.,44,44,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Supplementary Table 3,15 February 2024,ChiomaBlessing,ChiomaBlessing,Differential abundance of mothers one week after first dose of BNT162b2 when compared to baseline.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1224|1236|2887326|468|469|470;2|1239|91061|186826|33958|1578|151781;2|1239|526524|526525|128827|174708;2|1239|91061;2|1224|28216|80840|80864;2|1239|186801|3085636|186803|1407607;2|976|200643|171549|2005525|375288;2|1224|28216|80840|119060|48736;2|1239|526524|526525|2810281|191303;2|976|200643|171549|2005473,Complete,ChiomaBlessing
bsdb:835/5/1,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 5,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-second dose,Breastfeeding mothers at one week post-second dose of BNT162b2 vaccine.,44,43,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,supplementary table 3,24 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing",differential abundance of mothers at one week post second dose of BNT162b2 when compared to baseline.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas olei,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hominis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella atlantae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella porci,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus macerans,k__Bacteria|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae|g__Peredibacter|s__Peredibacter starrii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas|s__Roseomonas gilardii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Gemmobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Nautella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Neptunomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__uncultured Paraburkholderia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Pseudarcobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter",2|1224|1236|2887326|468|469|470;2|1224|1236|2887326|468|469|487316;2|1224|1236|2887326|468|469|108980;2|1224|28211|204458|76892|41275|657642;2|976|117743|200644|2762318|2782229|420404;2|1224|1236|2887326|468|475|34059;2|1224|1236|2887326|468|475|1288392;2|1239|91061|1385|186822|44249|44252;2|3018035|3031419|2024979|263369|263370|28202;2|976|200643|171549|171552|838|28132;2|1224|28211|204441|433|125216|257708;2|1224|1236|2887326|468|469;2|1224|1236|135625|712|713;2|1224|28211|204458|76892|41275;2|976|1853228|1853229|563835;2|1224|28211|204455|31989|204456;2|201174|1760|85007|85026|2053;2|1224|1236|91347|543|570;2|32066|203490|203491|1129771|32067;2|1239|909932|909929|1843491|158846;2|1224|28211|204455|2854170|481445;2|1224|1236|135619|135620|75687;2|1224|28211|356|118882|528;2|1224|28211|204455|31989;2|1239|1737404|1737405|1570339|162289;2|1224|1236|91347|1903411|613;2|1224|28216|206351|1499392|57739;2|1239|186801|244328;2|1224|28216|80840|119060|1822464|1822466;2|1239|186801|186802|1898207;2|1239|186801|186802|186806|1730;2|29547|3031852|213849|2808963|2321113;2|1224|28211|204457|2820280|56358,Complete,ChiomaBlessing
bsdb:835/5/2,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 5,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-second dose,Breastfeeding mothers at one week post-second dose of BNT162b2 vaccine.,44,43,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Table 3,15 February 2024,ChiomaBlessing,ChiomaBlessing,Differential abundance of mothers one week after second dose of BNT162b2 when compared to baseline.,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus nagyae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter russicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus aviarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas|s__Pseudoxanthomonas kaohsiungensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Myxococcota|o__Haliangiales|f__Kofleriaceae|g__Haliangium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Kurthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__uncultured Odoribacter sp.",2|1239|1737404|1737405|1570339|165779|1755241;2|1239|1737404|1737405|1570339|165779|54007;2|201174|1760|85006|1268|1663|172040;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|216572;2|201174|1760|85009|31957|1912216|33011;2|29547|3031852|213849|72293|209|59617;2|1239|91061|186826|33958|2767887|1606;2|1224|1236|135614|32033|83618|283923;2|201174|1760|85006|1268|32207|1885016;2|1239|186801|186802|186806|1730;2|74201|203494|48461|1647988|239934;2|1224|28216|80840|506|507;2|1239|526524|526525|128827|174708;2|1239|91061;2|976|200643|171549|815|816;2|1224|28216|80840|506|359336;2|1239;2|1239|186801|186802|1980681;2|201174|84998|84999|84107;2|200940|3031449|213115|194924;2|1239|526524|526525|128827|1937008;2|1239|186801|186802|216572|216851;2|2818505|3031714|224464|162027;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|1239|91061|1385|186818|1649;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005473;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|186801|3082720|186804;2|976|200643|171549|171552;2|1239|909932|1843489|31977|1567;2|1224|28216|80840|119060|48736;2|1239|186801|3082720|186804|1501226;2|1224|28216|80840|995019|40544;2|203691|203692|136|2845253|157;2|1239|526524|526525|2810281|191303;2|976|200643|171549|1853231|283168|876416,Complete,ChiomaBlessing
bsdb:835/6/1,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 6,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one month post second-dose,Breastfeeding mothers at one month post second-dose of BNT162b2 vaccine.,44,44,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,supplementary table 3,24 October 2023,Folakunmi,"Folakunmi,Chinelsy,ChiomaBlessing",differential abundance of mothers at one month post second dose of BNT162b2 when compared to baseline.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hominis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinobacterium|s__Marinobacterium marisflavi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella atlantae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Pseudoroseomonas|s__Pseudoroseomonas aestuarii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas|s__Roseomonas gilardii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas acidaminiphila,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Aeromicrobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Formosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Pseudarcobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",2|1224|1236|2887326|468|469|108980;2|29547|3031852|213849|72294|194|204;2|1239|186801|186802|1898207;2|1239|526524|526525|128827|1937008|1862672;2|976|117743|200644|2762318|2782229|420404;2|1224|1236|135619|135620|48075|434084;2|1224|1236|2887326|468|475|34059;2|1224|28216|206351|481|482|495;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|28132;2|1224|28211|204441|433|2870717|568898;2|1224|28211|204441|433|125216|257708;2|1224|1236|135614|32033|40323|128780;2|1224|28216|80840|80864|12916;2|201174|1760|85009|85015|2040;2|201174|84998|84999|1643824|1380;2|1224|28211|204458|76892|41275;2|201174|1760|85007|1653;2|201174|1760|85006|145357;2|976|117743|200644|49546|225842;2|201174|1760|85007|85026|2053;2|1239|186801|3085636|186803|1164882;2|1224|28211|356|119045|186650;2|1224|1236|2887326|468|475;2|1224|28216|206351|481;2|1224|28211|204457|41297|165696;2|1224|28211|204455|31989;2|1224|1236|135625|712;2|1239|91061|186826|33958|1253;2|1239|91061|1385|186818;2|29547|3031852|213849|2808963|2321113;2|1224|28211|356|82115;2|1224|1236|91347|1903411|613;2|1224|28211|204441|2829815|204447;2|1224|28211|204457|41297|13687;2|1224|28216|80840|114248;2|1239|186801|244328,Complete,ChiomaBlessing
bsdb:835/6/2,Study 835,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HK, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM , Tun HM",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 6,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one month post second-dose,Breastfeeding mothers at one month post second-dose of BNT162b2 vaccine.,44,44,None,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Table 3,16 February 2024,ChiomaBlessing,"ChiomaBlessing,Joan Chuks",Differential abundance of mothers at one month post second dose of BNT162b2 when compared to baseline.,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium|s__Aquabacterium citratiphilum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter russicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas aquatica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus aviarius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas|s__Pseudoxanthomonas kaohsiungensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae|g__Bdellovibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Flaviflexus,k__Bacteria|p__Myxococcota|o__Haliangiales|f__Kofleriaceae|g__Haliangium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__uncultured Odoribacter sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__uncultured Muribaculaceae bacterium",2|1239|1737404|1737405|1570339|165779|54007;2|1224|28216|80840|92793|70582;2|201174|1760|85006|1268|1663|172040;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|817;2|1239|186801|186802|31979|1898204;2|1224|28216|80840|80864|283|225991;2|1239|91061|186826|81852|1350|44008;2|29547|3031852|213849|72293|209|59617;2|32066|203490|203491|1129771|32067|104608;2|1239|91061|186826|33958|2767887|1606;2|976|200643|171549|815|909656|310298;2|1224|1236|135614|32033|83618|283923;2|201174|1760|85006|1268|32207|1885016;2|1239|186801|186802|216572|1263|1265;2|1239|91061|186826|186827|1375;2|74201|203494|48461|1647988|239934;2|1224|28216|80840|506|507;2|976|200643|171549|171550|239759;2|1239|526524|526525|128827|174708;2|1239|1737404|1737405|1570339|165779;2|1239;2;2|976|200643|171549|815|816;2|3018035|3031418|213481|213483|958;2|1224|28216|80840|506|359336;2|201174|84998|84999|84107;2|200940|3031449|213115|194924;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827|1937008;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350;2|1239|91061|1385|33986;2|1239|186801|186802|216572|216851;2|1239|526524|526525|128827|1573534;2|201174|1760|2037|2049|1522056;2|2818505|3031714|224464|162027;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|1239|526524|526525|128827|1573535;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1224|28216|80840|119060|47670;2|201174|1760|85006|85023|33882;2|1239|186801|3085656|3085657|2039302;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552;2|1239|909932|1843489|31977|1567;2|1224|28216|80840|119060|48736;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1200657;2|203691|203692|136|2845253|157;2|1239|526524|526525|2810281|191303;2|976|200643|171549|1853231|283168|876416;2|976|200643|171549|2005473|2301481,Complete,ChiomaBlessing
bsdb:836/1/1,Study 836,case-control,NA,10.3389/fcimb.2021.770913,https://www.frontiersin.org/articles/10.3389/fcimb.2021.770913/full,"Shuo Wang, Yuan Wei, Luyan Liu, Zailing Li",Association Between Breastmilk Microbiota and Food Allergy in Infants,NA,2022,"breast milk microbiome, breastfeeding, food allergies, butyrate, infant",Experiment 1,China,Homo sapiens,Milk,UBERON:0001913,Food allergy,EFO:1001890,non-allergy (NA) group,food allergy (FA) group,Group with food allergy.,22,11,"use of antibiotics or probiotics for 2 weeks
before or after delivery, resulted in being excluded from the study",16S,34,Illumina,LEfSe,0.05,NA,2,"gestational age,maternal age,race",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 4A,6 November 2023,Davvve,Davvve,"LEfSe analysis between the food allergy (FA) and non-allergy (NA) groups, showing genera with absolute values of linear discriminant analysis (LDA)
score.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286;2|201174|1760|85006|85019|1696,Complete,Folakunmi
bsdb:836/1/2,Study 836,case-control,NA,10.3389/fcimb.2021.770913,https://www.frontiersin.org/articles/10.3389/fcimb.2021.770913/full,"Shuo Wang, Yuan Wei, Luyan Liu, Zailing Li",Association Between Breastmilk Microbiota and Food Allergy in Infants,NA,2022,"breast milk microbiome, breastfeeding, food allergies, butyrate, infant",Experiment 1,China,Homo sapiens,Milk,UBERON:0001913,Food allergy,EFO:1001890,non-allergy (NA) group,food allergy (FA) group,Group with food allergy.,22,11,"use of antibiotics or probiotics for 2 weeks
before or after delivery, resulted in being excluded from the study",16S,34,Illumina,LEfSe,0.05,NA,2,"gestational age,maternal age,race",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,fig 4,6 November 2023,Davvve,Davvve,"LEfSe analysis between the food allergy (FA) and non-allergy (NA) groups, showing genera with absolute values of linear discriminant analysis (LDA)
score",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanoregulaceae|g__Methanolinea,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Thermovirgaceae|g__Thermovirga,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Thermodesulfobacteriota|c__Syntrophia|o__Syntrophales|f__Syntrophaceae|g__Syntrophus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Thermotogota|c__Thermotogae|o__Kosmotogales|f__Kosmotogaceae|g__Mesotoga,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Geodermatophilus",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803;2|1239|909932|909929|1843491|158846;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|459786;2|201174|84998|84999|1643824|1380;2|32066|203490|203491|203492|848;2|976|200643|171549|2005519|397864;2|976|200643|171549|171552|577309;2|1239|526524|526525|2810281|191303;2|1239|91061|186826|186827|66831;2157|28890|224756|2191|1198451|499551;2|508458|649775|649776|3029089|336260;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|3085642|580596;2|200940|3031648|2914038|213468|43773;2|201174|1760|85006|85021|53457;2|74152|641853|641854|641876|423604;2|1239|909932|1843489|31977|906;2|201174|84998|1643822|1643826|580024;2|200918|188708|1643946|1643948|1184396;2|976|200643|171549|1853231|283168;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|186807|2740;2|201174|1760|1643682|85030|1860,Complete,Folakunmi
bsdb:837/1/1,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men with coronary heart disease (CHD),Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study.",567,112,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig.1 B,23 January 2024,Andre,Andre,"Differently abundant taxa in CHD patients according to the sex, based on LEfSe analysis.",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|1239|526524|526525|128827;2|1239|186801|3085636|186803|28050;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:837/1/2,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men with coronary heart disease (CHD),Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study.",567,112,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig.1 B,24 January 2024,Andre,Andre,"Differently abundant taxa in CHD patients according to sex, based on LEfSe analysis.",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",2|201174;2|976|200643|171549|2005519|397864;2|976|200643|171549|2005519;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|35832;2|201174|84998|84999;2|201174|84998;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525,Complete,Chloe
bsdb:837/2/1,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Women without cardiovascular disease,"Women without cardiovascular disease, and enrolled in the ONCOVER study",242,87,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig. 2 B,24 January 2024,Andre,Andre,"Differently abundant taxa in non‑CVD patients according to sex, based on LEfSe analysis",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|976|200643|171549;2|976|200643;2|976;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107,Complete,Chloe
bsdb:837/2/2,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Women without cardiovascular disease,"Women without cardiovascular disease, and enrolled in the ONCOVER study",242,87,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig. 2 B,24 January 2024,Andre,Andre,"Differently abundant taxa in non‑CVD patients according to sex, based on LEfSe analysis",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|1239;2|1239|186801|3082768|990719;2|1239|186801|3082768;2|1239|186801|186802|216572;2|74201|203494;2|74201|203494|48461;2|74201,Complete,Chloe
bsdb:837/3/1,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Men with coronary heart disease (CHD),"Men with coronary heart disease, and enrolled in the CORDIOPREV study.",242,567,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 1,Fig. 4,24 January 2024,Andre,Andre,Linear discriminant analysis between CHD patients and non‑CVD subjects in Men,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",2|1239|909932|1843488|909930;2|1239|909932|1843488;2|201174;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|1239|91061;2|1239;2|95818|2093818|2093825;2|95818|2093818;2|1239|186801;2|201174|84998|84999;2|201174|84998;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|200940|3031449;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236|135625|712|724;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|909932;2|1239|186801|186802|216572;2|1224|1236|135625|712;2|1224|1236|135625;2;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|1239|909932|909929;2|1224|1236|91347|543|620;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|200940;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|909932|1843489;2|74201|203494|48461,Complete,Chloe
bsdb:837/3/2,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Men with coronary heart disease (CHD),"Men with coronary heart disease, and enrolled in the CORDIOPREV study.",242,567,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 2,Figure 4,24 January 2024,Andre,"Andre,MyleeeA",Linear discriminant analysis between CHD patients and non‑CVD subjects in Men,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|976|200643|171549|171550|239759;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976;2|976|200643|171549|2005519|397864;2|976|200643|171549|2005519;2|1239|186801|3085636|186803|572511;2|1224|28216|80840;2|976|200643|171549|1853231|574697;2|976|200643|171549|2005519|1348911;2|1239|526524|526525;2|976|200643|1970189|1573805;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1224|28216|80840|995019|577310;2|1239|186801|3082720;2|1224;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|1224|28216|80840|995019;2|976|200643|171549|2005525;2|1239|526524|526525|2810280|3025755;2|1239|1737404|1737405;2|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:837/4/1,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Women without cardiovascular disease,Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study",87,112,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 1,Figure 4,24 January 2024,Andre,Andre,Linear discriminant analysis between CHD patients and non‑CVD subjects in Women,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|909932|1843488|909930;2|1239|909932|1843488;2|201174;2|1239|91061;2|200940|3031449|213115|194924|35832;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|200940|3031449;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|909932;2|1239|909932|1843488|909930|33024;2|1224|1236|91347|543|620;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|200940;2|1239|909932|1843489|31977|29465,Complete,Chloe
bsdb:837/4/2,Study 837,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H, Arenas-de Larriva AP, Lopez-Moreno J, Gutierrez-Mariscal FM, Romero-Cabrera JL, Molina-Abril H, Torres-Peña JD, Rodriguez-Cano D, Malagon MM, Ordovas JM, Delgado-Lista J, Perez-Martinez P, Lopez-Miranda J , Camargo A",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Women without cardiovascular disease,Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study",87,112,1 month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 2,Figure 4,24 January 2024,Andre,Andre,Linear discriminant analysis between CHD patients and non‑CVD subjects in Women,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|976|200643|171549;2|976|200643;2|976;2|1239|186801|3085636|186803|572511;2|1224|28216|80840;2|976|200643|171549|1853231|574697;2|1239|526524|526525;2|976|200643|1970189|1573805;2|976|200643|171549|1853231|283168;2|1224|28216|80840|995019|577310;2|1239|186801|3082720;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019;2|1239|1737404|1737405;2|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:838/1/1,Study 838,case-control,26277095,10.1186/s12920-015-0121-1,NA,"Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE , Crandall KA",Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities,BMC medical genomics,2015,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Healthy controls,Asthma Samples,"Participants ranged between the ages of 6 and 20 years, with physician-diagnosed asthma for at least one year prior to the time of recruitment.",6,8,N/A,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,increased,decreased,NA,increased,Signature 1,"Figure 3b, and within result text (Microbial identification and relative abundance in asthma and control communities, paragraphs 2 and 3)",7 November 2023,MyleeeA,"MyleeeA,Folakunmi",Differential relative abundance between asthma and control communities,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. PRwf-1",2|1224|1236|91347|543|561|562;2|1224|1236|2887326|468|475|480;2|1224|1236|2887326|468|497|349106,Complete,Folakunmi
bsdb:838/1/2,Study 838,case-control,26277095,10.1186/s12920-015-0121-1,NA,"Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE , Crandall KA",Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities,BMC medical genomics,2015,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Healthy controls,Asthma Samples,"Participants ranged between the ages of 6 and 20 years, with physician-diagnosed asthma for at least one year prior to the time of recruitment.",6,8,N/A,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,increased,decreased,NA,increased,Signature 2,"Figure 3b, and within result text (Microbial identification and relative abundance in asthma and control communities, paragraphs 2 and 3)",7 November 2023,MyleeeA,"MyleeeA,Folakunmi",Differential relative abundance between asthma and control communities,decreased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,2|1239|1737404|1737405|1570339|165779|33034,Complete,Folakunmi
bsdb:839/1/3,Study 839,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z , Qiu J",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy control (HC),pre-treatment (focal epilepsy),These are individuals with newly diagnosed focal epilepsy before they started receiving treatment.,14,10,2 weeks,16S,45,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 3,Figure 2D,1 November 2023,Deacme,"Deacme,Chinelsy",Diversity and relative abundance of gut microbiota between the group before treatment and the control group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. cv1,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|976|200643|171549|171550|239759|1622071;2|1239|91061|1385;2|1239|91061;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|91061|1385|539738|1378;2|1239|91061|186826;2|1224|1236|91347|543|1940338,Complete,Folakunmi
bsdb:839/2/1,Study 839,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z , Qiu J",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy control (HC),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,unchanged,NA,increased,Signature 1,Fig.4D,15 November 2023,Chinelsy,Chinelsy,Diversity and relative abundance of gut microbiota between the group after treatment and the control group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,s__uncultured organism",2|976|200643|171549|1853231|574697;2|201174|84998|84999|84107|102106;2|201174|84998|84999;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171550|239759|626932;155900,Complete,Folakunmi
bsdb:839/3/1,Study 839,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z , Qiu J",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to oxcarbazepine,EFO:0009893,pre-treatment (focal epilepsy),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig.3D,15 November 2023,Chinelsy,Chinelsy,Diversity and relative abundance of gut microbiota between the groups before and after treatment,increased,"k__Bacteria|p__Lentisphaerota|c__Lentisphaeria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. G2,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|s__Victivallaceae bacterium NML 080035,k__Bacteria|s__uncultured rumen bacterium",2|256845|1313211;2|1239|186801|186802|216572|459786;2|1224|28216|80840|995019;2|256845|1313211|278082|255528;2|256845|1313211|278082;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|216572|459786|871666;2|256845|1313211|278082|255528|573638;2|136703,Complete,Folakunmi
bsdb:839/3/2,Study 839,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z , Qiu J",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to oxcarbazepine,EFO:0009893,pre-treatment (focal epilepsy),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig.3D,15 November 2023,Chinelsy,Chinelsy,Diversity and relative abundance of gut microbiota between the groups before and after treatment,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|91061;2|1239|91061|1385|539738|1378;2|1239|91061|186826;2|1239|186801|3082720|186804|1501226;2|1239|909932|909929;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|1940338;2|1239|91061|186826|33958,Complete,Folakunmi
bsdb:839/4/1,Study 839,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z , Qiu J",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy control (HC),pre-treatment (focal epilepsy),These are individuals with newly diagnosed focal epilepsy before they started receiving treatment.,14,10,2 weeks,16S,45,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 1,Supplementary Figure 1,17 January 2024,Folakunmi,Folakunmi,Significant results of Metastats analysis at the phyla and genus level,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|201174;2|1239|186801|186802|216572|216851;2|976|200643|171549|2005525|375288;2|1224|1236|91347|543|1940338;2|1239|909932|909929|1843491|158846;2|1239|91061|186826|1300|1301;2|1239|186801|3082720|186804|1501226;2|201174|84998|84999|84107|102106,Complete,Folakunmi
bsdb:839/5/1,Study 839,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z , Qiu J",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy control (HC),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,increased,unchanged,NA,increased,Signature 1,Supplementary Figure 3,17 January 2024,Folakunmi,Folakunmi,Significant results of Metastats analysis at the phyla and genus level,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|201174;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|459786;2|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:839/6/1,Study 839,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z , Qiu J",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to oxcarbazepine,EFO:0009893,pre-treatment (focal epilepsy),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,supplementary figure 3,17 January 2024,Folakunmi,Folakunmi,Significant results of Metastats analysis at the phyla and genus levels,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|201174;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|1940338;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|216572|459786;2|1239|91061|186826|1300|1301;2|1239|186801|3082720|186804|1501226;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|207244,Complete,Folakunmi
bsdb:840/1/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 1,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,2013 sampling period,2015 sampling period,The 2015 sampling period occurred from October 2015 through December 2015,42,33,NA,16S,4,Illumina,"Mann-Whitney (Wilcoxon),Welch's T-Test",0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Fig 6, Text",2 April 2024,Fiddyhamma,Fiddyhamma,"The volcano plot (center) depicts the differences between the 2013 and 2015 sampling periods for each detected ASV (red and black points). Taxa depicted in red are the most highly significant (P < 0.015). Overabundant ASVs from 2013 are located on the negative (left) side of the volcano plot, while overabundant ASVs from 2015 are located on the positive (right) side. The violin plots surrounding the volcano plot depict the CLR values of the most significant taxa from the volcano plot; left: overabundant taxa in 2013; right: overabundant taxa in 2015",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__Sarcina ventriculi,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter|s__Altererythrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas koreensis",2|201174|1760|85007|85025|1827|1831;2|1224|1236|2887326|468|469|472;2|1239|186801|186802|31979|1266|1267;2|1224|28211|204457|335929|361177|1872480;2|1224|1236|135614|32033|40323|266128,Complete,NA
bsdb:840/1/2,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 1,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,2013 sampling period,2015 sampling period,The 2015 sampling period occurred from October 2015 through December 2015,42,33,NA,16S,4,Illumina,"Mann-Whitney (Wilcoxon),Welch's T-Test",0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Fig 6, Text",2 April 2024,Fiddyhamma,Fiddyhamma,"The volcano plot (center) depicts the differences between the 2013 and 2015 sampling periods for each detected ASV (red and black points). Taxa depicted in red are the most highly significant (P < 0.015). Overabundant ASVs from 2013 are located on the negative (left) side of the volcano plot, while overabundant ASVs from 2015 are located on the positive (right) side. The violin plots surrounding the volcano plot depict the CLR values of the most significant taxa from the volcano plot; left: overabundant taxa in 2013; right: overabundant taxa in 2015",decreased,"k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Cecembia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides|s__Nocardioides aestuarii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus sp. (in: a-proteobacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella|s__Rickettsiella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera aromatica",2|976|768503|768507|563798|1187078;2|201174|1760|85009|85015|1839|252231;2|1224|28211|204455|31989|265|267;2|1224|1236|118969|118968|59195|2201268;2|1224|28216|206389|2008794|33057|59405,Complete,NA
bsdb:840/2/NA,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 2,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Non-Core microbiome social group (R),Non-Core microbiome social group (F),"The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features. The same core features were then removed from the complete microbiome table to output a “non-core” microbiome feature table. Core and non-core feature tables were then exported to biom format",NA,NA,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:840/3/NA,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 3,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Core microbiome social groups (V),Core microbiome social groups (F),"The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features.",NA,NA,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:840/4/NA,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 4,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Non-Core microbiome 2013 sampling period,Non-Core microbiome 2015 sampling period,"The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features. The same core features were then removed from the complete microbiome table to output a “non-core” microbiome feature table. Core and non-core feature tables were then exported to biom format",NA,NA,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:840/5/NA,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 5,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Core microbiome 2013 sampling period,Core microbiome 2015 sampling period,"The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features.",NA,NA,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:840/6/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 6,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Complete microbiome social group R,Complete microbiome social group F,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",11,43,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig 2B, text",4 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",increased,k__Bacteria|p__Cyanobacteriota,2|1117,Complete,NA
bsdb:840/6/2,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 6,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Complete microbiome social group R,Complete microbiome social group F,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",11,43,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Fig 2B, text",4 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota",2|201174;2|1239;2|1224,Complete,NA
bsdb:840/7/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 7,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Complete microbiome social group R,Complete microbiome social group V,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",11,12,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig 2B, text",4 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",decreased,k__Bacteria|p__Actinomycetota,2|201174,Complete,NA
bsdb:840/8/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 8,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Complete microbiome social group F,Complete microbiome social group KK,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",43,8,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig 2B, text",4 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota",2|201174;2|1224,Complete,NA
bsdb:840/9/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 9,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Complete microbiome social group F,Complete microbiome social group V,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",43,12,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig 2B, text",4 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",increased,k__Bacteria|p__Bacillota,2|1239,Complete,NA
bsdb:840/10/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 10,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Complete microbiome social group HH,Complete microbiome social group KK,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",4,8,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig 2B, text",4 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",increased,k__Bacteria|p__Pseudomonadota,2|1224,Complete,NA
bsdb:840/11/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 11,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,Complete microbiome social group V,Complete microbiome social group KK,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",12,8,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig 2B, text",4 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,NA
bsdb:840/12/1,Study 840,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML , Horvath JE",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 12,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Microbiome measurement,EFO:0007882,2013 sampling period (Complete microbiome),2015 sampling period (Complete microbiome),The 2015 sampling period occurred from October 2015 through December 2015,42,33,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 4B, text",6 April 2024,Fiddyhamma,Fiddyhamma,"Box plots representing the significant pairwise taxa using Wilcoxon tests on CLR transformed relative abundance values on phyla: Actinobacteria, Firmicutes, Deinococcus-Thermus, Fusobacteria, and Proteobacteria.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|201174;2|1224;2|1239;2|1297|188787|118964|183710|1298;2|32066|203490,Complete,NA
bsdb:841/1/1,Study 841,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM , Peng Q",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 1,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 35,Calves without dam on day 35,Calves without dam on day 35 of the whole 95 days formal experimental period.,8,8,none,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figures 5&6,3 November 2023,Folakunmi,Folakunmi,"Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|201174;2|976|117743|200644|49546|76831;2|201174|84998|1643822|1643826|651554;2|1239|186801|3082720|186804|1257,Complete,ChiomaBlessing
bsdb:841/1/2,Study 841,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM , Peng Q",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 1,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 35,Calves without dam on day 35,Calves without dam on day 35 of the whole 95 days formal experimental period.,8,8,none,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figures 5&6,4 November 2023,Folakunmi,Folakunmi,"Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|1224|1236|91347|543|1940338;2|976|200643|171549|2005525|375288,Complete,ChiomaBlessing
bsdb:841/2/1,Study 841,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM , Peng Q",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 2,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 65,Calves without dam on day 65,Calves without dam on day 65 of the whole 95 days formal experimental period.,8,8,none,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figures 5&6,4 November 2023,Folakunmi,Folakunmi,"Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|815|816;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:841/2/2,Study 841,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM , Peng Q",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 2,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 65,Calves without dam on day 65,Calves without dam on day 65 of the whole 95 days formal experimental period.,8,8,none,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figures 5&6,4 November 2023,Folakunmi,Folakunmi,"Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|186802|216572|3068309;2|203691|203692|136|2845253|157;2|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:841/3/1,Study 841,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM , Peng Q",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 3,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 95,Calves without dam on day 95,Calves without dam on day 95 of the whole 95 days formal experimental period.,8,8,none,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figures 5&6,4 November 2023,Folakunmi,Folakunmi,"Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|186801|186802|186806|1730|290054;2|203691|203692|136|2845253|157,Complete,ChiomaBlessing
bsdb:841/3/2,Study 841,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM , Peng Q",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 3,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 95,Calves without dam on day 95,Calves without dam on day 95 of the whole 95 days formal experimental period.,8,8,none,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figures 5&6,4 November 2023,Folakunmi,Folakunmi,"Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,2|1239|186801|186802|216572|3068309,Complete,ChiomaBlessing
bsdb:842/1/1,Study 842,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E, Gołębiewski M, Sikora M, Grzybowski T, Gorzkiewicz M, Popielarz M, Gawryjołek J , Krogulska A",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Control group,Food Allergy,Infants with food allergy,28,16,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3 and Table 4,2 November 2023,Peace Sandy,Peace Sandy,"Table 3. Differentially abundant OTUs , Table 4 Differentially represented OTUs—characteristic either for AD or FA.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465|39778,Complete,Folakunmi
bsdb:842/2/1,Study 842,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E, Gołębiewski M, Sikora M, Grzybowski T, Gorzkiewicz M, Popielarz M, Gawryjołek J , Krogulska A",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 2,Poland,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,Control group,Atopic dermatitis,Infants with atopic dermatitis,28,5,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3 and Table 4,4 November 2023,Peace Sandy,"Peace Sandy,Folakunmi","Table 3. Differentially abundant OTUs , Table 4 Differentially represented OTUs—characteristic either for AD or FA.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter variabilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",2|1224|1236|2887326|468|469|70346;2|976|200643|171549|2005525|375288;2|1224|1236|135614|32033|40323|40324;2|976|200643|171549|815|909656|357276,Complete,Folakunmi
bsdb:842/3/1,Study 842,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E, Gołębiewski M, Sikora M, Grzybowski T, Gorzkiewicz M, Popielarz M, Gawryjołek J , Krogulska A",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,"Food allergy,Dermatitis","EFO:1001890,MONDO:0002406",Control group,Atopic dermatitis and Food Allergy (ADFA),Infants with both Atopic dermatitis and Food Allergy,28,38,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3 and Table 4,13 November 2023,Peace Sandy,"Peace Sandy,Folakunmi","Table 3: Differentially abundant OTUs 
Table 4: Differentially represented OTUs—characteristic either for AD or FA",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter variabilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",2|1224|1236|2887326|468|469|70346;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|1239|909932|1843489|31977|29465|39778;2|976|200643|171549|815|909656|357276,Complete,Folakunmi
bsdb:842/4/1,Study 842,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E, Gołębiewski M, Sikora M, Grzybowski T, Gorzkiewicz M, Popielarz M, Gawryjołek J , Krogulska A",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,"Food allergy,Dermatitis","EFO:1001890,MONDO:0002406",Control group,Infants with Allergy Symptoms,"All infants with Allergy symptoms including Food Allergy, Atopic dermatitis, and both Atopic dermatitis and Food Allergy",28,59,1 month,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 5,26 December 2023,Folakunmi,Folakunmi,OTUs whose abundance on skin and in feces is correlated,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|1239|91061|186826|1300|1301|1306;2|1239|91061|1385|539738|1378;2|201174|1760|85004|31953|1678|158787;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|33958|1578|1596,Complete,Folakunmi
bsdb:842/4/2,Study 842,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E, Gołębiewski M, Sikora M, Grzybowski T, Gorzkiewicz M, Popielarz M, Gawryjołek J , Krogulska A",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,"Food allergy,Dermatitis","EFO:1001890,MONDO:0002406",Control group,Infants with Allergy Symptoms,"All infants with Allergy symptoms including Food Allergy, Atopic dermatitis, and both Atopic dermatitis and Food Allergy",28,59,1 month,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 5,26 December 2023,Folakunmi,Folakunmi,OTUs whose abundance on skin and in feces is correlated,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii",2|1224|1236|2887326|468|469|472;2|1239|91061|186826|1300|1301|1306;2|1239|91061|186826|33958|1578|1596;2|1224|1236|135625|712|724|726;2|976|200643|171549|815|816|28116;2|201174|1760|2037|2049|2529408|1660;2|201174|1760|2037|2049|1654|55565,Complete,Folakunmi
bsdb:843/1/NA,Study 843,case-control,36975801,10.1128/msystems.01003-22,NA,"Carter KA, Fodor AA, Balkus JE, Zhang A, Serrano MG, Buck GA, Engel SM, Wu MC , Sun S",Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition,mSystems,2023,"Lactobacillus crispatus, Lactobacillus iners, measurement error, metagenome inference, vaginal microbiome",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Premature birth,EFO:0003917,term birth(control),preterm birth (PTB),Cases were participants who experienced early preterm birth at <32 weeks of gestation.,37,35,None.,16S,123,Illumina,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:844/1/1,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",71,86,None,16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Supplemental Table S11,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the Indian substudy,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,2|1239|186801|3085636|186803|1506553,Complete,Folakunmi
bsdb:844/2/1,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",61,80,4 months,16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Supplemental Table S10b,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the Danish substudy,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,2|1224|1236|91347|543|1940338,Complete,Folakunmi
bsdb:844/3/1,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 3,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Indians (normoglycaemic controls and T2D patients),Denmark (normoglycaemic controls and T2D patients),Gut microbiota in Denmark participants,294,279,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S2b,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Joan Chuks",Differentially abundant taxa in the gut microbiome between Danes and Indians (normoglycaemic controls and T2D patients),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Merdibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|52784;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|1935176;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|200940|3031449|213115|194924|35832;2|1224|28211|356|41294|374;2|976|200643|171549|1853231|574697;2|1239|186801|3082768|990719|990721;2|976|200643|171549|2005519|1348911;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|877420;2|1239|526524|526525|128827|1935200;2|1239|186801|186802|216572|3028852;2|1239|1980693;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|119852;2|1224|28216|80840|75682|846;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186807|2740;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|216572|1017280;2|201174|1760|85007|85025|1827;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1508657|2053608;2|1239|186801|186802|216572|1263|41978;2|976|200643|171549|171551|1635148;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003;2|1239|186801|186802|216572|2895461,Complete,Folakunmi
bsdb:844/3/2,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 3,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Indians (normoglycaemic controls and T2D patients),Denmark (normoglycaemic controls and T2D patients),Gut microbiota in Denmark participants,294,279,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S2b,6 November 2023,ChiomaBlessing,ChiomaBlessing,Differentially abundant taxa in the gut microbiome between Danes and Indians (normoglycaemic controls and T2D patients),decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Kerstersia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia caballeronis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.",2|1224|28216|80840|506|222;2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|156454;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1407607;2|1239|91061|186826|186828|117563;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|404402;2|1224|28216|80840|506|257820;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|248744;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|265975;2|1224|28216|80840|119060|1822464|416943;2|201174|84998|84999|1643824|2082587;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841|166486;2|201174|84998|84999|84107|1473205;2|1224|1236|91347|1903411|613;2|1239|526524|526525|128827|123375;2|1239|186801|3082720|186804|1505652;2|1239|91061|186826|33958|46255;2|1239|186801|186802|216572|707003;2|976|200643|171549|171552|838|59823;2|1239|186801|3085636|186803|33042|2049024,Complete,Folakunmi
bsdb:844/4/1,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 4,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Metformin,CHEBI:6801,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",132,166,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Supplemental. TableS9,4 January 2024,Folakunmi,Folakunmi,Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the combined Danish-Indian group,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:844/4/2,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 4,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Metformin,CHEBI:6801,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",132,166,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 2,Supplemental. TableS9,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the combined Danish-Indian group,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,2|976|200643|171549|815|816|29523,Complete,Folakunmi
bsdb:844/5/1,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 5,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S3A,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|3085636|186803|653683;2|1239|186801|186802|3085642|580596;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263|41978;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:844/5/2,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 5,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental Table S3A & B,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|3085636|186803|33042|2049024;2|1239|186801|3085636|186803|189330;2|1239|1263031;2|1239|186801|3085636|186803|1506553;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|459786,Complete,Folakunmi
bsdb:844/6/1,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 6,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S4A and B,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|3085636|186803|653683;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|216572|292632,Complete,Folakunmi
bsdb:844/6/2,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 6,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S4A and B,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,increased,"k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|1263031;2|1239|186801|3085636|186803|1506553,Complete,Folakunmi
bsdb:844/7/1,Study 844,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M , Pedersen O",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months,16S,12345,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental Table S6A,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi",Differentially abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the Danish substudy,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,2|1239|186801|3085636|186803|1506553,Complete,Folakunmi
bsdb:845/1/1,Study 845,"cross-sectional observational, not case-control",37919319,10.1038/s41598-023-42474-7,NA,"Antonello G, Blostein F, Bhaumik D, Davis E, Gögele M, Melotti R, Pramstaller P, Pattaro C, Segata N, Foxman B , Fuchsberger C",Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population,Scientific reports,2023,NA,Experiment 1,Italy,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never smokers,Current smokers,Individuals who reported being smokers at the day of examination with daily smoking intensity at least 1 month prior to the visit.,880,326,12 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,number of teeth measurement,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,figure 1,7 November 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Heatmap of the 44 genera diferentially abundant between Current and Never smokers,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__uncultured Peptostreptococcus sp.",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|419014;2|201174|84998|84999|1643824|1380;2|976|200643;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|201174|84998|1643822|1643826|84162;2|1239|909932|1843489|31977|39948;2|1239|186801|3082720|3118655|44259;2|508458|649775|649776|3029087|1434006;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|544448|31969|2085|2092|2093;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|3085636|186803|1213720;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|1239|186801|3082720|186804|1257|169971,Complete,Folakunmi
bsdb:845/1/2,Study 845,"cross-sectional observational, not case-control",37919319,10.1038/s41598-023-42474-7,NA,"Antonello G, Blostein F, Bhaumik D, Davis E, Gögele M, Melotti R, Pramstaller P, Pattaro C, Segata N, Foxman B , Fuchsberger C",Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population,Scientific reports,2023,NA,Experiment 1,Italy,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never smokers,Current smokers,Individuals who reported being smokers at the day of examination with daily smoking intensity at least 1 month prior to the visit.,880,326,12 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,number of teeth measurement,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,figure 1,7 November 2023,OdigiriGreat,"OdigiriGreat,Folakunmi",Result of the Heatmap of the 44 genera diferentially abundant between Current and Never smokers.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Candidatus Absconditabacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__uncultured Peptostreptococcus sp.,k__Bacteria|p__Candidatus Gracilibacteria",2|1239|91061|186826|186827|46123;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313;2|976|117743|200644|2762318|59735;2|221235;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|1239|186801|3085636|186803|43996;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28216|206351|481|32257;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1224|28216|80840|80864|219181;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|1239|186801|3085636|186803|297314;2|1239|186801|3082720|186804|1257|169971;2|363464,Complete,Folakunmi
bsdb:845/2/NA,Study 845,"cross-sectional observational, not case-control",37919319,10.1038/s41598-023-42474-7,NA,"Antonello G, Blostein F, Bhaumik D, Davis E, Gögele M, Melotti R, Pramstaller P, Pattaro C, Segata N, Foxman B , Fuchsberger C",Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population,Scientific reports,2023,NA,Experiment 2,Italy,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never smokers,Former smokers,Individuals who quit smoking 17.96 years on average,880,395,12 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,number of teeth measurement,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:846/1/1,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Home Made Diet - H,Base Diet - B,"A raw meat diet with the addition of a complementary food, from here on called Base",30,56,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,Peace Sandy,"Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.

Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",2|976|200643|171549|815|816;2|32066|203490|203491|203492|848;2|1239|186801|186802|216572|1263;2|1239|526524|526525|128827|174708;2|1224|1236|135624|83763|13334;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|526524|526525|2810280|100883;2|1224|1236|91347|543|561;2|29547|3031852|213849|72293|209;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|186807|2740;2|1239|186801|3085636|186803|841;2|201174|84998|1643822|1643826|84108,Complete,Peace Sandy
bsdb:846/1/2,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Home Made Diet - H,Base Diet - B,"A raw meat diet with the addition of a complementary food, from here on called Base",30,56,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,Peace Sandy,"Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.

Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239;2|976|200643|171549;2|1239|186801|186802|186806|1730;2|976|200643|171549|171552|577309;2|201174|84998|1643822|1643826|447020;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803|2383;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:846/2/1,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 2,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Commercial moist complete diet - W,Complete diet - K,Commercial extruded complete diet (K),83,171,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,Peace Sandy,Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|189330;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:846/2/2,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 2,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Commercial moist complete diet - W,Complete diet - K,Commercial extruded complete diet (K),83,171,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,Peace Sandy,"Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.

Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|976|200643|171549|815|816;2|32066|203490;2|1239|186801|186802|186806|1730;2|976|200643|171549|171552|577309;2|1239|186801|186802|216572|1263;2|1239|526524|526525|128827|174708;2|1224|1236|135624|83763|13334;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|2383;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|216851;2|32066|203490|203491|203492|848;2|29547|3031852|213849|72293|209;2|1239|186801|3085636|186803|28050;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186807|2740;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|201174|84998|1643822|1643826|84108;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:846/3/1,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 3,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Spayed Female - FC,Whole Female - F,Whole Female,28,145,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5,26 February 2024,Peace Sandy,Peace Sandy,Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacteroidota",2|32066|203490;2|976,Complete,Peace Sandy
bsdb:846/3/2,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 3,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Spayed Female - FC,Whole Female - F,Whole Female,28,145,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5,26 February 2024,Peace Sandy,Peace Sandy,Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Peace Sandy
bsdb:846/4/1,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 4,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Castrated Male - MC,Whole Male - M,Whole Male,89,78,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5,26 February 2024,Peace Sandy,Peace Sandy,Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|976;2|32066|203490,Complete,Peace Sandy
bsdb:846/4/2,Study 846,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S , Sandri M",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 4,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Castrated Male - MC,Whole Male - M,Whole Male,89,78,NIL,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5,26 February 2024,Peace Sandy,Peace Sandy,"Relative Abundances (RA) for the category sex of the three represented phyla in the 
fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.",decreased,k__Bacteria|p__Bacillota,2|1239,Complete,Peace Sandy
bsdb:847/1/1,Study 847,case-control,34222034,10.3389/fcimb.2021.598093,https://pubmed.ncbi.nlm.nih.gov/34222034/,"Martínez-Cuesta MC, Del Campo R, Garriga-García M, Peláez C , Requena T",Taxonomic Characterization and Short-Chain Fatty Acids Production of the Obese Microbiota,Frontiers in cellular and infection microbiology,2021,"diversity, in vitro incubations, metabolic activity, microbiota, obesity, short-chain fatty acids",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight volunteers (N),Obese Volunteers (O),Obese adult volunteers with body mass index (BMI) > 30 kg/m^2,13,13,Volunteers who were on antibiotics six (6) months preceding the sample collection were excluded from the study,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 5,7 November 2023,Aleru002,"Aleru002,Peace Sandy",The significant differences in gut microbiota composition in normal weight (N) and obese (O) subjects.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|526524|526525|2810280|100883;2|1239|909932;2|1239|909932|909929;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827|123375,Complete,Peace Sandy
bsdb:847/1/2,Study 847,case-control,34222034,10.3389/fcimb.2021.598093,https://pubmed.ncbi.nlm.nih.gov/34222034/,"Martínez-Cuesta MC, Del Campo R, Garriga-García M, Peláez C , Requena T",Taxonomic Characterization and Short-Chain Fatty Acids Production of the Obese Microbiota,Frontiers in cellular and infection microbiology,2021,"diversity, in vitro incubations, metabolic activity, microbiota, obesity, short-chain fatty acids",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight volunteers (N),Obese Volunteers (O),Obese adult volunteers with body mass index (BMI) > 30 kg/m^2,13,13,Volunteers who were on antibiotics six (6) months preceding the sample collection were excluded from the study,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 5,7 November 2023,Aleru002,"Aleru002,Peace Sandy",The significant differences in gut microbiota composition in normal weight (N) and obese (O) subjects.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Verrucomicrobiota",2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|244127;2|1239;2|1239|91061|1385|186817|1386|1409;2;2|976|200643|171549|2005519|397864;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107;2|1239|1737404|1582879;2|976|117743|200644;2|976|117743;2|32066|203490|203491;2|32066|203490;2|1239|186801|186802|216572|596767;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1224|28216|80840|75682;2|1224|28216|80840|995019|577310;2|1239|1737404|1737405|1570339;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1904861;2|976|200643|171549|171551|836;2|1224|28211|204441;2|976|200643|171549|171550;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|44748;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810281|191303;2|74201,Complete,Peace Sandy
bsdb:848/1/1,Study 848,"cross-sectional observational, not case-control",37925571,10.1038/s41598-023-46566-2,NA,"He J, Gong X, Hu B, Lin L, Lin X, Gong W, Zhang B, Cao M, Xu Y, Xia R, Zheng G, Wu S , Zhang Y",Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder,Scientific reports,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing (TD) group,Constipated autism spectrum disorder (C-ASD) group,Children with autism spectrum disorder (ASD) while also experiencing constipation as an important gastrointestinal (GI) comorbidity.,40,40,"3 months, including probiotics, acid suppressors, or other drugs affecting the gut microbiota",16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 3,7 November 2023,Deacme,"Deacme,Folakunmi",Discriminative taxa between the typically developing (TD) group and constipated autism spectrum disorder (C-ASD) group  derived from LeFse analysis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|2005519|397864;2|1239|526524|526525|128827|1470349;2|1224|28216|80840|80864|283;2|976|200643|171549|2005519|1348911;2|1239|186801|3085636|186803|33042;2|200940|3031449|213115|194924|872;2|201174|84998|84999|84107|1472762;2|32066|203490|203491|203492|848;2|1239|909932|909929|1843491|158846;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1239|186801|3082720|3120161|1481960;2|1239|186801|186802|186807|2740;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|216572|1508657;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|216572|707003;2|1239|526524|526525|128827,Complete,Folakunmi
bsdb:848/1/2,Study 848,"cross-sectional observational, not case-control",37925571,10.1038/s41598-023-46566-2,NA,"He J, Gong X, Hu B, Lin L, Lin X, Gong W, Zhang B, Cao M, Xu Y, Xia R, Zheng G, Wu S , Zhang Y",Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder,Scientific reports,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing (TD) group,Constipated autism spectrum disorder (C-ASD) group,Children with autism spectrum disorder (ASD) while also experiencing constipation as an important gastrointestinal (GI) comorbidity.,40,40,"3 months, including probiotics, acid suppressors, or other drugs affecting the gut microbiota",16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 3,7 November 2023,Deacme,"Deacme,Folakunmi",Discriminative taxa between the typically developing (TD) group and constipated autism spectrum disorder (C-ASD) group derived from LeFse analysis.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|91061|186826|186827|1375;2|1239|186801|3085636|186803|207244;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186806|1730|39497;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|877420;2|1239|91061|186826|33958|1578;2|1239|91061|1385|186820|1637;2|200795|292625|292629|292628|475961;2|1239|186801|3085636|186803|248744;2|1224|28211|356|119045|407;2|201174|1760|85006|85023|33882;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|1224|28216|80840|119060|48736;2|1239|186801|186802|216572|1263;2|203691|203692|136|2791015|399320;2|1239|91061|1385|90964|1279;2|1239|526524|526525|2810280|3025755;2|203691|203692|136|2845253|157;2|1239|186801|3085636|186803|1506577;2|1239|186801|186802|543314|35517;2|1239|186801|3085636|186803|2316020|33038;2|201174|84998|84999|84107;2|1239|526524|526525|128827;2|1239|186801|3085636|186803;2|976|200643|171549|171552,Complete,Folakunmi
bsdb:849/1/1,Study 849,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S , Dao MC","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 1,United States of America,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Age,EFO:0000246,Non-T2D(prediabetes),type 2 diabetes (T2D),"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency.",29,21,6 months,WMS,NA,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 1,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 2, line 3-6, figure 3",12 November 2023,Chinelsy,"Chinelsy,MyleeeA,Folakunmi","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with age.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|815|816;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:849/1/2,Study 849,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S , Dao MC","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 1,United States of America,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Age,EFO:0000246,Non-T2D(prediabetes),type 2 diabetes (T2D),"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency.",29,21,6 months,WMS,NA,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 2,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 2, line 3-6, figure 3",17 December 2023,Folakunmi,Folakunmi,"Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with age.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853,Complete,Folakunmi
bsdb:849/2/1,Study 849,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S , Dao MC","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 2,United States of America,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Cytokine,EFO:0003786,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 1,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 3, Figure 3",13 November 2023,MyleeeA,"MyleeeA,Folakunmi","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory
bacteria and  anti-inflammatory/SCFA-producing bacteria correlated with the inflammatory cytokine TNF-a",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288,Complete,Folakunmi
bsdb:849/2/2,Study 849,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S , Dao MC","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 2,United States of America,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Cytokine,EFO:0003786,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 2,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 3, Figure 3",13 November 2023,MyleeeA,"MyleeeA,Folakunmi","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with the inflammatory cytokine TNF-a",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",2|976|200643|171549|171552|838;2|201174|84998|84999|84107|102106|74426,Complete,Folakunmi
bsdb:849/3/1,Study 849,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S , Dao MC","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 3,United States of America,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Diet,EFO:0002755,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 1,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 4, Figure 3",17 December 2023,Folakunmi,Folakunmi,"Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with dietary fiber.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:849/4/1,Study 849,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S , Dao MC","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 4,United States of America,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",HbA1c measurement,EFO:0004541,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 1,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraphs 3 and 4, Figure 3",17 December 2023,Folakunmi,Folakunmi,"Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with HbA1c",increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:849/4/2,Study 849,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S , Dao MC","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 4,United States of America,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",HbA1c measurement,EFO:0004541,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 2,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraphs 3 and 4, Figure 3",17 December 2023,Folakunmi,Folakunmi,"Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with HbA1c",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:850/1/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 1,"Canada,China",Bos taurus,"Nasopharynx,Lung","UBERON:0001728,UBERON:0002048",Population,IDOMAL:0001254,Nasopharyngeal swabs from Canada and bronchoalveolar lavage from Canada,Nasopharyngeal swabs from China,Nasopharyngeal swabs from two cities (Qiqihaer and Guangan) in China from the study of Cui et al (2021).,127,18,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,figure 2,12 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing",Differentially abundant taxa in the nasopharyngeal samples (NPS) of China (Qiqihaer and Guangan) when compared with the nasopharyngeal samples of Saskatoon in Canada and bronchoalveolar lavage samples (BAL) of Alberta in Canada.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium efficiens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glutamicum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma conjunctivae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter arcticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. PRwf-1,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",2|201174|1760|85007|1653|1716|152794;2|201174|1760|85007|1653|1716|1718;2|1224|28211|356|212791|225324;2|544448|2790996|2895623|2923352|45361;2|1224|1236|2887326|468|475|480;2|1224|1236|2887326|468|497|334543;2|1224|1236|2887326|468|497|349106;2|1224|1236|2887326|468|469|470;2|1224|1236|91347|543|570|573,Complete,ChiomaBlessing
bsdb:850/2/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 2,"Canada,China",Bos taurus,"Nasopharynx,Lung","UBERON:0001728,UBERON:0002048",Population,IDOMAL:0001254,Nasopharyngeal swabs from China and bronchoalveolar lavage from Canada,"Nasopharyngeal swabs from Saskatoon, Canada.",Nasopharyngeal swabs from Saskatoon in Canada from the study of Malmuthuge et al. (2021).,33,112,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,figure 2,12 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing","Differentially abundant taxa in the nasopharyngeal samples (NPS) of Saskatoon, Canada when compared with the NPS of China and bronchoalveolar lavage samples (BAL) of Alberta in Canada.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ambifaria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cenocepacia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia dolosa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia lata,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia multivorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia vietnamiensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phymatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans",2|1224|28216|80840|119060|32008|152480;2|1224|28216|80840|119060|32008|95486;2|1224|28216|80840|119060|32008|152500;2|1224|28216|80840|119060|32008|482957;2|1224|28216|80840|119060|32008|87883;2|1224|28216|80840|119060|32008|101571;2|1224|28216|80840|119060|32008|60552;2|1224|28216|80840|119060|1822464|148447;2|1224|28216|80840|119060|1822464|36873,Complete,ChiomaBlessing
bsdb:850/3/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 3,"Canada,China",Bos taurus,"Nasopharynx,Lung","UBERON:0001728,UBERON:0002048",Sampling site,EFO:0000688,Nasopharyngeal swabs from Canada and Nasopharyngeal swabs from China,"Bronchoalveolar lavage from Alberta, Canada","Bronchoalveolar lavage collected from feedlot calves which died from bovine respiratory disease in Alberta, Canada from the study of Klima et al. (2019).",130,15,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2,12 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing","Differentially abundant taxa in the bronchoalveolar lavage samples (BAL) of Alberta in Canada when compared with the nasopharyngeal samples (NPS) of China and NPS of Saskatoon, Canada .",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus pleuropneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus succinogenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Glaesserella|s__Glaesserella parasuis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus|s__Histophilus somni,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia haemolytica,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma arthritidis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma|s__Mycoplasma mycoides,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis agalactiae,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis bovis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella bryantii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__[Haemophilus] ducreyi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Basfia|s__[Mannheimia] succiniciproducens",2|1224|1236|135625|712|713|715;2|1224|1236|135625|712|713|67854;2|1239|186801|186802|31979|1485|1502;2|1224|1236|135625|712|2094023|738;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|214906|731;2|1224|1236|135625|712|75984|75985;2|544448|2790996|2895623|2895509|2111;2|544448|2790996|2895623|2895509|2098;2|544448|31969|2085|2092|2093|2102;2|544448|2790996|2895623|2767358|2110;2|544448|2790996|2895623|2767358|28903;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|2974251|77095;2|976|200643|171549|171552|2974251|28126;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171552|2974251|28135;2|976|200643|171549|171552|558436|839;2|1224|1236|135625|712|724|730;2|1224|1236|135625|712|697331|157673,Complete,ChiomaBlessing
bsdb:850/4/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 4,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),Before loading for short distance transportation,"calves before loading to truck for transportation at short distance. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation",10,10,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,supplementary figure S4,13 November 2023,Folakunmi,Folakunmi,Signature microbiota in calves before loading into trucks for transportation at a short distance,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia|s__Nocardia farcinica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina|s__Idiomarina loihiensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. e14,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis|s__Sodalis glossinidius",2|201174|1760|85007|85025|1817|37329;2|1224|1236|135622|267893|135575|135577;2|201174|1760|85011|2062|1883|645465;2|1224|1236|91347|2812006|84565|63612,Complete,ChiomaBlessing
bsdb:850/5/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 5,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),unloading after short distance transportation,"calves at the time of unloading from truck after transportation at short distance. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation",10,10,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,supplementary figure S4,13 November 2023,Folakunmi,Folakunmi,Signature microbiota in calves at the time of unloading from trucks after transportation at a short distance.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium etli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas|s__Marinomonas sp. MED121,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Yoonia|s__Yoonia vestfoldensis",2|1224|28211|356|82115|379|29449;2|1224|1236|135619|135620|28253|314277;2|1224|28211|204455|31989|2211641|245188,Complete,ChiomaBlessing
bsdb:850/6/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 6,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),7 days after placement and adaptive feeding (short distance),"calves 7 days after placement and adaptive feeding following transportation at short distance. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,10,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,supplementary figure S4,14 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing",calves 7 days after placement and adaptive feeding following transportation at short distance.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus|s__Dermacoccus sp. Ellin185,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geotalea|s__Geotalea uraniireducens,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Microscillaceae|g__Microscilla|s__Microscilla marina,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsaceae|g__Nocardiopsis|s__Nocardiopsis dassonvillei,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma linguale,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces avermitilis",2|201174|1760|85006|145357|57495|188626;2|200940|3031651|3031668|213422|2910589|351604;2|976|768503|768507|1937962|1023|1027;2|201174|1760|85012|83676|2013|2014;2|976|768503|768507|89373|107|108;2|201174|1760|85011|2062|1883|33903,Complete,ChiomaBlessing
bsdb:850/7/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 7,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),before loading for long distance transportation,"calves before loading into truck for long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,18,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,supplementary figure S4,14 November 2023,Folakunmi,Folakunmi,"calves before loading for long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium radiotolerans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Rhizorhabdus|s__Rhizorhabdus wittichii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum extorquens",2|1224|28216|206351|481|71|72;2|1224|28211|356|119045|407|31998;2|1224|1236|72274|135621|286|294;2|1224|28211|204457|41297|1649486|160791;2|1224|28211|356|119045|2282523|408,Complete,ChiomaBlessing
bsdb:850/8/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 8,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),unloading from long distance transportation,"calves at the time of unloading from truck after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,18,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,supplementary figure S4,14 November 2023,Folakunmi,Folakunmi,"abundant taxa in calves at the time of unloading from truck after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baylyi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus minor,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus pleuropneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus succinogenes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Glaesserella|s__Glaesserella parasuis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus|s__Histophilus somni,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia haemolytica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella dagmatis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter arcticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter cryohalolentis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. PRwf-1,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__[Haemophilus] ducreyi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Basfia|s__[Mannheimia] succiniciproducens,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Riemerella|s__Riemerella anatipestifer",2|1224|1236|2887326|468|469|202950;2|1224|1236|135625|712|713|51047;2|1224|1236|135625|712|713|715;2|1224|1236|135625|712|713|67854;2|1224|28211|356|212791|225324;2|1224|1236|135625|712|2094023|738;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|214906|731;2|1224|28216|206351|481|32257|505;2|1224|1236|135625|712|75984|75985;2|1224|1236|2887326|468|475|480;2|1224|28216|206351|481|482|485;2|1224|28216|206351|481|482|486;2|1224|28216|206351|481|482|487;2|1224|1236|135625|712|745|754;2|1224|1236|135625|712|745|747;2|1224|1236|2887326|468|497|334543;2|1224|1236|2887326|468|497|330922;2|1224|1236|2887326|468|497|349106;2|1224|1236|135625|712|724|730;2|1224|1236|135625|712|697331|157673;2|976|117743|200644|2762318|34084|34085,Complete,ChiomaBlessing
bsdb:850/9/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 9,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),7 days after placement and adaptive feeding(long distance),"calves at  7 days after placement and adaptive feeding after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,18,none,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,supplementary figure S4,15 November 2023,Folakunmi,"Folakunmi,Davvve,ChiomaBlessing","abundant taxa in calves at 7 days after placement and adaptive feeding after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio thermocellus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus viridans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium tumefaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter sp. FB24,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas subvibrioides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium sp. AT7,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter vibrioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium ammoniagenes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium diphtheriae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium efficiens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria rhizophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcoides|s__Macrococcoides caseolyticum,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma conjunctivae,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyopneumoniae,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides|s__Nocardioides sp. JS614,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mendocina,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium leguminosarum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas|s__Rhodopseudomonas palustris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora|s__Saccharopolyspora erythraea,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus saprophyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus",2|1239|186801|186802|216572|35829|1515;2|1239|91061|186826|186827|1375|1377;2|1239|186801|3085636|186803|1766253|39491;2|1224|28211|356|82115|357|358;2|201174|1760|85006|1268|1663|290399;2|1224|28211|204458|76892|41275|74313;2|1239|91061|186826|186828|2747|333990;2|1224|28211|204458|76892|75|155892;2|1239|186801|186802|31979|1485|1491;2|201174|1760|85007|1653|1716|1697;2|201174|1760|85007|1653|1716|43765;2|201174|1760|85007|1653|1716|169292;2|201174|1760|85007|1653|1716|1717;2|201174|1760|85007|1653|1716|152794;2|201174|1760|85007|1653|1716|38289;2|1239|91061|186826|81852|1350|1352;2|1224|1236|91347|543|561|562;2|201174|1760|85006|1268|57493|72000;2|1239|186801|3085636|186803|1506553|66219;2|1239|186801|3085636|186803|2719231|84030;2|1239|91061|1385|90964|3076173|69966;2|544448|2790996|2895623|2923352|45361;2|544448|2790996|2895623|2923352|2099;2|544448|2790996|2895623|2923352|2100;2|201174|1760|85009|85015|1839|196162;2|1239|186801|186802|216572|1017280|106588;2|1224|1236|72274|135621|286|300;2|1224|28211|356|82115|379|384;2|1224|28211|356|41294|1073|1076;2|1239|186801|186802|216572|552398;2|1239|186801|186802|216572|1263|1264;2|201174|1760|85010|2070|1835|1836;2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|29385;2|1224|1236|72274|135621|2901164|316;2|1239|186801|3085636|186803|830|43305,Complete,ChiomaBlessing
bsdb:850/10/1,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 10,Canada,Bos taurus,Nasopharynx,UBERON:0001728,"Breastfeeding duration,Transport","EFO:0006864,GO:0006810",suckling calves (control),weaning+short transportation,"These were the calves in the treatment group that got weaned and transported at short distance. Metagenomics of the bovine respiratory microbiome in treatment groups on days 0 (prior to weaning and short-distance transportation), 2, 4, 8, 14, and 28 was used to compare with the control group that stayed with their dams (suckling).",10,10,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,figure 7,16 November 2023,Folakunmi,Folakunmi,Significantly abundant taxa in the weaning+short-transport group on day 14 when compared to the suckling group on day 14.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,2|1224|1236|135625|712|75984,Complete,ChiomaBlessing
bsdb:850/10/2,Study 850,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J, Liu X, Usdrowski H, Deng F, Li Y , Zhao J","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 10,Canada,Bos taurus,Nasopharynx,UBERON:0001728,"Breastfeeding duration,Transport","EFO:0006864,GO:0006810",suckling calves (control),weaning+short transportation,"These were the calves in the treatment group that got weaned and transported at short distance. Metagenomics of the bovine respiratory microbiome in treatment groups on days 0 (prior to weaning and short-distance transportation), 2, 4, 8, 14, and 28 was used to compare with the control group that stayed with their dams (suckling).",10,10,none,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,figure 7,16 November 2023,Folakunmi,Folakunmi,Significantly abundant taxa in the weaning+short-transport group on day 14 when compared to the suckling group on day 14.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,2|1224|1236|2887326|468|475,Complete,ChiomaBlessing
bsdb:851/1/1,Study 851,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes JD, Van Domselaar G , Bernstein CN",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 1,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0003346,UBERON:0000331",Crohn's disease,EFO:0000384,non-inflammatory bowel disease who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,non-inflamed crohn's disease,biopsies collected from patients with crohn's disease at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.,7,15,N/A,16S,6,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Table 2,9 November 2023,Yjung24,Yjung24,"Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|459786,Complete,Peace Sandy
bsdb:851/2/1,Study 851,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes JD, Van Domselaar G , Bernstein CN",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 2,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0003346,UBERON:0000331",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,non-inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.,7,21,N/A,16S,6,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Table 2,9 November 2023,Yjung24,Yjung24,"Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|201174|1760|2037|2049|1654;2|1239;2|1224|1236|72274|2887365|2742;2|1224;2|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:851/2/2,Study 851,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes JD, Van Domselaar G , Bernstein CN",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 2,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0003346,UBERON:0000331",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,non-inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.,7,21,N/A,16S,6,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Table 2,9 November 2023,Yjung24,Yjung24,"Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:851/3/1,Study 851,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes JD, Van Domselaar G , Bernstein CN",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 3,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0003346,UBERON:0000331",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as inflamed as per the clinical pathologist.,27,26,N/A,16S,6,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,increased,increased,decreased,Signature 1,Table 2,9 November 2023,Yjung24,Yjung24,"Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224;2|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:851/3/2,Study 851,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes JD, Van Domselaar G , Bernstein CN",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 3,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0003346,UBERON:0000331",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as inflamed as per the clinical pathologist.,27,26,N/A,16S,6,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,increased,increased,decreased,Signature 2,Table 2,9 November 2023,Yjung24,Yjung24,"Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976;2|976|200643|171549|171550|239759;2|976|200643|171549|2005525|375288,Complete,Peace Sandy
bsdb:852/1/1,Study 852,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J, Park T, Kim HJ, An S , Sul WJ",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 1,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3A",10 November 2023,Deacme,"Deacme,Folakunmi",Result of linear discriminant analysis effect size (LEfSe) for bacteria in the cheek between acne and healthy groups,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|1236|135624|84642;2;2|201174|1760|85007|1653|1716;2|1224|1236|135614|32033|40323,Complete,Folakunmi
bsdb:852/1/2,Study 852,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J, Park T, Kim HJ, An S , Sul WJ",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 1,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3A",10 November 2023,Deacme,"Deacme,Davvve,Folakunmi",Result of linear discriminant analysis effect size (LEfSe)for bacteria in the cheek between acne and healthy groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Candidatus Korobacteraceae|g__Candidatus Korobacter|s__Candidatus Korobacter versatilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota",2|201174|1760|2037|2049|1654;2|57723|204432|204433|3121618|658061|658062;2|201174|1760|85007|1653|1716|61592;2|201174|1760|85007|85029|37914;2|1224|1236|91347|543|561|562;2|1239|1737404|1737405|1570339|150022;2|32066|203490|203491|1129771|32067;2|1239|186801|3085636|186803|437755;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2759,Complete,Folakunmi
bsdb:852/2/1,Study 852,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J, Park T, Kim HJ, An S , Sul WJ",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 2,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3), Figure S3B",10 November 2023,Deacme,"Deacme,Folakunmi",Result of linear discriminant analysis effect size (LEfSe) for bacteria in the forehead between acne and healthy groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836,Complete,Folakunmi
bsdb:852/3/1,Study 852,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J, Park T, Kim HJ, An S , Sul WJ",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 3,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2),Figure S3C",10 November 2023,Deacme,"Deacme,Folakunmi",Result of linear discriminant analysis effect size (LEfSe) for fungi in the cheek microbiome between acne and healthy groups.,increased,"k__Eukaryota|k__Fungi|p__Mucoromycota|c__Endogonomycetes|o__Endogonales|f__Densosporaceae|g__Densospora,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",2759|4751|1913637|2212702|4869|2052797|2570834;2759|4751|5204|1538075|162474|742845|55193|76773,Complete,Folakunmi
bsdb:852/3/2,Study 852,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J, Park T, Kim HJ, An S , Sul WJ",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 3,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3C",10 November 2023,Deacme,"Deacme,Folakunmi",Result of linear discriminant analysis effect size (LEfSe) for fungi in the cheek microbiome between acne and healthy groups.,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia slooffiae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae",2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|5204|1538075|162474|742845|55193|76776;2759|4751|5204|1538075|162474;2759|4751|4890|4891|4892|4893|4930|4932,Complete,Folakunmi
bsdb:852/4/1,Study 852,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J, Park T, Kim HJ, An S , Sul WJ",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 4,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3),Figure S3D",10 November 2023,Deacme,"Deacme,Folakunmi",Result of linear discriminant analysis effect size (LEfSe)for fungi in the forehead mycobiome between acne and healthy groups,increased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,2759|4751|5204|1538075|162474|742845|55193|76773,Complete,Folakunmi
bsdb:852/4/2,Study 852,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J, Park T, Kim HJ, An S , Sul WJ",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 4,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3), Figure S3D",10 November 2023,Deacme,"Deacme,Folakunmi",Result of linear discriminant analysis effect size (LEfSe)for fungi in the forehead mycobiome between acne and healthy groups,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Schizoporaceae|g__Xylodon|s__Xylodon flaviporus",2759|4751|5204|1538075|162474|742845|55193|76773;2759|4751|5204|155619|139380|574935|1124675|2173181,Complete,Folakunmi
bsdb:853/1/NA,Study 853,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West KA, Yin X, Rutherford EM, Wee B, Choi J, Chrisman BS, Dunlap KL, Hannibal RL, Hartono W, Lin M, Raack E, Sabino K, Wu Y, Wall DP, David MM, Dabbagh K, DeSantis TZ , Iwai S",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 1,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,neurotypical (NT),Autism Spectrum Disorder (ASD),The study focuses on the composition of the human gut microbiome in children with ASD compared to neurotypical children.,NA,NA,NA,16S,4,Illumina,DESeq2,NA,NA,NA,age,"age,sex",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:853/2/NA,Study 853,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West KA, Yin X, Rutherford EM, Wee B, Choi J, Chrisman BS, Dunlap KL, Hannibal RL, Hartono W, Lin M, Raack E, Sabino K, Wu Y, Wall DP, David MM, Dabbagh K, DeSantis TZ , Iwai S",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 2,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,neurotypical (NT),Autism Spectrum Disorder (ASD),The study focuses on the composition of the human gut microbiome in children with ASD compared to neurotypical children.,NA,NA,NA,WMS,NA,Illumina,NA,NA,NA,NA,age,"age,sex",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:853/3/NA,Study 853,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West KA, Yin X, Rutherford EM, Wee B, Choi J, Chrisman BS, Dunlap KL, Hannibal RL, Hartono W, Lin M, Raack E, Sabino K, Wu Y, Wall DP, David MM, Dabbagh K, DeSantis TZ , Iwai S",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 3,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,neurotypical (NT),Autism Spectrum Disorder (ASD),The study focuses on the composition of the human gut microbiome in children with ASD compared to neurotypical children.,20,20,NA,16S,23,NA,DESeq2,0.05,NA,NA,age,"age,sex",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:854/1/1,Study 854,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H, Xiao K, Chen Z , Long Q",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,39,23,"Application of antibiotic or immunomodulatory eyedrops in the
previous 4 weeks,",16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota",2|1224|1236|2887326|468|469;2|1239|186801|186802|31979|1485;2|201174|1760|85007|1653|1716;2|1239,Complete,Peace Sandy
bsdb:854/1/2,Study 854,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H, Xiao K, Chen Z , Long Q",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,39,23,"Application of antibiotic or immunomodulatory eyedrops in the
previous 4 weeks,",16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota",2|1239|91061|1385|186817|1386;2|976;2|1117;2|1224,Complete,Peace Sandy
bsdb:854/2/1,Study 854,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H, Xiao K, Chen Z , Long Q",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Non Sjogrens Syndrome Dry Eye (NSSDE),Patients with Non-Sjogrens Syndrome Dry Eye,39,36,"Application of antibiotic or immunomodulatory eyedrops in the
previous 4 weeks,",16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Tables 3 and 4,10 November 2023,Mary Bearkland,Mary Bearkland,"TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224;2|201174;2|1224|1236|2887326|468|469;2|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:854/2/2,Study 854,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H, Xiao K, Chen Z , Long Q",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Non Sjogrens Syndrome Dry Eye (NSSDE),Patients with Non-Sjogrens Syndrome Dry Eye,39,36,"Application of antibiotic or immunomodulatory eyedrops in the
previous 4 weeks,",16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Tables 3 and 4,10 November 2023,Mary Bearkland,Mary Bearkland,"TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Cyanobacteriota",2|1239|91061|1385|186817|1386;2|1117,Complete,Peace Sandy
bsdb:854/3/1,Study 854,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H, Xiao K, Chen Z , Long Q",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 3,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Non Sjogrens Syndrome Dry Eye (NSSDE),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,36,23,"Application of antibiotic or immunomodulatory eyedrops in the
previous 4 weeks,",16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Tables 3 and 4,10 November 2023,Mary Bearkland,Mary Bearkland,"TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",increased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Peace Sandy
bsdb:854/3/2,Study 854,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H, Xiao K, Chen Z , Long Q",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 3,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Non Sjogrens Syndrome Dry Eye (NSSDE),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,36,23,"Application of antibiotic or immunomodulatory eyedrops in the
previous 4 weeks,",16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Tables 3 and 4,10 November 2023,Mary Bearkland,Mary Bearkland,"TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota",2|1239|186801|186802|31979|1485;2|1224,Complete,Peace Sandy
bsdb:855/1/1,Study 855,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S, Vani G, Donthineni PR, Basu S , Arunasri K",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 1,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Dry Eye Disease patients,Both Sjogren's and non-Sjogren's patients with Dry Eye Disease,18,24,No medications in the past month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2A,18 November 2023,Mary Bearkland,Mary Bearkland,Table S2A: Discriminative genera in SS and NSS compared to HC,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Marinococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea",2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|1737404|1582879;2|1239|186801|186802|216572|236752;2|201174|1760|85004|31953|2701;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|1224|1236|135614|32033|83614;2|1239|91061|1385|186817|1370;2|201174|1760|85007|85025|1817;2|1239|1737404|1737405|1570339|543311;2|1224|28211|356|2843305|1632780;2|1224|1236|72274|135621|286;2|1224|28211|204455|31989|1060;2|201174|84998|1643822|1643826|84108;2|1224|28211|204457|41297|165695;2|32066|203490|203491|1129771|34104;2|201174|1760|85011|2062|1883;2|201174|1760|85007|85028|2060;2|1224|28216|206389|2008794|349,Complete,Peace Sandy
bsdb:855/1/2,Study 855,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S, Vani G, Donthineni PR, Basu S , Arunasri K",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 1,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Dry Eye Disease patients,Both Sjogren's and non-Sjogren's patients with Dry Eye Disease,18,24,No medications in the past month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2A,18 November 2023,Mary Bearkland,Mary Bearkland,Table S2A: Discriminative genera in SS and NSS compared to HC,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae|g__Aureimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae|g__Microbispora|s__Microbispora rosea|s__Microbispora rosea subsp. aerata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|28216|80840|80864|12916;2|1224|1236|2887326|468|469;2|1224|1236|135624|84642|642;2|1224|1236|135622|72275|111142;2|976|200643|171549|171552|1283313;2|201174|1760|85006|1268|1663;2|1224|28211|356|255475|414371;2|1239|91061|1385|186817|1386;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1224|1236|1706369|1706371|10;2|976|117743|200644|2762318|59732;2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216;2|1224|28216|80840|80864|80865;2|1239|91061|186826|186828|82800;2|201174|1760|85007|85029|37914;2|1239|91061|1385|186817|1433999;2|976|117743|200644|2762318|59734;2|1224|28211|356|212791;2|201174|1760|85007|85026|2053;2|1239|91061|186826|186828|117563;2|1224|28211|204455|31989|366614;2|1224|1236|135619|28256|2745;2|201174|1760|85006|85021|53457;2|1224|1236|91347|543|570;2|201174|1760|85006|1268|57493;2|201174|1760|85006|2805426|57499;2|1239|91061|186826|33958|1578;2|201174|1760|85007|2805586|1847725;2|32066|203490|203491|1129771|32067;2|1224|1236|135614|32033|68;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045|407;2|201174|1760|85006|85023|33882;2|201174|1760|85012|2004|2005|58117|2010;2|201174|1760|85006|1268|1269;2|201174|1760|85007|1762|1763;2|1239|91061|1385|186822|44249;2|1224|28211|204455|31989|265;2|1224|28211|356|69277|28100;2|201174|1760|85006|85018|985001;2|201174|1760|85009|31957|1085622;2|1224|1236|135614|32033|83618;2|1224|28211|204457|335929|1855416;2|201174|1760|85006|1268|32207;2|1224|1236|91347|1903411|613;2|1224|1236|135622|267890|22;2|1224|28211|204441|2829815|204447;2|1224|1236|135614|32033|40323,Complete,Peace Sandy
bsdb:855/2/1,Study 855,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S, Vani G, Donthineni PR, Basu S , Arunasri K",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 2,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Sjogren's patients with Dry Eye Disease,Sjogren's patients with Dry Eye Disease,18,9,No medications in the past month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2B,19 November 2023,Mary Bearkland,Mary Bearkland,Table S2B: Discriminative genera in SS compared to HC,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Marinococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,k__Bacteria|s__uncultured bacterium",2|976|117743|200644|2762318|59735;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|1737404|1582879;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|1578;2|1224|28216|80840|119060|47670;2|1239|91061|1385|186817|1370;2|1239|1737404|1737405|1570339|543311;2|1224|28211|356|2843305|1632780;2|1224|28211|356|69277|28100;2|1224|1236|72274|135621|286;2|1224|28211|204455|31989|1060;2|1224|1236|91347|543|590;2|1224|28211|204457|41297|165695;2|201174|1760|85011|2062|1883;2|201174|1760|85007|85028|2060;2|77133,Complete,Peace Sandy
bsdb:855/2/2,Study 855,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S, Vani G, Donthineni PR, Basu S , Arunasri K",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 2,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Sjogren's patients with Dry Eye Disease,Sjogren's patients with Dry Eye Disease,18,9,No medications in the past month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2B,19 November 2023,Mary Bearkland,Mary Bearkland,Table S2B: Discriminative genera in SS compared to HC,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea",2|1224|28216|80840|80864|12916;2|1224|1236|135622|72275|111142;2|976|200643|171549|171552|1283313;2|1239|1737404|1737405|1570339|165779;2|201174|1760|85006|1268|1663;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1224|1236|1706369|1706371|10;2|976|117743|200644|2762318|59732;2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216;2|1224|28216|80840|80864|80865;2|1239|91061|186826|186828|82800;2|201174|1760|85007|85029|37914;2|1239|91061|1385|186817|1433999;2|1224|28211|356|212791;2|1239|91061|1385|33986;2|1239|91061|1385|539738|1378;2|201174|1760|85007|85026|2053;2|1239|91061|186826|186828|117563;2|1224|28211|204455|31989|366614;2|1224|1236|135619|28256|2745;2|201174|1760|85006|2805426|57499;2|201174|1760|85007|2805586|1847725;2|32066|203490|203491|1129771|32067;2|1224|1236|135614|32033|83614;2|1224|1236|135614|32033|68;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045|407;2|201174|1760|85006|85023|33882;2|201174|1760|85006|1268|1269;2|201174|1760|85007|1762|1763;2|1224|28211|204455|31989|265;2|201174|1760|85006|85018|985001;2|201174|1760|85009|31957|1085622;2|1224|28211|204457|335929|1855416;2|201174|1760|85006|1268|32207;2|1224|1236|91347|1903411|613;2|1224|1236|135622|267890|22;2|1224|28211|204441|2829815|204447;2|1224|1236|135614|32033|40323;2|1224|1236|135623|641|662;2|1239|91061|186826|33958|46255;2|1224|28216|206389|2008794|349,Complete,Peace Sandy
bsdb:855/3/1,Study 855,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S, Vani G, Donthineni PR, Basu S , Arunasri K",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 3,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Non-Sjogren's Syndrome patients with Dry Eye Disease,Non-Sjogren's patients with Dry Eye Disease,18,15,No medications in the past month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2C,19 November 2023,Mary Bearkland,"Mary Bearkland,Muqtadirat",Table S2C: Discriminative genera in NSS compared to HC,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Marinococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas|s__Roseomonas gilardii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|s__Rhodobacteraceae bacterium HIMB11",2|976|117743|200644|2762318|59735;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|1737404|1582879;2|1239|186801|186802|216572|236752;2|201174|1760|85004|31953|2701;2|1224|28216|80840|119060|47670;2|1224|1236|135614|32033|83614;2|1239|91061|1385|186817|1370;2|201174|1760|85006|85023|33882;2|201174|1760|85007|85025|1817;2|1239|1737404|1737405|1570339|543311;2|1224|28211|356|69277|28100;2|1224|1236|72274|135621|286;2|1224|28211|204455|31989|1060;2|1224|28211|204441|433|125216|257708;2|201174|1760|85006|1268|32207;2|1224|1236|91347|1903411|613;2|1224|28211|204457|41297|165695;2|32066|203490|203491|1129771|34104;2|201174|1760|85011|2062|1883;2|1239|186801|186802|216572|292632;2|201174|1760|85007|85028|2060;2|1224|28216|206389|2008794|349;2|1224|28211|204455|31989|1366046,Complete,Peace Sandy
bsdb:855/3/2,Study 855,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S, Vani G, Donthineni PR, Basu S , Arunasri K",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 3,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Non-Sjogren's Syndrome patients with Dry Eye Disease,Non-Sjogren's patients with Dry Eye Disease,18,15,No medications in the past month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2C,19 November 2023,Mary Bearkland,Mary Bearkland,Table S2C: Discriminative genera in NSS compared to HC,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Mangrovibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|28216|80840|80864|12916;2|1224|1236|2887326|468|469;2|1224|1236|135624|84642|642;2|1224|1236|135622|72275|111142;2|976|200643|171549|171552|1283313;2|1239|91061|1385|186817|150247;2|1239|91061|1385|186817|1386;2|201174|1760|85004|31953|1678;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1224|28211|204458|76892|41275;2|1224|1236|1706369|1706371|10;2|976|117743|200644|2762318|59732;2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216;2|1224|28216|80840|80864|80865;2|1239|91061|186826|186828|82800;2|201174|1760|85007|85029|37914;2|1239|91061|1385|186817|1433999;2|976|117743|200644|2762318|59734;2|1224|28211|356|212791;2|201174|1760|85007|85026|2053;2|1224|28211|204455|31989|366614;2|1224|1236|135625|712|724;2|1224|1236|135619|28256|2745;2|201174|1760|85006|85021|53457;2|1224|1236|91347|543|570;2|201174|1760|85006|1268|57493;2|201174|1760|85006|2805426|57499;2|201174|1760|85007|2805586|1847725;2|32066|203490|203491|1129771|32067;2|1224|1236|135614|32033|68;2|1224|1236|91347|543|451512;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045|407;2|201174|1760|85006|1268|1269;2|201174|1760|85007|1762|1763;2|1239|91061|1385|186822|44249;2|1224|28211|204455|31989|265;2|201174|1760|85006|85018|985001;2|201174|1760|85009|31957|1085622;2|1224|1236|135614|32033|83618;2|1224|28211|204457|335929|1855416;2|1224|1236|135622|267890|22;2|1224|28211|204441|2829815|204447;2|201174|84998|1643822|1643826|84108;2|1224|1236|135614|32033|40323,Complete,Peace Sandy
bsdb:856/1/1,Study 856,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z, Xiao Y, Jia Y, Lin Q, Qian Y, Cui L, Xiang Z, Li M, Yang C , Zou H",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,LEfSe,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 3g and Results within text (Page 7, Last 6 lines, Under subheading: Composition and difference analysis of the ocular microbiome)",11 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing","Fig 3g: Species composition with significant difference
at the species level between the NDM and DM-DE groups (top 20)",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides|s__Mycobacteroides abscessus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium nitrogenifigens,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium sp. Fuku2-ISO-50,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus odorifer,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio agarivorans",2|201174|1760|85007|1762|670516|36809;2|1224|28211|204457|41297|165696|378548;2|1224|28211|204457|41297|165696|1739114;2|1239|91061|1385|186822|44249|189426;2|1239|91061|1385|90964|1279|1280;2|1239|91061|186826|1300|1301|1302;2|1224|1236|135623|641|662|153622,Complete,ChiomaBlessing
bsdb:856/1/2,Study 856,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z, Xiao Y, Jia Y, Lin Q, Qian Y, Cui L, Xiang Z, Li M, Yang C , Zou H",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,LEfSe,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 3g and Results within text (Page 7, Last 6 lines, Under subheading: Composition and difference analysis of the ocular microbiome)",11 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing","Figure 3g Species composition with significant difference
at the species level between the NDM and DM-DE groups (top 20)",increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Cordyceps|s__Cordyceps militaris,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter mori,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc sp. DORA_2,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio vulnificus",2759|4751|4890|147550|5125|474943|45234|73501;2|1224|1236|91347|543|547|539813;2|1239|91061|186826|33958|1243|1403934;2|1224|1236|91347|543|590|28901;2|1224|1236|135623|641|662|672,Complete,ChiomaBlessing
bsdb:856/2/1,Study 856,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z, Xiao Y, Jia Y, Lin Q, Qian Y, Cui L, Xiang Z, Li M, Yang C , Zou H",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,ANOSIM,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Text on page 5; Under subheading ""Composition and difference analysis of the ocular microbiome""",18 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Composition and Differential analysis of the ocular microbiome between NDM and DM-DE groups,increased,"k__Bacteria|p__Actinomycetota,k__Eukaryota|p__Apicomplexa,k__Eukaryota|k__Fungi|p__Ascomycota,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc sp. DORA_2,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium leprae,k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae|g__Plasmodium|s__Plasmodium ovale,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",2|201174;2759|5794;2759|4751|4890;2|204428|204429|51291|809|810|813;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561|562;2|1239|91061|186826|33958|1243|1403934;2|201174|1760|85007|1762|1763|1769;2759|5794|422676|5819|1639119|5820|36330;2|1224|1236|91347|543|590|28901;2|1224|1236|135623|641|662,Complete,ChiomaBlessing
bsdb:856/2/2,Study 856,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z, Xiao Y, Jia Y, Lin Q, Qian Y, Cui L, Xiang Z, Li M, Yang C , Zou H",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,ANOSIM,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Text on page 5; Under subheading ""Composition and difference analysis of the ocular microbiome""",18 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing",Composition and Differential analysis of the ocular microbiome between NDM and DM-DE groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",2|1224|1236|2887326|468|469|40214;2|1239;2|1239|91061|186826|81852|1350|1351;2|1224;2|1239|91061|1385|90964|1279|1280;2|1239|91061|186826|1300|1301|1313,Complete,ChiomaBlessing
bsdb:857/1/1,Study 857,case-control,28536926,10.1007/s11427-016-9001-4,NA,"Li W, Wu X, Hu X, Wang T, Liang S, Duan Y, Jin F , Qin B",Structural changes of gut microbiota in Parkinson's disease and its correlation with clinical features,Science China. Life sciences,2017,"16S rRNA sequencing, gastrointestinal dysfunction, gut-brain-axis, microbiome, short chain fatty acids, α-synuclein",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease,14,24,3 months,16S,345,Illumina,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,12 April 2024,MyleeeA,"MyleeeA,Scholastica",Significantly abundant genera in Parkinson's disease (PD) compared to healthy control (HC) group,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|909932|1843488|909930|904;2|1224|1236|2887326|468|469;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1224|1236|91347|1903414|583;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:857/1/2,Study 857,case-control,28536926,10.1007/s11427-016-9001-4,NA,"Li W, Wu X, Hu X, Wang T, Liang S, Duan Y, Jin F , Qin B",Structural changes of gut microbiota in Parkinson's disease and its correlation with clinical features,Science China. Life sciences,2017,"16S rRNA sequencing, gastrointestinal dysfunction, gut-brain-axis, microbiome, short chain fatty acids, α-synuclein",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease,14,24,3 months,16S,345,Illumina,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,13 April 2024,Shulamite,"Shulamite,Scholastica",Significantly abundant genera in Parkinson's disease (PD) compared to healthy control (HC) group,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:858/1/1,Study 858,case-control,36941248,10.1038/s41398-023-02325-5,NA,"Butler MI, Bastiaanssen TFS, Long-Smith C, Morkl S, Berding K, Ritz NL, Strain C, Patangia D, Patel S, Stanton C, O'Mahony SM, Cryan JF, Clarke G , Dinan TG",The gut microbiome in social anxiety disorder: evidence of altered composition and function,Translational psychiatry,2023,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Social anxiety disorder,EFO:1001917,Healthy controls,Patients with Social Anxiety Disorder (SAD),Patients with Social Anxiety Disorder (SAD),31,18,4 weeks,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex","age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Fig 2, Text",16 November 2023,Chinelsy,"Chinelsy,Peace Sandy",Genus and species level differences between SAD and healthy controls.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter",2|1239|186801|186802|3082771|1924093;2|1239|186801|186802|3082771|1924093|1965604;2|201174|84998|1643822|1643826|644652,Complete,Peace Sandy
bsdb:858/1/2,Study 858,case-control,36941248,10.1038/s41398-023-02325-5,NA,"Butler MI, Bastiaanssen TFS, Long-Smith C, Morkl S, Berding K, Ritz NL, Strain C, Patangia D, Patel S, Stanton C, O'Mahony SM, Cryan JF, Clarke G , Dinan TG",The gut microbiome in social anxiety disorder: evidence of altered composition and function,Translational psychiatry,2023,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Social anxiety disorder,EFO:1001917,Healthy controls,Patients with Social Anxiety Disorder (SAD),Patients with Social Anxiety Disorder (SAD),31,18,4 weeks,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex","age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Fig 2, Text",28 December 2023,Peace Sandy,Peace Sandy,Genus and species level differences between SAD and healthy controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis",2|1224|28216|80840|995019|577310;2|1224|28216|80840|995019|577310|487175,Complete,Peace Sandy
bsdb:859/1/1,Study 859,time series / longitudinal observational,37184522,10.1097/HC9.0000000000000151,NA,"Waldner B, Aldrian D, Zöggeler T, Oberacher H, Oberhuber R, Schneeberger S, Messner F, Schneider AM, Kohlmaier B, Lanzersdorfer R, Huber WD, Entenmann A, Müller T , Vogel GF",The influence of liver transplantation on the interplay between gut microbiome and bile acid homeostasis in children with biliary atresia,Hepatology communications,2023,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,Children with BA before - [pre],Post24 + m,The impact of LT and reestablishment of bile flow on gut microbiome–bile acid homeostasis in children with BA for more than 24 months (post24 + m) after liver transplantation (LT),10,12,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,NA,NA,increased,increased,increased,NA,increased,Signature 1,FIGURE 3,9 February 2024,Peace Sandy,Peace Sandy,"Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (C) Cladogram of LEfSe analysis results of pre and post24 + m groups on the taxonomic order level. Over-representation of taxa is color-coded in red (post24 + m) and green (pre). Radiating circle depicts phylum to order level. (E) Barchart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|976|200643|171549;2|976|200643;2|1239|186801;2|201174|84998|84999;2|201174|84998;2|28221;2|200940|3031449|213115;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802,Complete,Peace Sandy
bsdb:859/1/2,Study 859,time series / longitudinal observational,37184522,10.1097/HC9.0000000000000151,NA,"Waldner B, Aldrian D, Zöggeler T, Oberacher H, Oberhuber R, Schneeberger S, Messner F, Schneider AM, Kohlmaier B, Lanzersdorfer R, Huber WD, Entenmann A, Müller T , Vogel GF",The influence of liver transplantation on the interplay between gut microbiome and bile acid homeostasis in children with biliary atresia,Hepatology communications,2023,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,Children with BA before - [pre],Post24 + m,The impact of LT and reestablishment of bile flow on gut microbiome–bile acid homeostasis in children with BA for more than 24 months (post24 + m) after liver transplantation (LT),10,12,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,NA,NA,increased,increased,increased,NA,increased,Signature 2,Fig 3,9 February 2024,Peace Sandy,Peace Sandy,"Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (C) Cladogram of LEfSe analysis results of pre and post24 + m groups on the taxonomic order level. Over-representation of taxa is color-coded in red (post24 + m) and green (pre). Radiating circle depicts phylum to order level. (E) Barchart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli",2|201174|1760|85006;2|29547|3031852|213849;2|1239|91061|1385;2|1239|91061|186826;2|1239|91061,Complete,Peace Sandy
bsdb:859/2/1,Study 859,time series / longitudinal observational,37184522,10.1097/HC9.0000000000000151,NA,"Waldner B, Aldrian D, Zöggeler T, Oberacher H, Oberhuber R, Schneeberger S, Messner F, Schneider AM, Kohlmaier B, Lanzersdorfer R, Huber WD, Entenmann A, Müller T , Vogel GF",The influence of liver transplantation on the interplay between gut microbiome and bile acid homeostasis in children with biliary atresia,Hepatology communications,2023,NA,Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,post 24 + m Control,Post24 + m,The impact of LT and reestablishment of bile flow on gut microbiome–bile acid homeostasis in children with BA for more than 24 months (post24 + m) after liver transplantation (LT),19,12,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,FIGURE 3,9 February 2024,Peace Sandy,Peace Sandy,"Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (D) Cladogram of LEfSe analysis results of post24 + m and age-matched control groups (p24 + m control) on the taxonomic order level.
Over-representation of taxa is color-coded in red (p24 + m control) and green (post24 + m). Radiating circle depicts phylum to order level.  Bar chart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m in (F)",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|1224|1236|91347;2|1224|1236,Complete,Peace Sandy
bsdb:859/2/2,Study 859,time series / longitudinal observational,37184522,10.1097/HC9.0000000000000151,NA,"Waldner B, Aldrian D, Zöggeler T, Oberacher H, Oberhuber R, Schneeberger S, Messner F, Schneider AM, Kohlmaier B, Lanzersdorfer R, Huber WD, Entenmann A, Müller T , Vogel GF",The influence of liver transplantation on the interplay between gut microbiome and bile acid homeostasis in children with biliary atresia,Hepatology communications,2023,NA,Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,post 24 + m Control,Post24 + m,The impact of LT and reestablishment of bile flow on gut microbiome–bile acid homeostasis in children with BA for more than 24 months (post24 + m) after liver transplantation (LT),19,12,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3,9 February 2024,Peace Sandy,Peace Sandy,"Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (D) Cladogram of LEfSe analysis results of post24 + m and age-matched control groups (p24 + m control) on the taxonomic order level. Over-representation of taxa is color-coded in red (p24 + m control) and green (post24 + m). Radiating circle depicts phylum to order level. Bar chart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m in (F)",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia",2|201174|1760|85004;2|201174;2|1239|186801|186802;2|1239|186801,Complete,Peace Sandy
bsdb:860/1/1,Study 860,time series / longitudinal observational,34766210,10.1007/s00248-021-01914-5,NA,"Sanseverino I, Pretto P, António DC, Lahm A, Facca C, Loos R, Skejo H, Beghi A, Pandolfi F, Genoni P , Lettieri T",Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese,Microbial ecology,2022,"Algal bloom, Freshwater, Lyngbya, Metagenomics, Microbial populations, Water quality",Experiment 1,Italy,Not specified,NA,NA,NA,NA,No healthy samples,2017 samples,"2017 samples are samples obtained from the three river depths(Meso, Secchi, and surface depth) during the cyanobacterial bloom in 2017.",NA,3,non,16S,34,Illumina,NA,0.05,NA,NA,NA,NA,decreased,decreased,unchanged,decreased,NA,decreased,Signature 1,Figure 3,7 March 2024,Imaspecial,Imaspecial,"Taxonomic analysis at the phylum level showed that, in most of the samples, Proteobacteria was the predominant taxonomic group followed by Actinobacteriota, Cyanobacteria and Bacteroidota .",increased,NA,NA,Complete,NA
bsdb:861/1/NA,Study 861,time series / longitudinal observational,34711536,10.1183/13993003.01932-2021,https://erj.ersjournals.com/content/59/1/2101932.long,"Cuthbertson L, James P, Habibi MS, Thwaites RS, Paras A, Chiu C, Openshaw PJM, Cookson WOC , Moffatt MF",Resilience of the respiratory microbiome in controlled adult RSV challenge study,The European respiratory journal,2022,NA,Experiment 1,United Kingdom,Homo sapiens,"Nasal cavity,Throat","UBERON:0001707,UBERON:0000341",Respiratory Syncytial Virus Infection,EFO:1001413,NA,Healthy non-smoking adults,Healthy non-smoking adults between 18 and 50 years of age.,NA,37,NA,16S,4,Illumina,"DESeq2,Mann-Whitney (Wilcoxon),PERMANOVA,ANOVA",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:862/1/1,Study 862,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker AJ, Lonergan M, Keir HR, Smith AH, Pollock J, Finch S, Cassidy AJ, Huang JTJ , Chalmers JD",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 1,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,MONDO:0004822,Less severe bronchiectasis,Severe bronchiectasis,Stable sputum samples with more severe bronchiectasis severity index (BSI) score [BSI ≥ 9],281,281,None,16S,34,Illumina,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2C,9 March 2024,Scholastica,Scholastica,Random forest plot indicating the bacterial taxa associated with a more severe BSI score and a less severe BSI score,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|1236|91347|543;2|1224|1236|72274|135621|286;2|1224|1236|135614|32033|40323,Complete,NA
bsdb:862/1/2,Study 862,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker AJ, Lonergan M, Keir HR, Smith AH, Pollock J, Finch S, Cassidy AJ, Huang JTJ , Chalmers JD",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 1,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,MONDO:0004822,Less severe bronchiectasis,Severe bronchiectasis,Stable sputum samples with more severe bronchiectasis severity index (BSI) score [BSI ≥ 9],281,281,None,16S,34,Illumina,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2C,9 March 2024,Scholastica,Scholastica,Random forest plot indicating the bacterial taxa associated with a more severe BSI score and a less severe BSI score,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2;2|1239|526524|526525|128827|118747;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|32257;2|1239|186801|3085636|186803;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|186801|3085636|186803|437755;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1239|186801|3085636|186803|265975;2|976|200643|171549|2005523|346096;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|970;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174|1760|85006|1268|32207,Complete,NA
bsdb:862/2/1,Study 862,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker AJ, Lonergan M, Keir HR, Smith AH, Pollock J, Finch S, Cassidy AJ, Huang JTJ , Chalmers JD",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 2,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,MONDO:0004822,Non-frequent exacerbating stable patients,Frequent exacerbating stable patients,Frequent exacerbating stable patients (≥ 3 exacerbation),281,281,None,16S,34,Illumina,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3C,9 March 2024,Scholastica,Scholastica,Random forest plot showing the bacterial taxa associated with three or more exacerbations in the previous year and those associated with fewer exacerbations,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236|91347|543;2|1224|1236|72274|135621|286,Complete,NA
bsdb:862/2/2,Study 862,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker AJ, Lonergan M, Keir HR, Smith AH, Pollock J, Finch S, Cassidy AJ, Huang JTJ , Chalmers JD",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 2,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,MONDO:0004822,Non-frequent exacerbating stable patients,Frequent exacerbating stable patients,Frequent exacerbating stable patients (≥ 3 exacerbation),281,281,None,16S,34,Illumina,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3C,9 March 2024,Scholastica,Scholastica,Random forest plot showing the bacterial taxa associated with three or more exacerbations in the previous year and those associated with fewer exacerbations,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|416916;2|201174|84998|84999|1643824|1380;2;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1224|28216|80840|80864;2|201174|1760|85007|1653|1716;2|976|117743|200644|49546;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|32257;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1224|1236|2887326|468|475;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1239|186801|3085636|186803|265975;2|976|200643|171549|2005523|346096;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|970;2|1239|91061|1385|90964|1279;2|1224|1236|135614|32033|40323;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|976|117743|200644|2762318;2|201174|1760|85006|1268|32207,Complete,NA
bsdb:862/3/1,Study 862,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker AJ, Lonergan M, Keir HR, Smith AH, Pollock J, Finch S, Cassidy AJ, Huang JTJ , Chalmers JD",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 3,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,MONDO:0004822,Stable samples,Exacerbation samples,Sputum samples at onset of exacerbation,64,64,None,16S,34,Illumina,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4C,10 March 2024,Scholastica,Scholastica,"Random forest plot showing the bacterial taxa associated with exacerbation samples, and those associated with stable samples from 64 pairs of one stable and one exacerbation sample per patient.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|1224|28216|206351|481|538;2|1239|91061|186826|186828|117563,Complete,NA
bsdb:862/3/2,Study 862,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker AJ, Lonergan M, Keir HR, Smith AH, Pollock J, Finch S, Cassidy AJ, Huang JTJ , Chalmers JD",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 3,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,MONDO:0004822,Stable samples,Exacerbation samples,Sputum samples at onset of exacerbation,64,64,None,16S,34,Illumina,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4C,10 March 2024,Scholastica,Scholastica,"Random forest plot showing the bacterial taxa associated with exacerbation samples, and those associated with stable samples from 64 pairs of one stable and one exacerbation sample per patient.",decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1224|28211|356|82115|357;2|29547|3031852|213849|72294|194;2|976|117743|200644|2762318|59732;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174|1760|85006|1268|32207,Complete,NA
bsdb:863/1/1,Study 863,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su YJ, Luo SD, Hsu CY , Kuo HC","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Urticaria","HP:0000964,EFO:0005531",Chronic urticaria (hives),Atopic dermatitis (eczema),Patients with atopic dermatitis (eczema),9,19,Those with a history of antibiotics,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Figure 5,15 February 2024,Peace Sandy,Peace Sandy,"Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549;2|1239|186801|3082720|186804|1501226;2|1224|28216|80840|995019|40544;2|976|200643,Complete,Peace Sandy
bsdb:863/1/2,Study 863,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su YJ, Luo SD, Hsu CY , Kuo HC","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Urticaria","HP:0000964,EFO:0005531",Chronic urticaria (hives),Atopic dermatitis (eczema),Patients with atopic dermatitis (eczema),9,19,Those with a history of antibiotics,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Fig 5,15 February 2024,Peace Sandy,Peace Sandy,"Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:863/2/1,Study 863,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su YJ, Luo SD, Hsu CY , Kuo HC","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Allergic rhinitis","HP:0000964,EFO:0005854",Allergic rhinitis,Atopic dermatitis (eczema),Patients with atopic dermatitis (eczema),9,19,Those with a history of antibiotics,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Fig 5,15 February 2024,Peace Sandy,Peace Sandy,"Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549;2|976|200643;2|1239|186801|3082720|186804|1501226;2|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:863/2/2,Study 863,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su YJ, Luo SD, Hsu CY , Kuo HC","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Allergic rhinitis","HP:0000964,EFO:0005854",Allergic rhinitis,Atopic dermatitis (eczema),Patients with atopic dermatitis (eczema),9,19,Those with a history of antibiotics,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Figure 5,15 February 2024,Peace Sandy,Peace Sandy,"Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|201174|84998|84999|1643824|1380;2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186806|1730|290054;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:864/1/1,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 1,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1230 h,The post-fed group consists of fish fed at 1230 hours. (1.5 hours postfeeding),17,18,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Table S2,6 March 2024,Muqtadirat,"Muqtadirat,Victoria",The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Balneolota|c__Balneolia|o__Balneolales|f__Balneolaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Pseudidiomarina,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Roseinatronobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae|g__Sporanaerobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Ureibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",2|1224|28216|80840|506;2|1239|91061|1385|186817|150247;2|29547|3031852|213849|2808963|28196;2|1224|28216|206389|2008794|12960;2|1239|91061|1385;2|1239|91061|1385|186817|1386;2|976|200643|171549;2|1936987|1853221|1853223|1813606;2|1224|28211|356|45404;2|32066|203490|203491|203492|180162;2|1224|1236|135613|1046;2|1224|1236|91347|543|544;2|976|117743|200644|246874;2|1224|1236|91347|1903409|551;2|1239|186801|186802;2|1239|91061|1385|186817|129337;2|1224|28216|80840|80864|47420;2|1239|91061|1385|90964|227979;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|1224|1236|135622|267891|58050;2|201174|1760|85012|83676;2|74201|414999;2|1224|28211|204455|31989|265;2|1224|1236|135625|712;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1224|1236|135623|641|657;2|1239|91061|1385|186818;2|976|200643|171549|171552|838;2|1224|1236|91347|1903414|583;2|1224|1236|135622|267893|2800384;2|32066|203490|203491|203492|623282;2|1224|1236|2887326|468|497;2|1224|1236|135622|267894|67572;2|1224|28211|204455|31989|119541;2|1239|1737404|1737405|2992718|165812;2|1239|91061|1385|186818|1569;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|2992719|285105;2|1297|188787|68933|188786|270;2|1239|91061|1385|186818|160795;2|1239|91061|186826|81852|2737;2|1239|909932|1843489|31977;2|1224|1236|135623|641;2|1239|91061|1385|186817|84406;2|1224|1236|135614|32033;2|1224|1236|91347|1903411|629,Complete,Chloe
bsdb:864/1/2,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 1,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1230 h,The post-fed group consists of fish fed at 1230 hours. (1.5 hours postfeeding),17,18,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Table S2,7 March 2024,Muqtadirat,"Muqtadirat,Victoria",The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,2|1224|1236|135622,Complete,Chloe
bsdb:864/2/1,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 2,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1400 h,The post-fed group consists of fish fed at 1400 hours. (3 hours post-feeding),17,18,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental Table S2,11 April 2024,Victoria,Victoria,The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Verrucomicrobiota|c__Opitutia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsaceae,k__Bacteria|p__Balneolota|c__Balneolia|o__Balneolales|f__Balneolaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Ureibacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Pseudidiomarina,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Roseinatronobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae|g__Sporanaerobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae",2|1224|1236|135623|641|657;2|1224|1236|135623|641;2|29547|3031852|213849|2808963|28196;2|1224|28211|204455|31989|265;2|1224|1236|135622|267894|67572;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578;2|1224|1236|2887326|468|497;2|32066|203490|203491|203492|180162;2|1239|91061|186826|1300|1301;2|1239|91061|1385|186817|1386;2|1239|91061|186826|1300|1357;2|1239|91061|1385|186817|129337;2|1297|188787|68933|188786|270;2|1224|1236|135625|712;2|1239|91061|1385;2|1224|28216|80840|80864|47420;2|1224|1236|91347|543|544;2|1224|28216|80840|506;2|1239|1737404|1737405|2992719|285105;2|1239|91061|186826;2|74201|414999;2|1239|91061|1385|186818;2|1239|91061|1385|90964;2|976|117743|200644|246874;2|1239|186801|3082720|186804;2|976|200643|171549|171552|838;2|1224|1236|135614|32033;2|1239|909932|1843489|31977;2|1224|1236|91347|1903414|583;2|1239|91061|1385|186817|150247;2|1239|186801|3082720|186804|1257;2|1224|1236|135613|1046;2|1239|91061|186826|81852|2737;2|1239|91061|186826|33958|1243;2|1239|91061|1385|90964|227979;2|1224|1236|91347|1903409|551;2|976|200643|171549;2|1224|1236|91347|1903411|629;2|1224|1236|135622|267891|58050;2|32066|203490|203491|203492|623282;2|1239|91061|186826|33958;2|1239|91061|1385|186817|84406;2|1239|186801|186802;2|1239|91061|1385|186818|1569;2|201174|1760|85012|83676;2|1936987|1853221|1853223|1813606;2|1239|91061|1385|186818|160795;2|1224|28216|206389|2008794|12960;2|1224|1236|135622|267893|2800384;2|1224|28211|204455|31989|119541;2|1239|1737404|1737405|2992718|165812;2|1224|28211|356|45404,Complete,Chloe
bsdb:864/2/2,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 2,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1400 h,The post-fed group consists of fish fed at 1400 hours. (3 hours post-feeding),17,18,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental Table S2,12 April 2024,Victoria,Victoria,The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,2|1224|1236|135622,Complete,Chloe
bsdb:864/3/1,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 3,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1600 h,The post-fed group consists of fish fed at 1600 hours. (5 hours postfeeding),17,18,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Table S2,12 April 2024,Victoria,Victoria,The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsaceae,k__Bacteria|p__Balneolota|c__Balneolia|o__Balneolales|f__Balneolaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Ureibacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Pseudidiomarina,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Roseinatronobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae|g__Sporanaerobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae",2|1224|1236|91347|1903411|629;2|976|200643|171549;2|1224|1236|91347|1903409|551;2|1239|91061|1385|90964|227979;2|1239|91061|186826|33958|1243;2|1239|91061|186826|81852|2737;2|1224|1236|135613|1046;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|186817|150247;2|1224|1236|91347|1903414|583;2|1239|909932|1843489|31977;2|1224|1236|135614|32033;2|976|200643|171549|171552|838;2|1239|186801|3082720|186804;2|1239|91061|1385|90964;2|1239|91061|1385|186818;2|74201|414999;2|1239|91061|186826;2|1239|91061|1385;2|1239|1737404|1737405|2992719|285105;2|1224|28216|80840|506;2|1224|1236|91347|543|544;2|1224|28216|80840|80864|47420;2|1224|1236|135625|712;2|1297|188787|68933|188786|270;2|1239|91061|1385|186817|129337;2|1239|91061|186826|1300|1357;2|1239|91061|1385|186817|1386;2|1239|91061|186826|1300|1301;2|32066|203490|203491|203492|180162;2|1224|1236|2887326|468|497;2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1224|1236|135622|267894|67572;2|1224|28211|204455|31989|265;2|29547|3031852|213849|2808963|28196;2|1224|1236|135623|641;2|1224|1236|135623|641|657;2|1224|1236|135622|267891|58050;2|32066|203490|203491|203492|623282;2|1239|91061|186826|33958;2|1239|91061|1385|186817|84406;2|1239|186801|186802;2|1239|91061|1385|186818|1569;2|201174|1760|85012|83676;2|1936987|1853221|1853223|1813606;2|1239|91061|1385|186818|160795;2|1224|28216|206389|2008794|12960;2|1224|1236|135622|267893|2800384;2|1224|28211|204455|31989|119541;2|1239|1737404|1737405|2992718|165812;2|1224|28211|356|45404,Complete,Chloe
bsdb:864/3/2,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 3,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1600 h,The post-fed group consists of fish fed at 1600 hours. (5 hours postfeeding),17,18,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Table S2,12 April 2024,Victoria,Victoria,The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales",2|976|117743|200644|246874;2|1224|1236|135622,Complete,Chloe
bsdb:864/4/1,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 4,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 2000 h,The post-fed group consists of fish fed at 2000 hours. (9 hours post-feeding),17,17,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table S2,12 April 2024,Victoria,Victoria,The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Balneolota|c__Balneolia|o__Balneolales|f__Balneolaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Pseudidiomarina,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Roseinatronobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae|g__Sporanaerobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Ureibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1224|28216|80840|506;2|1239|91061|1385|186817|150247;2|29547|3031852|213849|2808963|28196;2|1224|28216|206389|2008794|12960;2|1239|91061|1385;2|1239|91061|1385|186817|1386;2|976|200643|171549;2|1936987|1853221|1853223|1813606;2|1224|28211|356|45404;2|32066|203490|203491|203492|180162;2|1224|1236|135613|1046;2|1224|1236|91347|543|544;2|1224|1236|91347|1903409|551;2|1239|186801|186802;2|1239|91061|1385|186817|129337;2|1224|28216|80840|80864|47420;2|1239|91061|1385|90964|227979;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|1224|1236|135622|267891|58050;2|201174|1760|85012|83676;2|1224|28211|204455|31989|265;2|1224|1236|135625|712;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1224|1236|135623|641|657;2|1239|91061|1385|186818;2|976|200643|171549|171552|838;2|1224|1236|91347|1903414|583;2|1224|1236|135622|267893|2800384;2|32066|203490|203491|203492|623282;2|1224|1236|2887326|468|497;2|1224|1236|135622|267894|67572;2|1224|28211|204455|31989|119541;2|1239|1737404|1737405|2992718|165812;2|1239|91061|1385|186818|1569;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|1737404|1737405|2992719|285105;2|1297|188787|68933|188786|270;2|1239|91061|1385|186818|160795;2|1239|91061|186826|81852|2737;2|1239|909932|1843489|31977;2|1224|1236|135623|641;2|1239|91061|1385|186817|84406;2|1224|1236|91347|1903411|629;2|1224|1236|135614|32033,Complete,Chloe
bsdb:864/4/2,Study 864,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris DJ, Morgan MM , Stewart FJ",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 4,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 2000 h,The post-fed group consists of fish fed at 2000 hours. (9 hours post-feeding),17,17,NA,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table S2,12 April 2024,Victoria,Victoria,The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135622;2|976|117743|200644|246874;2|74201|414999;2|1239|91061|186826|1300|1301,Complete,Chloe
bsdb:865/1/1,Study 865,randomized controlled trial,33708251,10.1155/2021/6645970,NA,"Liu L, Yang M, Dong W, Liu T, Song X, Gu Y, Wang S, Liu Y, Abla Z, Qiao X, Liu W, Jiang K, Wang B, Zhang J , Cao H",Gut Dysbiosis and Abnormal Bile Acid Metabolism in Colitis-Associated Cancer,Gastroenterology research and practice,2021,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer cell line,BTO:0001616,control group at week 10 (C10 group),azoxymethane/dextran sodiumsulfate (AOM/DSS) group at week 10 (AD10 group),"C57BL/6mice aged 7 weeks were obtained from Beijing Huafukang Bioscience Co. Inc. and acclimatized 1 week before the experiment. Intraperitoneal injection of 10mg/kg azoxymethane(AOM) was applied to the AOM/DSS group. After seven days, the AOM/DSS group was given1.5% dextran sodium sulfate (DSS) in drinking water on days 8–13, 27–32, and 46–51, and each cycle of DSS treatment was followed by 14-day drinking water. This was to create the colitis-induced colorectal cancer (CAC) model in the mice. Group 1 is the mice that developed CAC and had their fecal sample collected before being euthanized on day 70 (week 10).",5,5,none,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4c,29 November 2023,Yjung24,"Yjung24,ChiomaBlessing",The LefSe analysis listed bacteria with significant differences at different levels in AD10 group vs C10 group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|171550|239759;2|976|200643|171549;2|976|200643;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803;2|976|200643|171549|1853231|283168;2|976|200643|171549|171551;2|976|200643|171549|171550,Complete,ChiomaBlessing
bsdb:865/1/2,Study 865,randomized controlled trial,33708251,10.1155/2021/6645970,NA,"Liu L, Yang M, Dong W, Liu T, Song X, Gu Y, Wang S, Liu Y, Abla Z, Qiao X, Liu W, Jiang K, Wang B, Zhang J , Cao H",Gut Dysbiosis and Abnormal Bile Acid Metabolism in Colitis-Associated Cancer,Gastroenterology research and practice,2021,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer cell line,BTO:0001616,control group at week 10 (C10 group),azoxymethane/dextran sodiumsulfate (AOM/DSS) group at week 10 (AD10 group),"C57BL/6mice aged 7 weeks were obtained from Beijing Huafukang Bioscience Co. Inc. and acclimatized 1 week before the experiment. Intraperitoneal injection of 10mg/kg azoxymethane(AOM) was applied to the AOM/DSS group. After seven days, the AOM/DSS group was given1.5% dextran sodium sulfate (DSS) in drinking water on days 8–13, 27–32, and 46–51, and each cycle of DSS treatment was followed by 14-day drinking water. This was to create the colitis-induced colorectal cancer (CAC) model in the mice. Group 1 is the mice that developed CAC and had their fecal sample collected before being euthanized on day 70 (week 10).",5,5,none,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4c,29 November 2023,Yjung24,"Yjung24,ChiomaBlessing",The LefSe analysis listed bacteria with significant differences at different levels in AD10 group vs C10 group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|815;2|976|200643|171549|815|816;2|29547|3031852|213849;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|29547|3031852;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1239|186801|186802|1392389;2|976|200643|171549|2005525|375288;2|1224;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:866/1/1,Study 866,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z, Li J, Engel AF , Molloy MP",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 1,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,Patients who had taken antibiotics up to four weeks before the colonoscopy.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 7a , 7c",29 November 2023,Yjung24,"Yjung24,Peace Sandy",LEfSe differential abundance plot for short-read samples,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter butyricus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|909932|1843488|909930|904|187327;2|976|200643|171549|171550|239759|1501391;2|1239|186801|3085636|3118652|2039240|2358141;2|976|200643|171549|815|816;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|820;2|201174|84998|84999|84107|102106|74426;2|1224|1236|91347|543|1940338;2|1239|186801|186802|1918454|1417852;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|216572|1263,Complete,Peace Sandy
bsdb:866/1/2,Study 866,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z, Li J, Engel AF , Molloy MP",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 1,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,Patients who had taken antibiotics up to four weeks before the colonoscopy.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 7a , 7c",29 November 2023,Yjung24,"Yjung24,Peace Sandy",LEfSe differential abundance plot for short read samples,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosacchariphilus",2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|572511;2|1239|186801|3082768|424536;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|2316020|592978;2|1224|28216|80840|995019|40544|40545;2|1239|186801|3085636|186803|2676048;2|1239|186801|3085636|186803|2678884,Complete,Peace Sandy
bsdb:866/2/1,Study 866,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z, Li J, Engel AF , Molloy MP",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 2,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,Patients who had taken antibiotics up to four weeks before the colonoscopy.,16S,123456789,PacBio RS,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 7b, 7d",29 November 2023,Yjung24,"Yjung24,Peace Sandy",Pacbio Long Read LefSe differential abundance plot between polyp and no polyp specimens.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",2|1239|186801|3085636|186803|2316020|33038;2|201174|1760|85004|31953|1678|216816;2|1224|28216|80840|995019|40544|40545;2|976|200643|171549|171552|1283313;2|1239|909932|1843488|909930|33024|33025,Complete,Peace Sandy
bsdb:866/2/2,Study 866,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z, Li J, Engel AF , Molloy MP",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 2,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,Patients who had taken antibiotics up to four weeks before the colonoscopy.,16S,123456789,PacBio RS,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,"7b, 7d",29 November 2023,Yjung24,"Yjung24,Peace Sandy",Pacbio Long Read LefSe differential abundance plot between polyp and no polyp specimens.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae",2|976|200643|171549|2005525|375288|46503;2|1239|909932|1843489|31977|29465|2682456,Complete,Peace Sandy
bsdb:867/1/1,Study 867,case-control,37960281,10.3390/nu15214628,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10649662/,"Altinok Dindar D, Chun B, Palma A, Cheney J, Krieger M, Kasschau K, Stagaman K, Mitri ZI, Goodyear SM, Shannon J, Karstens L, Sharpton T , Zhang Z",Association between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor,Nutrients,2023,"Acidaminococus, Hungatella, Tyzzerella, breast cancer, gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls,Breast cancer patients,"Biopsy-confirmed diagnosis of breast cancer prior to initiating any treatment, including surgery, chemotherapy, or radiation therapy.",44,42,Not mentioned,16S,4,Illumina,LEfSe,0.05,FALSE,2,age,body mass index,decreased,decreased,NA,NA,decreased,NA,Signature 1,Figure 2,30 November 2023,Andre,Andre,Linear discriminant analysis effect size (LEfSe) analysis of fecal microbiome at genus level of the participants in the control and BCa group samples,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2|1239|909932|1843488|909930|904;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|1506577,Complete,Folakunmi
bsdb:867/1/2,Study 867,case-control,37960281,10.3390/nu15214628,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10649662/,"Altinok Dindar D, Chun B, Palma A, Cheney J, Krieger M, Kasschau K, Stagaman K, Mitri ZI, Goodyear SM, Shannon J, Karstens L, Sharpton T , Zhang Z",Association between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor,Nutrients,2023,"Acidaminococus, Hungatella, Tyzzerella, breast cancer, gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls,Breast cancer patients,"Biopsy-confirmed diagnosis of breast cancer prior to initiating any treatment, including surgery, chemotherapy, or radiation therapy.",44,42,Not mentioned,16S,4,Illumina,LEfSe,0.05,FALSE,2,age,body mass index,decreased,decreased,NA,NA,decreased,NA,Signature 2,Figure 2,30 November 2023,Andre,"Andre,Folakunmi",Linear discriminant analysis effect size (LEfSe) analysis of fecal microbiome at genus level of the participants in the control and BCa group samples,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|g__Candidatus Galligastranaerophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A144,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|s__rumen bacterium NK4A214",2|1239|186801|186802|216572|52784;2|2840511;2|1239|186801|3082768|990719;2|201174|84998|84999;2|1239|909932|1843489|31977|39948;2|976|117743|200644;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|3068309;2|1239|186801|3085636|186803|877421;2|1239|186801|186802|216572;2|877428,Complete,Folakunmi
bsdb:868/1/1,Study 868,case-control,33748490,10.1016/j.heliyon.2021.e06432,NA,"Gryaznova MV, Solodskikh SA, Panevina AV, Syromyatnikov MY, Dvoretskaya YD, Sviridova TN, Popov ES , Popov VN",Study of microbiome changes in patients with ulcerative colitis in the Central European part of Russia,Heliyon,2021,"Inflammatory bowel disease, Intestinal microbiota, Russian population, Sequencing, Ulcerative colitis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Ulcerative colitis,Patients with ulcerative colitis,10,10,NIL,PCR,NA,Ion Torrent,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and Figure 3,12 December 2023,Yjung24,"Yjung24,Peace Sandy","Quantitative changes in the bacteria generic composition of the intestinal microbiome in patients with ulcerative colitis relative to control group.

Changes in species composition of intestinal microbiome in patients with ulcerative colitis relative to control group (∗Pvalue≤0.05, ∗∗Pvalue≤0.01, ∗∗∗Pvalue≤0.001).",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|3085636|186803|830;2|1224|1236|91347|543|158483;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|877420;2|1239|1980693;2|201174|84998|84999|1643824|133925;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|976|200643|171549|815|909656|310298;2|1239|909932|1843488|909930|33024|626940;2|1239|909932|1843489|31977|39948|487173;2|1224|28216|80840|995019|40544|40545;2|1239|186801|186802|216572|216851|853,Complete,Peace Sandy
bsdb:868/1/2,Study 868,case-control,33748490,10.1016/j.heliyon.2021.e06432,NA,"Gryaznova MV, Solodskikh SA, Panevina AV, Syromyatnikov MY, Dvoretskaya YD, Sviridova TN, Popov ES , Popov VN",Study of microbiome changes in patients with ulcerative colitis in the Central European part of Russia,Heliyon,2021,"Inflammatory bowel disease, Intestinal microbiota, Russian population, Sequencing, Ulcerative colitis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Ulcerative colitis,Patients with ulcerative colitis,10,10,NIL,PCR,NA,Ion Torrent,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and Figure 3,12 December 2023,Yjung24,"Yjung24,Peace Sandy","Quantitative changes in the bacteria generic composition of the intestinal microbiome in patients with ulcerative colitis relative to control group.

Changes in species composition of intestinal microbiome in patients with ulcerative colitis relative to control group (∗Pvalue≤0.05, ∗∗Pvalue≤0.01, ∗∗∗Pvalue≤0.001).",decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Falsochrobactrum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans",2|1224|28211|204458|76892|41275;2|976|200643|171549|1853231|574697;2|976|200643|171549|2005519|1348911;2|201174|1760|85009|31957|1912216;2|1239|186801|3085636|186803|1432051;2|1224|28211|356|118882|1649292;2|1239|186801|3085636|186803|1407607;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|1224|1236|91347|1903411|629;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1407607|1150298,Complete,Peace Sandy
bsdb:869/1/1,Study 869,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H, Takagi T, Naito Y, Inoue R, Azuma Y, Torii T, Mizushima K, Doi T, Inoue K, Dohi O, Yoshida N, Kamada K, Uchiyama K, Ishikawa T, Konishi H , Itoh Y",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,quiescent ulcerative colitis patients,consecutive recruitment of patients with quiescent UC in our outpatient clinic from November 2016 to September 2017. Clinical remission was defined as a Lichtiger index score of ≤4.,59,59,no history of antibiotic use within three months,16S,34,Illumina,LEfSe,0.05,NA,4,"age,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 1f,12 December 2023,Yjung24,"Yjung24,Peace Sandy","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Yellow-shaded areas indicate taxa that characterize UC, and green-shaded areas indicate taxa that characterize HCs. Linear discriminant analysis (LDA) scores for identified taxa of patient of UCs (7 taxa) and HC (6 taxa) was shown. ** p < 0.01.",increased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|201174|84992;2|201174;2|1239|91061;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|91061|186826,Complete,Peace Sandy
bsdb:869/1/2,Study 869,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H, Takagi T, Naito Y, Inoue R, Azuma Y, Torii T, Mizushima K, Doi T, Inoue K, Dohi O, Yoshida N, Kamada K, Uchiyama K, Ishikawa T, Konishi H , Itoh Y",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,quiescent ulcerative colitis patients,consecutive recruitment of patients with quiescent UC in our outpatient clinic from November 2016 to September 2017. Clinical remission was defined as a Lichtiger index score of ≤4.,59,59,no history of antibiotic use within three months,16S,34,Illumina,LEfSe,0.05,NA,4,"age,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 1f,12 December 2023,Yjung24,"Yjung24,Peace Sandy","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Yellow-shaded areas indicate taxa that characterize UC, and green-shaded areas indicate taxa that characterize HCs. Linear discriminant analysis (LDA) scores for identified taxa of patient of UCs (7 taxa) and HC (6 taxa) was shown. ** p < 0.01.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|976|200643|171549;2|976|200643;2|976;2|1239|186801;2|1239|186801|186802,Complete,Peace Sandy
bsdb:869/2/1,Study 869,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H, Takagi T, Naito Y, Inoue R, Azuma Y, Torii T, Mizushima K, Doi T, Inoue K, Dohi O, Yoshida N, Kamada K, Uchiyama K, Ishikawa T, Konishi H , Itoh Y",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Disease progression measurement,EFO:0008336,sustained remission of ulcerative colitis group,relapsed ulcerative colitis group,Patients who had clinically relapsed during the 3.5 year-long follow-up period. Clinical relapse was defined as clinical or endoscopic deterioration requiring therapeutic modification.,40,19,NA,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2g,12 December 2023,Yjung24,"Yjung24,Peace Sandy","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Red-shaded areas indicate taxathat characterize relapse group, and blue-shaded areas indicate taxa that characterize SusRem group. Linear discriminant analysis (LDA) scores for identified taxa of SusRem (2 taxa) and Relapse (6 taxa)",increased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|201174|84992;2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:869/2/2,Study 869,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H, Takagi T, Naito Y, Inoue R, Azuma Y, Torii T, Mizushima K, Doi T, Inoue K, Dohi O, Yoshida N, Kamada K, Uchiyama K, Ishikawa T, Konishi H , Itoh Y",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Disease progression measurement,EFO:0008336,sustained remission of ulcerative colitis group,relapsed ulcerative colitis group,Patients who had clinically relapsed during the 3.5 year-long follow-up period. Clinical relapse was defined as clinical or endoscopic deterioration requiring therapeutic modification.,40,19,NA,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2g,12 December 2023,Yjung24,"Yjung24,Peace Sandy","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Red-shaded areas indicate taxa that characterize relapse group, and blue-shaded areas indicate taxa that characterize SusRem group. Linear discriminant analysis (LDA) scores for identified taxa of SusRem (2 taxa) and Relapse (6 taxa)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Peace Sandy
bsdb:870/1/1,Study 870,case-control,37077242,10.3389/fmicb.2023.1113174,https://pubmed.ncbi.nlm.nih.gov/37077242/,"Huang D, Wang J, Zeng Y, Li Q , Wang Y",Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches,Frontiers in microbiology,2023,"bone mineral density, feature selection, gut microbiota, microbial biomarker, postmenopausal osteoporosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postmenopausal osteoporosis,EFO:0003854,Healthy controls,Postmenopausal osteoporosis (PMOP) patients,Patients with Postmenopausal osteoporosis (PMOP),37,21,Subjects who were on antibiotics one (1) month preceding the sample collection were excluded from the study,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.1,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table S2, Figure 1",20 December 2023,Aleru002,"Aleru002,Folakunmi",Gut microbiota compositions between healthy controls and patients with postmenopausal osteoporosis (PMOP),increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|91061;2|1239|186801|186802|31979|1485|84024;2|1239|526524;2|32066|203490;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|526524|526525;2|1239|91061|186826|33958|2767887|1624;2|1239|186801|186802,Complete,Folakunmi
bsdb:870/1/2,Study 870,case-control,37077242,10.3389/fmicb.2023.1113174,https://pubmed.ncbi.nlm.nih.gov/37077242/,"Huang D, Wang J, Zeng Y, Li Q , Wang Y",Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches,Frontiers in microbiology,2023,"bone mineral density, feature selection, gut microbiota, microbial biomarker, postmenopausal osteoporosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postmenopausal osteoporosis,EFO:0003854,Healthy controls,Postmenopausal osteoporosis (PMOP) patients,Patients with Postmenopausal osteoporosis (PMOP),37,21,Subjects who were on antibiotics one (1) month preceding the sample collection were excluded from the study,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.1,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table S2,20 December 2023,Aleru002,"Aleru002,Folakunmi",Gut microbiota compositions and statistical results between healthy controls and patients with postmenopausal osteoporosis (PMOP),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|815|816|28111;2|1239|186801|186802|216572,Complete,Folakunmi
bsdb:871/1/1,Study 871,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C, Desilets A, Tonneau M, El Ouarzadi O, De Figueiredo Sousa M, Bahig H, Filion É, Nguyen-Tan PF, Christopoulos A, Benlaïfaoui M, Derosa L, Alves Costa Silva C, Ponce M, Malo J, Belkad W, Charpentier D, Aubin F, Hamilou Z, Jamal R, Messaoudene M, Soulières D , Routy B",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,Oral mucositis CTCAE grade 1-2 (mild),Oral mucositis CTCAE grade 3 (severe),Patients with severe mucositis following chemoradiation therapy,30,22,NA,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Fig. 2.,20 December 2023,Andre,Andre,Fig. 2. Gut microbiome profiling with shotgun metagenomic sequencing by development of severe mucositis,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1D1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilicoli|s__Massilicoli timonensis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota|s__Massilimicrobiota timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",2|1239|186801|3085636|186803|207244|105841;2|1239|186801|1697794;2|1239|186801|186802|31979|1485|29363;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|3085636|186803|1649459|154046;2|1239|526524|526525|128827|2683202|2015901;2|1239|526524|526525|128827|1924110|1776392;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|3085636|186803|1769710|1653434;2|1239|526524|526525|2810280|3025755|1547,Complete,Chloe
bsdb:871/1/2,Study 871,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C, Desilets A, Tonneau M, El Ouarzadi O, De Figueiredo Sousa M, Bahig H, Filion É, Nguyen-Tan PF, Christopoulos A, Benlaïfaoui M, Derosa L, Alves Costa Silva C, Ponce M, Malo J, Belkad W, Charpentier D, Aubin F, Hamilou Z, Jamal R, Messaoudene M, Soulières D , Routy B",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,Oral mucositis CTCAE grade 1-2 (mild),Oral mucositis CTCAE grade 3 (severe),Patients with severe mucositis following chemoradiation therapy,30,22,NA,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Fig. 2,20 December 2023,Andre,Andre,Fig. 2. Gut microbiome profiling with shotgun metagenomic sequencing by development of severe mucositis,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. chh4-2,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella marseillensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium",2|1239|186801|3085636|186803|1766253|39491;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|1288121;2|201174|1760|85004|31953|419014|419015;2|1239|186801|186802|1715004;2|1239|186801|186802|31979|1485|2293011;2|1239|186801|186802|31979|1485|2067550;2|1239|186801|3085636|186803|28050|28052;2|976|200643|171549|815|909656|204516;2|976|200643|171549|171552|838|2479840;2|201174|84998|84999|84107|1473205|1473216;2|1239|186801|3085636|186803|2316020|46228;2|200940|3031449|213115|194924|2049043,Complete,Chloe
bsdb:871/2/1,Study 871,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C, Desilets A, Tonneau M, El Ouarzadi O, De Figueiredo Sousa M, Bahig H, Filion É, Nguyen-Tan PF, Christopoulos A, Benlaïfaoui M, Derosa L, Alves Costa Silva C, Ponce M, Malo J, Belkad W, Charpentier D, Aubin F, Hamilou Z, Jamal R, Messaoudene M, Soulières D , Routy B",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No enteral feeding plus mild mucositis,Enteral feeding plus mucositis of any grade,Head and neck squamous cell carcinoma with severe mucositis and enteral feeding need,27,13,NA,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Fig 3,3 January 2024,Andre,Andre,Gut microbiome profiling with shotgun metagenomic sequencing by co-occurrence of development of severe mucositis and enteral feeding,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. YY7918,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An181,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum",2|1239|186801|3085636|186803|207244|105841;2|201174|84998|1643822|1643826|84111|502558;2|1239|186801|3085636|186803|2719313|1531;2|1239|91061|186826|81852|1350|1351;2|201174|1760|85006|2805426|57499|1276;2|1239|186801|3085636|186803|1506553|1965575;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|3085636|186803|1769710|1653434;2|1239|526524|526525|2810280|3025755|1547;2|1239|526524|526525|128827|1522,Complete,Chloe
bsdb:871/2/2,Study 871,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C, Desilets A, Tonneau M, El Ouarzadi O, De Figueiredo Sousa M, Bahig H, Filion É, Nguyen-Tan PF, Christopoulos A, Benlaïfaoui M, Derosa L, Alves Costa Silva C, Ponce M, Malo J, Belkad W, Charpentier D, Aubin F, Hamilou Z, Jamal R, Messaoudene M, Soulières D , Routy B",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No enteral feeding plus mild mucositis,Enteral feeding plus mucositis of any grade,Head and neck squamous cell carcinoma with severe mucositis and enteral feeding need,27,13,NA,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Fig3.,3 January 2024,Andre,Andre,NA,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|186802|1715004;2|1239|186801|186802|31979|1485|2293011;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802|186806|1730|39496;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|204516;2|1239|186801|3085636|186803|841|166486;2|201174|84998|84999|84107|1473205|1473216;2|1224|28216|80840|995019|40544|40545,Complete,Chloe
bsdb:871/3/1,Study 871,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C, Desilets A, Tonneau M, El Ouarzadi O, De Figueiredo Sousa M, Bahig H, Filion É, Nguyen-Tan PF, Christopoulos A, Benlaïfaoui M, Derosa L, Alves Costa Silva C, Ponce M, Malo J, Belkad W, Charpentier D, Aubin F, Hamilou Z, Jamal R, Messaoudene M, Soulières D , Routy B",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No Enteral feeding tube placement,Enteral feeding tube placement,Patients needing enteral feeding,27,13,NA,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplemental Figure 10,3 January 2024,Andre,Andre,Gut microbiome profiling in patients with enteral feeding versus without,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. YY7918,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella sp. OF01-20,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena contorta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Isoptericola|s__Isoptericola variabilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An181,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum",2|1239|186801|3085636|186803|207244|105841;2|1239|186801|3085636|186803|572511|1322;2|1239|186801|3085636|186803|572511|33035;2|201174|84998|1643822|1643826|84111|502558;2|1239|186801|3085636|186803|1432051|2292348;2|1239|186801|3085636|186803|2719313|1531;2|1239|91061|186826|81852|1350|1351;2|1239|186801|3085636|186803|2005359|39482;2|1239|186801|3085636|186803|2005355|1912855;2|201174|1760|85006|85017|254250|139208;2|201174|1760|85006|2805426|57499|1276;2|1239|186801|3085636|186803|1506553|1965575;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|1905344|1550024;2|1239|526524|526525|2810280|3025755|1547;2|1239|909932|1843489|31977|29465|29466;2|1239|526524|526525|128827|1522,Complete,Chloe
bsdb:871/3/2,Study 871,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C, Desilets A, Tonneau M, El Ouarzadi O, De Figueiredo Sousa M, Bahig H, Filion É, Nguyen-Tan PF, Christopoulos A, Benlaïfaoui M, Derosa L, Alves Costa Silva C, Ponce M, Malo J, Belkad W, Charpentier D, Aubin F, Hamilou Z, Jamal R, Messaoudene M, Soulières D , Routy B",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No Enteral feeding tube placement,Enteral feeding tube placement,Patients needing enteral feeding,27,13,NA,WMS,NA,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplemental Figure 10,3 January 2024,Andre,Andre,Gut microbiome profiling in patients with enteral feeding versus without,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AF36-15AT,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|572511|40520;2|976|200643|171549|1853231|574697|1472416;2|1239|186801|186802|1715004;2|1239|186801|186802|31979|1485|2293011;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|189330|2292041;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|2005359|290055;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|204516;2|1239|186801|3085636|186803|841|166486,Complete,Chloe
bsdb:872/1/1,Study 872,case-control,NA,https://doi.org/10.1186/s13041-023-01014-0,NA,"Wenwu Zhang, Siyun Zhang, Jiewen Chen, kejun He, Changming Zhang",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"Spinal cord injury, Gut microbiota, 16S rRNA gene sequencing, Untargeted metabolomics",Experiment 1,China,Homo sapiens,NA,NA,NA,NA,typically healthy control group,spinal cord injury patient,"Spinal cord injury (SCI) is an insult to the spinal cord resulting in a change, either temporary or permanent, in the cord's normal motor, sensory, or autonomic function",10,11,NA,16S,34,DNA-DNA Hybridization,"LEfSe,T-Test,ANOSIM",0.05,FALSE,3,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,12 March 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Alterations in the gut microbiota at the phylum and genus levels between the two groups.,increased,"k__Bacteria|p__Synergistota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|508458;2|201174|84998|1643822|1643826|84111,Complete,NA
bsdb:872/1/2,Study 872,case-control,NA,https://doi.org/10.1186/s13041-023-01014-0,NA,"Wenwu Zhang, Siyun Zhang, Jiewen Chen, kejun He, Changming Zhang",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"Spinal cord injury, Gut microbiota, 16S rRNA gene sequencing, Untargeted metabolomics",Experiment 1,China,Homo sapiens,NA,NA,NA,NA,typically healthy control group,spinal cord injury patient,"Spinal cord injury (SCI) is an insult to the spinal cord resulting in a change, either temporary or permanent, in the cord's normal motor, sensory, or autonomic function",10,11,NA,16S,34,DNA-DNA Hybridization,"LEfSe,T-Test,ANOSIM",0.05,FALSE,3,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,12 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Ayibatari",Alterations in the gut microbiota at the phylum and genus levels between the two groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|877420;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|1236|91347|543|1940338,Complete,NA
bsdb:873/1/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint B0 (in the morning before the Bruce Treadmill Test),19,15,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,7 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint B0 (in the morning before the Bruce Treadmill Test),increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis",2|1239|526524|526525|2810280|135858|2292991;2|1239|186801|186802|31979|1485|1650661,Complete,Folakunmi
bsdb:873/2/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics (in the morning before the Bruce Treadmill Test),19,13,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,7 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at time point B0(in the morning before the Bruce Treadmill Test),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena",2|1239|186801|3085636|186803|572511|2292961;2|1239|186801|3085636|186803|189330|88431,Complete,Folakunmi
bsdb:873/3/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,15,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AF41-9",2|1239|186801|3085636|186803|33042|116085;2|201174|1760|85006|1268|32207|43675;2|1239|186801|186802|216572|1263|2292069,Complete,Folakunmi
bsdb:873/3/2,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,15,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,2|976|200643|171549|815|816|674529,Complete,Folakunmi
bsdb:873/4/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at time point W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,13,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at time point W1 (the same day after the repeated lower body 30s-all-out wingate's test),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,2|1239|186801|3085636|186803|1407607|1150298,Complete,Folakunmi
bsdb:873/4/2,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at time point W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,13,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W1  (the same day after the repeated lower body 30s-all-out wingate's test),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,2|976|200643|171549|815|816|674529,Complete,Folakunmi
bsdb:873/5/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 5,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint W2 (morning fasting after the WT on an empty stomach),19,15,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W2 (morning fasting after the WT on an empty stomach),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,2|976|200643|171549|815|909656|204516,Complete,Folakunmi
bsdb:873/6/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 6,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at timepoint W2 (morning fasting after the WT on an empty stomach),19,13,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W2  (morning fasting after the WT on an empty stomach),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,2|1239|186801|3085636|186803|572511|2292961,Complete,Folakunmi
bsdb:873/6/2,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 6,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at timepoint W2 (morning fasting after the WT on an empty stomach),19,13,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W2  (morning fasting after the WT on an empty stomach),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,2|976|200643|171549|815|909656|204516,Complete,Folakunmi
bsdb:873/7/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 7,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint B1 (the same day after the Bruce Treadmill Test),19,15,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at timepoint B1 (the same day after the Bruce Treadmill Test),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,2|1239|186801|186802|1898207,Complete,Folakunmi
bsdb:873/8/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 8,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics  at timepoint B1 (the same day after the Bruce Treadmill Test),19,13,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at timepoint B1 (the same day after the Bruce Treadmill Test),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei",2|1239|186801|3085636|186803|572511|2292961;2|1239|91061|186826|33958|2759736|1597,Complete,Folakunmi
bsdb:873/9/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 9,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics  at timepoint B2 (morning after the Bruce Treadmill Test on an empty stomach),19,15,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint B2 (morning after the Bruce Treadmill Test on an empty stomach),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. MSK.20.85,2|1239|186801|3085636|186803|572511|2709718,Complete,Folakunmi
bsdb:873/10/1,Study 873,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A , Kosciolek T",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 10,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics  at timepoint B2 (morning after the Bruce Treadmill Test on an empty stomach),19,13,Individuals who were on antibiotics six (6) months before the start of the study.,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint B2 (morning after the Bruce Treadmill Test),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,2|1239|186801|3085636|186803|572511|2292961,Complete,Folakunmi
bsdb:874/1/1,Study 874,case-control,25023578,https://doi.org/10.1097/MPG.0000000000000495,NA,"Walia R, Garg S, Song Y, Girotra M, Cuffari C, Fricke WF , Dutta SK",Efficacy of fecal microbiota transplantation in 2 children with recurrent Clostridium difficile infection and its impact on their growth and gut microbiome,Journal of pediatric gastroenterology and nutrition,2014,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,NA,Children with recurrent Clostridium difficile Infection,Efficacy of Fecal Microbiota Transplantation on Children with Recurrent Clostridium difficile Infection.,NA,2,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,"age,antibiotic exposure,cesarean section,premature birth",NA,increased,NA,NA,NA,NA,Signature 1,Figure 2b,5 March 2024,Victoria,Victoria,Histograms showing relative abundances of microbiota members at the taxonomic phylum level.,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,NA
bsdb:874/1/2,Study 874,case-control,25023578,https://doi.org/10.1097/MPG.0000000000000495,NA,"Walia R, Garg S, Song Y, Girotra M, Cuffari C, Fricke WF , Dutta SK",Efficacy of fecal microbiota transplantation in 2 children with recurrent Clostridium difficile infection and its impact on their growth and gut microbiome,Journal of pediatric gastroenterology and nutrition,2014,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,NA,Children with recurrent Clostridium difficile Infection,Efficacy of Fecal Microbiota Transplantation on Children with Recurrent Clostridium difficile Infection.,NA,2,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,"age,antibiotic exposure,cesarean section,premature birth",NA,increased,NA,NA,NA,NA,Signature 2,Figure 2b,5 March 2024,Victoria,Victoria,Histograms showing relative abundances of microbiota members at the taxonomic phylum level.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Actinomycetota",2|1239;2|1224;2|74201;2|201174,Complete,NA
bsdb:875/1/1,Study 875,case-control,29756631,10.2340/00015555-2968,NA,"Deng Y, Wang H, Zhou J, Mou Y, Wang G , Xiong X",Patients with Acne Vulgaris Have a Distinct Gut Microbiota in Comparison with Healthy Controls,Acta dermato-venereologica,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Acne,EFO:0003894,Healthy control group,Acne vulgaris group,"Patients with mild, moderate, severe and very severe acne",43,43,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 3A,6 March 2024,Scholastica,"Scholastica,ChiomaBlessing",Bacterial taxa significantly enriched in acne samples (AS) compared to healthy control samples (CS),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota",2|976|200643|171549;2|976|200643;2|976,Complete,ChiomaBlessing
bsdb:875/1/2,Study 875,case-control,29756631,10.2340/00015555-2968,NA,"Deng Y, Wang H, Zhou J, Mou Y, Wang G , Xiong X",Patients with Acne Vulgaris Have a Distinct Gut Microbiota in Comparison with Healthy Controls,Acta dermato-venereologica,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Acne,EFO:0003894,Healthy control group,Acne vulgaris group,"Patients with mild, moderate, severe and very severe acne",43,43,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 3A,6 March 2024,Scholastica,"Scholastica,ChiomaBlessing",Bacterial taxa significantly abundant in acne samples (AS) compared to healthy control samples (CS),decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|1239|186801|3082720|3118656|114627;2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061|1385|186817|1386;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|91061|186826|186828;2|1239|91061|186826|186828|2747;2|1239|186801;2|1239|186801|186802|31979;2|28221;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1224|28211|356|212791;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803;2|1239|91061|186826|1300|1357;2|1239|91061|1385|186817|400634;2|1239|91061|1385|186817|182709;2|1224|28216|80840|75682|846;2|1239|91061|1385|186822;2|1239|91061|1385|186822|44249;2|976|200643|171549|171552|577309;2|1239|91061|1385|186818;2|1239|186801|186802|216572|1263;2|1239;2|1239|186801|186802;2|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:876/1/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 1,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Men with 0-3 sexual partners,Men with >3 sexual partners,Men in the risk increasing category with more than 3 sexual partners (in the last 12 months).,38,29,6 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 4 (c) and Supplementary Table S4,5 March 2024,Uhabiba14,"Uhabiba14,Fiddyhamma,MyleeeA",Species-level taxonomic biomarkers identified using LEfSe to associate with behaviors having >3 (and 0–3) sexual partners.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Neoanaerotignum|s__Candidatus Neoanaerotignum tabaqchaliae,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|s__Methanomassiliicoccales archaeon,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia",2|1239|186801|3085636|186803|572511|1737424;2|1239|186801|2721109|2721136;2|1239|186801|2044939;2|1239|186801|3085636|186803|28050|28052;2157|2283796|183967|1235850|1906667;2|1239|186801|186802|216572|459786;2|976|200643|171549;2|1239|186801,Complete,Svetlana up
bsdb:876/1/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 1,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Men with 0-3 sexual partners,Men with >3 sexual partners,Men in the risk increasing category with more than 3 sexual partners (in the last 12 months).,38,29,6 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 4C and SupplementaryTable S4,5 March 2024,Uhabiba14,"Uhabiba14,MyleeeA,Fiddyhamma","Species-level taxonomic biomarkers identified using LEfSe58 to associate with behaviors having ( 0–3) sexual partners. Only taxonomically known
species are displayed",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira pilosicoli,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|s__Campylobacteraceae bacterium,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis",2|1239|186801|3085636|3118652|2039240|2358141;2|976|200643|171549|815|2212467;2|203691|203692|1643686|143786|29521|52584;2|29547|3031852|213849|72294|2268179;2|1798710|1906119|2137880;2|1239|186801|3085636|186803|2719231|253257;2|1239|186801|186802|216572|2485925;2|976|200643|171549|171552|838|1602169;2|976|200643|171549|171552|1926672|1852370,Complete,Svetlana up
bsdb:876/2/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 2,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Condom use (Always during RAI),No Condom use (during RAI),Men in the risk increasing category who never use Condom during Receptive Anal intercourse.,12,37,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Supplementary Table S4,13 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe to associate with Condom use (Always during RAI) and No Condom use (during RAI).,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803|1898203;2|1239|186801|3085636|186803;2|976|200643|171549|171550|2049048;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|2049040;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:876/2/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 2,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Condom use (Always during RAI),No Condom use (during RAI),Men in the risk increasing category who never use Condom during Receptive Anal intercourse.,12,37,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Supplementary Table S4,13 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe to associate with Condom use (Always during RAI) and No Condom use (during RAI).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza",2|1239|186801|186802|2527773|2500537;2|1239|186801|2044939;2|1239|186801|3085636|186803|28050|28052,Complete,Svetlana up
bsdb:876/3/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 3,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No Oral Sex,Yes Oral Sex,Men in the risk increasing category who practice Oral sex.,21,42,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S4,13 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe to associate with No Oral sex and Yes Oral sex.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|976|200643|171549|815|2212467;2|1239|186801|2044939;2|200940|3031449|213115|194924|872|901;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|171552|838|1602169;2|976|200643|171549|171552|838|59823;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|2485925;2|1239|186801;2|976|200643|171549|171550;2|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:876/3/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 3,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No Oral Sex,Yes Oral Sex,Men in the risk increasing category who practice Oral sex.,21,42,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S4,13 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe to associate with No Oral sex and Yes Oral sex.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas|s__Merdimonas faecis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Mesosutterella|s__Mesosutterella multiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli",2|976|200643|171549|815|816|818;2|201174|1760|85004|31953|1678|1681;2|200940|3031449|213115|194924|35832|35833;2|29547|3031852|213849|72294|194|824;2|1239|186801|2720800|2720821;2|1239|186801|2044939;2|1239|186801|186802|31979|1485|84024;2|1239|526524|526525|128827|2049044;2|1239|186801|3085636|186803|1898203;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|815|909656|204516;2|1239|186801|186802|3082771|1924093|1924094;2|1239|186801|3085636|186803|2023266|1653435;2|1224|28216|80840|995019|2494213|2259133;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|186802|216572|2485925;2|1239|91061,Complete,Svetlana up
bsdb:876/4/NA,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 4,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Condom use (Sometimes during RAI),No Condom use (during RAI),Men in the risk increasing category who never use Condom during Receptive Anal intercourse.,15,37,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:876/5/NA,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 5,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Condom use (Always during RAI),Condom use (Sometimes during RAI),Men in the risk increasing category who sometimes use Condom during Receptive Anal intercourse.,12,15,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:876/6/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 6,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,STI Negative,STI Positive,Men in the risk increasing category who were positive to sexually transmitted infection.,44,23,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S4,15 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe associated with Positive STI  and Negative STI .,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella seckii",2|1239|186801|3085636|186803|841|301302;2|1224|28216|80840|995019|40544|40545;2|1239|186801|186802|216572;2|1224|28216|80840|995019|40544|1944635,Complete,Svetlana up
bsdb:876/6/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 6,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,STI Negative,STI Positive,Men in the risk increasing category who were positive to sexually transmitted infection.,44,23,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S4,15 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe associated with Positive STI and Negative STI,increased,"k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira pilosicoli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium",2|1239|186801|2044939;2|203691|203692|1643686|143786|29521|52584;2|1239|186801|186802|216572;2|1239|91061;2|976|200643|171549|171550;2|256845|1313211|2053569;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|186806|2049045,Complete,Svetlana up
bsdb:876/7/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 7,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No RAI,Yes RAI,Men in the risk increasing category who practice Receptive Anal intercourse.,21,46,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S4,15 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe to associate with No Receptive Anal Intercourse and Yes Receptive Anal Intercourse.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|186801|186802|31979|1485|1506;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|171550,Complete,Svetlana up
bsdb:876/7/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 7,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No RAI,Yes RAI,Men in the risk increasing category who practice Receptive Anal intercourse.,21,46,6 Months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S4,15 April 2024,MyleeeA,MyleeeA,Species-level taxonomic biomarkers identified using LEfSe to associate with No Receptive Anal Intercourse and Yes Receptive Anal Intercourse.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Mesosutterella|s__Mesosutterella multiformis,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|s__Mycoplasmatales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia",2|976|200643|171549|171550|239759|214856;2|201174|1760|85004|31953|1678|216816;2|1239|186801|2720800|2720821;2|1239|186801|2044939;2|1224|28216|80840|995019|2494213|2259133;2|1239|91061;2|544448|31969|2085|2023991;2|1239|186801|186802|216572|2485925;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801,Complete,Svetlana up
bsdb:876/8/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 8,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Westernized,"Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.",93,93,6 Months,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S3,17 April 2024,MyleeeA,MyleeeA,Species enriched in MSM and Westernized.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|s__Alphaproteobacteria bacterium,k__Bacteria|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Eukaryota|c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira pilosicoli,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|s__Campylobacteraceae bacterium,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus massiliensis,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|s__Opitutales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium freudenreichii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|s__Helicobacteraceae bacterium",2|1224|28211|1913988;2|1239|91061|1903720;2|976|200643|171549|815|2212467;2|976|200643|171549|2030927;2759|2683628|42740|2547934|12967;2|203691|203692|1643686|143786|29521|52584;2|29547|3031852|213849|72294|2268179;2|1798710|1906119|2137880;2|1239|186801|2044939;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485|1506;2|200940|3031449|213115|194924|2049043;2|1239|186801|3085636|186803|189330|88431;2|1224|28216|80840|995019|1980697|1852381;2|74201|414999|415000|2026772;2|1239|186801|186802|216572|2485925;2|201174|1760|85009|31957|1743|1744;2|1239|909932|909929|2137878;2|256845|1313211|278082|255528|172900|172901;2|976|200643|171549;2|1239|186801;2|201174|84998;2|29547|3031852|213849|72293|2212472,Complete,Svetlana up
bsdb:876/8/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 8,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Westernized,"Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.",93,93,6 Months,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S3,17 April 2024,MyleeeA,MyleeeA,Species enriched in MSM and Westernized.,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella marseillensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|s__Coriobacteriia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Avimonas|s__Candidatus Avimonas narfae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira hominis (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter|s__Neglectibacter timonensis,k__Bacteria|p__Bacillota|g__Negativibacillus|s__Negativibacillus massiliensis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|1501391;2|1239|186801|3085636|186803|207244|105841;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|371601;2|201174|1760|85004|31953|1678|1681;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|871665;2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|2044939;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|1432051|1720294;2|1239|186801|186802|186806|2049045;2|1239|186801|186802|186806|1730|142586;2|1239|186801|3085636|186803|2316020|342942;2|1239|186801|3082720|3030910|86331|114527;2|1239|186801|3085656|3085657|2039302|1981510;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|838|2479840;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|3085636|186803|1769710|1653434;2|1239|526524|526525|128827|123375;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1306;2|1239|526524|526525|2810281|191303|154288;2|1239|909932|1843489|31977|29465|423477;2|1239|91061;2|201174|84998|2052159;2|1239|186801|2720801|2720820;2|1239|186801;2|1239|186801|3085636|186803|1506553|29347;2|1239|186801|3085636|186803|28050|2763051;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|186802|216572|2172004|2763053;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|186802|216572|1924105|1776382;2|1239|1980693|1871035;2|1239|526524|526525|2810280|3025755|1547;2|1239|526524|526525|128827|1522,Complete,Svetlana up
bsdb:876/9/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 9,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Non MSM,MSM,Men who have sex with Men (Prevotella Family comparison),24,84,6 Months,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S2,17 April 2024,MyleeeA,MyleeeA,Species differentially enriched in MSM relative to non-MSM. Log2-transformed abundances of Prevotellaceae members with a minimum abundance of 0.1 at 90th percentile in all subjects.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|976|200643|171549|171552|577309|454154;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|1602169;2|976|200643|171549|171552|838|59823,Complete,Svetlana up
bsdb:876/10/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 10,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Non MSM,MSM,Men who have sex with Men,31,93,6 Months,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Supplementary Table S3,17 April 2024,MyleeeA,MyleeeA,Species enriched in MSM and Non MSM.,increased,"k__Bacteria|p__Bacillota|s__Bacillota bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|s__Methanomassiliicoccales archaeon,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. Marseille,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira aalborgi,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis",2|1239|1879010;2|976|200643|171549|815|2212467;2|1239|186801|2044939;2|200940|3031449|213115|194924|872|901;2|1239|186801|186802|186806|1730|142586;2|1239|186801|186802|216572|216851|853;2|32066|203490|203491|203492|848|850;2|1239|186801|3085636|186803|1898203;2|1239|526524|526525|128827|1573535|1735;2|256845|1313211|2053569;2157|2283796|183967|1235850|1906667;2|1239|909932|909929|1843491|52225|187979;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|1602169;2|976|200643|171549|171550|2049048;2|1239|186801|3085636|186803|841|2049040;2|201174|84998|1643822|1643826|84108|572010;2|1239|91061|186826|1300|1301|1318;2|1239|186801;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|976|200643|171549|171550;2|976|200643|171549|171552|838|304215;2|1239|526524|526525|2810280|135858|2049022;2|976|200643|171549|171552|838|59823;2|203691|203692|1643686|143786|29521|29522;2|1239|909932|1843489|31977|906|2023260;2|1239|91061|1903720;2|976|200643|171549|171552|2974251|2518605,Complete,Svetlana up
bsdb:876/10/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 10,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Non MSM,MSM,Men who have sex with Men,31,93,6 Months,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Supplementary Table S3,18 April 2024,MyleeeA,MyleeeA,Species enriched in MSM and Non MSM.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|s__Acidaminococcaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Mesosutterella|s__Mesosutterella multiformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum",2|1239|909932|1843488|909930|2049052;2|1239|186801|186802|3085642|2048137|1628085;2|976|200643|171549|171550|239759|2585118;2|976|200643|171549|171550|239759|1501391;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|3118652|2039240|2358141;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|976|200643|171549|2005519|397864|487174;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|871665;2|1239|186801|3085636|186803|572511|418240;2|1798710|1906119|2137880;2|1239|186801|2044939;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|31979|1485|1506;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|2211178|2211183;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|204475;2|1239|186801|3085636|186803|2316020|33038;2|1224|28216|80840|995019|2494213|2259133;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171552|577309|454154;2|1224|28216|80840|995019|577310;2|1224|28216|80840|995019|577310|487175;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|1239|186801|186802|216572|1263|3062497;2|1239|186801|186802|216572|1263|40519;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801;2|1239|186801|186802|31979|1485|2126740,Complete,Svetlana up
bsdb:876/11/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 11,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,481,6 Months,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S3,18 April 2024,MyleeeA,MyleeeA,Species enriched in MSM and Non Westernized.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus massiliensis (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira pilosicoli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Alangreenwoodia|s__Candidatus Alangreenwoodia gallinarii,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Allobutyricicoccus|s__Candidatus Allobutyricicoccus pentlandensis,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Allochristensenella|s__Candidatus Allochristensenella caecavium,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Avimonas|s__Candidatus Avimonas narfae,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Geddesella|s__Candidatus Geddesella stercoravicola,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Metalachnospira|s__Candidatus Metalachnospira gallinarum,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Neochristensenella|s__Candidatus Neochristensenella gallicola,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Neoruminococcus|s__Candidatus Neoruminococcus faecicola,k__Bacteria|p__Bacillota|c__Clostridia|g__Candidatus Pseudolachnospira|s__Candidatus Pseudolachnospira avium,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Hydrogeniiclostridium|s__Hydrogeniiclostridium mannosilyticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia|s__Massiliimalia timonensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas|s__Merdimonas faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium freudenreichii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides|s__Sanguibacteroides justesenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota|s__Massilimicrobiota sp.",2|1239|186801|186802|216572|244127|2321404;2|1239|186801|186802|216572|1935176|1871018;2|976|200643|171549|815|816|291644;2|201174|1760|85004|31953|1678|1686;2|203691|203692|1643686|143786|29521|52584;2|976|200643|171549|1853231|574697;2|1239|186801|2720809|2720823;2|1239|186801|2720794|2720824;2|1239|186801|2720795|2720825;2|1239|186801|2720801|2720820;2|1239|186801|2720808|2720834;2|1239|186801|2721107|2721132;2|1239|186801|2721110|2721137;2|1239|186801|2721112|2721139;2|1239|186801|2721118|2721148;2|1239|186801|2044939;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485|1506;2|976|200643|171549|2005519|1348911|1099853;2|1239|186801|3085636|186803|1432051|1432052;2|1239|526524|526525|128827|2049044;2|1239|186801|186802|186806|1730|142586;2|1239|186801|186802|216572|946234|2049025;2|1239|526524|526525|128827|61170|61171;2|1239|186801|186802|3082771|2764317|2764322;2|1239|186801|186802|1392389|1673721;2|1239|186801|186802|1392389|1689270;2|1239|186801|3085636|186803|1506553|2028282;2|1239|186801|3085636|186803|1898203;2|1239|186801|186802|216572|2895461|1987501;2|1239|909932|1843489|31977|906|907;2|1239|186801|186802|216572|3028852|2897707;2|1239|186801|3085636|186803|2023266|1653435;2|1239|186801|186802|216572|459786|1945593;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|838|28125;2|201174|1760|85009|31957|1743|1744;2|201174|1760|85006|1268|32207|43675;2|976|200643|171549|171551|1635148|1547597;2|1239|186801|186802|216572;2|1239|186801|186802|216572|2485925;2|1239|526524|526525|128827|1924110|1924111,Complete,Svetlana up
bsdb:876/11/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 11,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,481,6 Months,WMS,NA,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S3,19 April 2024,MyleeeA,MyleeeA,Species enriched in MSM and Non Westernized.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 348,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Nanosynsacchari|s__Candidatus Nanosynsacchari sp. TM7_ANC_38.39_G1_1,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|s__Elusimicrobiales bacterium,k__Bacteria|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus plantarum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|s__Spirochaetia bacterium",2|201174|1760|2037|2049|1654|29317;2|976|200643|171549|815|2212467;2|976|200643|171549|171552|1926672|1852370;2|976|200643|171549|171552|838|59823;2|1798710|1906119|2137880;2|95818|671231;2|95818|2093818|2093825|2171986|2789662|1986206;2|74152|641853|641854|2478488;2|1239|91061|1903720;2|1239|91061;2|1239|91061|186826|33958|1243;2|1239|91061|186826|1300|1357|1940789;2|1239|91061|186826|1300|1357|1365;2|1239|91061|186826|1300|1301|1306;2|1239|186801|2044939;2|1239|186801;2|1239|186801|186802|31979|1485|84024;2|1239|186801|186802|31979|1485|1506;2|1239|186801|3082720|3030910|86331|114527;2|1239|186801|186802|186806|2049045;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|871665;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|1898203;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|841|2049040;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572;2|1239|186801|186802|216572|1263|3062497;2|1239|526524|526525|128827|2049044;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|423477;2|256845|1313211|2053569;2|1224|1236|91347|543|561|1499973;2|203691|203692|2053615,Complete,Svetlana up
bsdb:876/12/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 12,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Westernized,"Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.",93,481,6 Months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,17 April 2024,MyleeeA,MyleeeA,"Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,Svetlana up
bsdb:876/12/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 12,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Westernized,"Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.",93,481,6 Months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,17 April 2024,MyleeeA,MyleeeA,"Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:876/13/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 13,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,389,6 Months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,17 April 2024,MyleeeA,MyleeeA,"Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:876/13/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 13,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,389,6 Months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,17 April 2024,MyleeeA,MyleeeA,"Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,Svetlana up
bsdb:876/14/1,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 14,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,China (Urban),Two Chinese cities - GuangDong and TangShan - which are located in Southern China and have been experiencing rapid urbanization in the last decade. They were used to represent populations from non-Western but relatively urbanized communities.,93,66,6 Months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,17 April 2024,MyleeeA,MyleeeA,"Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,Svetlana up
bsdb:876/14/2,Study 876,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T , Kehrmann J",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 14,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,China (Urban),Two Chinese cities - GuangDong and TangShan - which are located in Southern China and have been experiencing rapid urbanization in the last decade. They were used to represent populations from non-Western but relatively urbanized communities.,93,66,6 Months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,17 April 2024,MyleeeA,MyleeeA,"Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:877/1/NA,Study 877,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E , Ghensi P",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (case samples),Mucositis group (case samples),Healthy species/ biomarkers enriched or significant in mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,28,intake of systemic antibiotics  within the past 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:877/2/1,Study 877,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E , Ghensi P",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 2,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (case samples),Peri-implantitis group (case samples),Healthy species/ biomarkers enriched or significant in peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,31,intake of systemic antibiotics  within the past 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a and text (paragraph 4),7 March 2024,EniolaAde,"EniolaAde,Folakunmi",LEFSE-identified healthy microbiome composition significantly enriched after treatment  in healthy group patients compared with peri-implantitis patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria",2|201174|1760|2037|2049|1654|544580;2|201174|1760|85007|1653|1716|43768;2|201174|1760|85006|1268|32207|172042,Complete,Folakunmi
bsdb:877/3/1,Study 877,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E , Ghensi P",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 3,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (case samples),Peri-implantitis group (case samples),Peri-implantitis species/ biomarkers enriched or significant in peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,31,intake of systemic antibiotics  within the past 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2c,7 March 2024,EniolaAde,"EniolaAde,Folakunmi",LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis patients,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae",2|32066|203490|203491|203492|848|851;2|976|200643|171549|171551|836|837;2|200795|292625|292629|292628,Complete,Folakunmi
bsdb:877/4/1,Study 877,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E , Ghensi P",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 4,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (contralateral site samples),Mucositis group (contralateral site samples),Healthy species/ biomarkers enriched or significant in mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,28,intake of systemic antibiotics  within the past 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,23 March 2024,Folakunmi,Folakunmi,LEFSE-identified healthy microbiome composition significantly enriched after treatment in  mucositis patients compared with healthy group patients,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,2|1239|91061|186826|1300|1301|1303,Complete,Folakunmi
bsdb:877/5/1,Study 877,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E , Ghensi P",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 5,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (contralateral site samples),Peri-implantitis group (contralateral site samples),Healthy species/ biomarkers enriched or significant in Peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,31,intake of systemic antibiotics  within the past 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,23 March 2024,Folakunmi,Folakunmi,LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis patients,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,2|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:877/6/1,Study 877,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E , Ghensi P",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 6,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group  (contralteral samples),Peri-implantitis and mucositis groups (contralteral samples),Peri-implantitis species/ biomarkers enriched or significant in peri-implantitis and mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,59,intake of systemic antibiotics  within the past 6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2d,28 March 2024,Folakunmi,Folakunmi,LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis and mucositis patients,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,2|976|200643|171549|171552|838|28131,Complete,Folakunmi
bsdb:878/1/1,Study 878,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, Huttenhower C, Garrett WS , Meyerson M",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 1,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,9,9,N/A,WMS,NA,Illumina,LEfSe,0.05,FALSE,1.8,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1C,8 April 2024,MyleeeA,MyleeeA,"Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by whole-genome sequencing in nine individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus",2|32066|203490|203491|203492;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|1300;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|732,Complete,Svetlana up
bsdb:878/1/2,Study 878,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, Huttenhower C, Garrett WS , Meyerson M",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 1,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,9,9,N/A,WMS,NA,Illumina,LEfSe,0.05,FALSE,1.8,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 1C,8 April 2024,MyleeeA,MyleeeA,"Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by whole-genome sequencing in nine individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.",2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|547;2|1224|1236|2887326|468|469|470;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|472,Complete,Svetlana up
bsdb:878/2/1,Study 878,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, Huttenhower C, Garrett WS , Meyerson M",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 2,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,95,95,N/A,16S,345,Roche454,LEfSe,0.05,FALSE,4.2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2C,8 April 2024,MyleeeA,MyleeeA,"Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by 16S rDNA sequencing in 95 individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490|203491|203492|848;2|32066|203490,Complete,Svetlana up
bsdb:878/2/2,Study 878,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, Huttenhower C, Garrett WS , Meyerson M",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 2,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,95,95,N/A,16S,345,Roche454,LEfSe,0.05,FALSE,4.2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2C,8 April 2024,MyleeeA,MyleeeA,"Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by 16S rDNA sequencing in 95 individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota",2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|976|200643|171549|815;2|1239|186801|186802|216572;2|976|200643;2|976|200643|171549;2|1239|186801|186802;2|1239|186801;2|1239,Complete,Svetlana up
bsdb:879/1/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 1,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Oral ulcer,HP:0000155,Covid-19 patients without oral lesions,Covid-19 with oral lesions,COVID-19 patients with the presence of oral lesions,101,14,NA,16S,4,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Fourth paragraph in section 3.3,6 March 2024,Nekembe,"Nekembe,Aleru Divine",Significant difference found in Covid-10 patients who had oral lesions.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
bsdb:879/2/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 2,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Illness severity status,EFO:0007863,Non severe COVID patients,Severe COVID patients,COVID-19 patients with severe symptoms,NA,NA,NA,16S,4,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Fourth paragraph in section 3.3,7 March 2024,Nekembe,"Nekembe,Aleru Divine",Significant differences found in Covid-10 patients who had severe symptoms.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:879/3/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 3,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Antimicrobial agent,CHEBI:33281,No antibiotics use,Antibiotics use,COVID-19 patients who had antibiotic therapy in the previous 3 months.,NA,NA,NA,16S,4,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Paragraph 4 in section 3.3 and Paragraph 5 in the discussion section,7 March 2024,Nekembe,"Nekembe,Aleru Divine",Significant differences found in Covid-10 patients who were on antibiotic therapy in the previous 3 months.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|186826|33958|1578;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:879/4/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 4,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Oxygen,CHEBI:15379,No oxygen therapy,Oxygen therapy,COVID-19 patients who had oxygen therapy.,NA,NA,NA,16S,4,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,Paragraph 4 in section 3.3 and Paragraph 5 in the discussion section,7 March 2024,Nekembe,"Nekembe,Aleru Divine",Significant differences found in Covid-10 patients who were on oxygen therapy.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:879/5/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 5,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Illness severity status,EFO:0007863,Non ICU patients,ICU patients,COVID-19 patients who were in intensive care units.,NA,NA,NA,16S,4,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section,29 March 2024,Aleru Divine,Aleru Divine,Significant differences found in Covid-10 patients who were in the Intensive Care Unit (ICU).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:879/5/2,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 5,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Illness severity status,EFO:0007863,Non ICU patients,ICU patients,COVID-19 patients who were in intensive care units.,NA,NA,NA,16S,4,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section,29 March 2024,Aleru Divine,Aleru Divine,Significant differences found in Covid-10 patients who were in the Intensive Care Unit (ICU).,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,NA
bsdb:879/6/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 6,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Diet,EFO:0002755,Non enteral diet,Covid-19 patients on enteral diet,COVID-19 patients who were on the enteral diet.,NA,NA,NA,16S,4,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section,29 March 2024,Aleru Divine,Aleru Divine,Significant differences found in Covid-10 patients who were on enteral diet.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135615|868|2717;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171551|836;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:880/1/1,Study 880,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B, Thänert R, Wallace MA, Burnham CD , Dantas G",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No Growth,Culture Positive,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,51,48,2 Weeks,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573,Complete,Folakunmi
bsdb:880/1/2,Study 880,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B, Thänert R, Wallace MA, Burnham CD , Dantas G",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No Growth,Culture Positive,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,51,48,2 Weeks,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2759|4751|4890;2|201174|1760|85009|31957|1912216|1747,Complete,Folakunmi
bsdb:880/2/1,Study 880,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B, Thänert R, Wallace MA, Burnham CD , Dantas G",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Insignificant Samples,Culture Positive Samples,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,17,48,2 Weeks,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,2|1224|1236|91347|543|570|573,Complete,Folakunmi
bsdb:880/2/2,Study 880,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B, Thänert R, Wallace MA, Burnham CD , Dantas G",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Insignificant Samples,Culture Positive Samples,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,17,48,2 Weeks,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|976|200643|171549|815|816|28116;2|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:880/3/1,Study 880,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B, Thänert R, Wallace MA, Burnham CD , Dantas G",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 3,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic,Insignificant Samples,Patients with specimen with bacterial growth <10^5 CFU/mL present during culturing but below the threshold for significance,10,17,2 Weeks,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 3,6 March 2024,MyleeeA,MyleeeA,Significantly enriched microbiota in suspected Urinary Tract Infections specimens from different clinical categories.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,Folakunmi
bsdb:880/4/1,Study 880,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B, Thänert R, Wallace MA, Burnham CD , Dantas G",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 4,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic,No Growth,Patients with urine samples with no visible Microorganism growth (Bacterial/Fungal),10,51,2 Weeks,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 3 and Table S3,6 March 2024,MyleeeA,MyleeeA,LefSe enrichment results; Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,2|201174|1760|85009|31957|1912216|1747,Complete,Folakunmi
bsdb:880/4/2,Study 880,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B, Thänert R, Wallace MA, Burnham CD , Dantas G",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 4,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic,No Growth,Patients with urine samples with no visible Microorganism growth (Bacterial/Fungal),10,51,2 Weeks,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 3 and Table S3,6 March 2024,MyleeeA,MyleeeA,LefSe enrichment results; Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,2|1239|186801|186802|216572|292632|2053618,Complete,Folakunmi
bsdb:881/1/NA,Study 881,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S, Valles-Colomer M, Foxx CL, Vieira-Silva S, van den Heuvel LL, Raes J, Seedat S, Lowry CA , Hemmings SMJ",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Post-traumatic stress disorder,EFO:0001358,Trauma exposed controls (TECs),Post Traumatic Stress Disorder (PTSD),"Individuals with Post Traumatic Stress Disorder (PTSD). 
Post traumatic stress disorder (PTSD) cases met the DSM-5 criteria of PTSD, in accordance with diagnostic evaluation using the Clinician Administered Post Traumatic Stress Disorder Scale for DSM–5 (CAPS-5) and had a CAPS 5 severity score greater than 23.",58,79,Antibiotic use within 4 weeks before stool sampling.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:881/2/1,Study 881,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S, Valles-Colomer M, Foxx CL, Vieira-Silva S, van den Heuvel LL, Raes J, Seedat S, Lowry CA , Hemmings SMJ",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Individuals not using psychotropic medication,Individuals using psychotropic medication,Individuals using psychotropic medication that may associate with the gut microbiome of the sample.,6,21,Antibiotic use within 4 weeks before stool sampling.,16S,4,Illumina,Linear Regression,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, C and D",7 March 2024,Keamy,"Keamy,ChiomaBlessing",Relative abundance (clr-transformed and filtered) of specific taxa at the genus and phylum level in individuals who were using psychotropic medication at the time of sample collection compared to individuals not using psychotropic medication,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239;2|976;2|1239|186801|186802|216572|1263,Complete,ChiomaBlessing
bsdb:881/2/2,Study 881,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S, Valles-Colomer M, Foxx CL, Vieira-Silva S, van den Heuvel LL, Raes J, Seedat S, Lowry CA , Hemmings SMJ",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Individuals not using psychotropic medication,Individuals using psychotropic medication,Individuals using psychotropic medication that may associate with the gut microbiome of the sample.,6,21,Antibiotic use within 4 weeks before stool sampling.,16S,4,Illumina,Linear Regression,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B and 4E,7 March 2024,Keamy,"Keamy,ChiomaBlessing",Relative abundance (clr-transformed and filtered) of specific taxa at the genus and phylum level in individuals who were using psychotropic medication at the time of sample collection compared to individuals not using psychotropic medication,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|74201,Complete,ChiomaBlessing
bsdb:881/3/1,Study 881,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S, Valles-Colomer M, Foxx CL, Vieira-Silva S, van den Heuvel LL, Raes J, Seedat S, Lowry CA , Hemmings SMJ",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Individuals without MDD diagnoses,Individuals with MDD diagnoses,Individuals diagnosed with Major Depressive Disorder (MDD). The MINI was used to diagnose MDD.,2,20,Antibiotic use within 4 weeks before stool sampling.,16S,4,Illumina,Linear Regression,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,7 March 2024,Keamy,"Keamy,ChiomaBlessing",GLM box plot showing relative abundance levels (clr-transformed and filtered) of the phylum Bacteroidetes in individuals who have MDD compared to those who did not have MDD,increased,k__Bacteria|p__Bacteroidota,2|976,Complete,ChiomaBlessing
bsdb:882/1/1,Study 882,"cross-sectional observational, not case-control,laboratory experiment",36627678,10.1186/s13578-023-00956-1,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832664,"Fu J, Shan J, Cui Y, Yan C, Wang Q, Han J , Cao G",Metabolic disorder and intestinal microflora dysbiosis in chronic inflammatory demyelinating polyradiculoneuropathy,Cell & bioscience,2023,"Arachidonic acid, Bile acids, Chronic inflammatory demyelinating polyradiculoneuropathy, Gut microbial dysbiosis, Metabolic disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic inflammatory demyelinating polyradiculoneuropathy,EFO:1000868,Healthy controls (non-CIDP),Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP),"Patients with chronic inflammatory demyelinating polyradiculoneuropathy (CIDP), a rare acquired immune-mediated neuropathy",33,31,None,WMS,NA,DNBSEQ-T7,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 6A,12 March 2024,Zheeburg,"Zheeburg,Scholastica",Bacterial species abundance in the stools of the chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) group versus non-CIDP group.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|906|907;2|1239|909932|1843489|31977|29465|39777;2|1239|186801|3085636|186803|2316020|33038;2|1239|909932|1843488|909930|33024|33025;2|1239|91061|186826|33958|1578|1604;2|1239|909932|909929|1843491|158846|437897;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|570|244366;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|2767887|1624;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|547|158836;2|1224|1236|91347|543|570|1463165;2|1239|91061|186826|1300|1301|1343,Complete,Svetlana up
bsdb:882/1/2,Study 882,"cross-sectional observational, not case-control,laboratory experiment",36627678,10.1186/s13578-023-00956-1,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832664,"Fu J, Shan J, Cui Y, Yan C, Wang Q, Han J , Cao G",Metabolic disorder and intestinal microflora dysbiosis in chronic inflammatory demyelinating polyradiculoneuropathy,Cell & bioscience,2023,"Arachidonic acid, Bile acids, Chronic inflammatory demyelinating polyradiculoneuropathy, Gut microbial dysbiosis, Metabolic disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic inflammatory demyelinating polyradiculoneuropathy,EFO:1000868,Healthy controls (non-CIDP),Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP),"Patients with chronic inflammatory demyelinating polyradiculoneuropathy (CIDP), a rare acquired immune-mediated neuropathy",33,31,None,WMS,NA,DNBSEQ-T7,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 6A,12 March 2024,Zheeburg,"Zheeburg,Scholastica",Bacterial species abundance in the stools of the chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) group versus non-CIDP group.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides coprosuis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zoogleoformans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. PHL 2737,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CT06,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. M10,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes dispar,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171552|577309|454155;2|976|200643|171549|815|909656|821;2|976|200643|171549|815|816|151276;2|976|200643|171549|815|909656|376805;2|976|200643|171549|815|816|28119;2|976|200643|171549|815|816|2162637;2|976|200643|171549|2005525|375288|2025876;2|976|200643|171549|815|816|2763022;2|976|200643|171549|815|816|28116;2|976|200643|171549|171550|239759|2585119;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|816|47678,Complete,Svetlana up
bsdb:883/1/1,Study 883,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A , Mukherjee S",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 1,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Healthy Controls,COVID-19 patients,Patients infected with COVID-19 virus (Delta and Omicron),19,43,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,FIG 2,12 March 2024,ModinatG,"ModinatG,Folakunmi",LEfSe analysis of core  species of COVID-19 patients and healthy controls.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas shioyasakiensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas gelatinilytica,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum|s__Ochrobactrum sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera|s__Rheinheimera pleomorphica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tritonius,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Vreelandella|s__Vreelandella piezotolerans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium|s__Pelagibacterium halotolerans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1224|1236|135614|32033|40323|40324;2|1224|1236|135622|267888|53246|1190813;2|1224|1236|135622|267888|53246|1703256;2|1224|28211|356|118882|528|42190;2|1224|1236|135614|32033|40323|69392;2|1224|1236|72274|135621|286|306;2|1239|91061|1385|90964|1279|29380;2|1224|1236|135613|1046|67575|2703963;2|1224|1236|135623|641|662|1435069;2|976|117743|200644|2762318|59732|1871047;2|1224|1236|135619|28256|3137766|2609667;2|1224|28211|356|2831106|1082930|531813;2|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:883/1/2,Study 883,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A , Mukherjee S",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 1,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Healthy Controls,COVID-19 patients,Patients infected with COVID-19 virus (Delta and Omicron),19,43,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,FIG 2,12 March 2024,ModinatG,"ModinatG,Folakunmi",Relative abundances of bacteria in upper respiratory tract (URT) of Covid-19 patients and healthy group,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus symci,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella equi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus toyakuensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",2|201174|1760|85004|31953|1678|216816;2|32066|203490|203491|203492|848|2663009;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482|33053;2|976|200643|171549|171552|838|28132;2|1239|91061|186826|1300|1301|2588991;2|1239|909932|1843489|31977|29465|2682456;2|1239|909932|1843489|31977|29465|1110546;2|1224|1236|135625|712|713|41114;2|201174|1760|85007|1653|1716|38284;2|1224|1236|2887326|468|475|60442;2|1239|91061|186826|1300|1301|2819619;2|1239|909932|1843489|31977|29465|423477;2|1224|28216|206351|481|482|28449;2|32066|203490|203491|1129771|32067|157687;2|1239|909932|1843489|31977|29465|39777,Complete,Folakunmi
bsdb:883/2/1,Study 883,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A , Mukherjee S",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 2,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Healthy Controls,Delta and Omicron-infected patients,Patients infected with the Delta and Omicron variants of  SARS-CoV-2,19,43,1 month,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,FIG 6,14 March 2024,ModinatG,"ModinatG,Folakunmi","Taxonomic difference among healthy controls, Delta-, and Omicron-infected patients.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae",2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482|33053;2|32066|203490|203491|203492|848|2663009;2|1224|28216|206351|481|482|28449;2|1239|909932|1843489|31977|29465|423477;2|1239|909932|1843489|31977|29465|2682456,Complete,Folakunmi
bsdb:883/3/1,Study 883,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A , Mukherjee S",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 3,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Omicron-infected patients,Delta-infected patients,Patients infected with Delta virus,19,24,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,FIG 5,12 March 2024,ModinatG,ModinatG,Upper respiratory tract (URT) microbiome composition between Delta and Omicron infected patients.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter mori,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter quasihormaechei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus toyakuensis",2|1224|1236|2887326|468|469|470;2|976|117743|200644|2762318|59732|1871047;2|1224|1236|91347|543|547|208224;2|1224|1236|91347|543|547|539813;2|1224|1236|91347|543|547|2529382;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|1463165;2|1224|1236|91347|543|570|244366;2|1224|1236|135614|32033|40323|69392;2|1239|91061|186826|1300|1301|2819619,Complete,Folakunmi
bsdb:883/3/2,Study 883,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A , Mukherjee S",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 3,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Omicron-infected patients,Delta-infected patients,Patients infected with Delta virus,19,24,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,FIG 5,12 March 2024,ModinatG,ModinatG,Upper respiratory tract (URT) microbiome composition between Delta and Omicron infected patients.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum|s__Ochrobactrum sp.,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium|s__Pelagibacterium halotolerans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus symci,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tritonius",2|1224|28216|206351|481|482|33053;2|1224|28211|356|118882|528|42190;2|1224|28211|356|2831106|1082930|531813;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|28132;2|1224|1236|72274|135621|286|287;2|1224|1236|72274|135621|286|306;2|201174|1760|85006|1268|32207|43675;2|1239|91061|1385|90964|1279|29380;2|1239|91061|186826|1300|1301|1156431;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|2588991;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|2682456;2|1239|909932|1843489|31977|29465|1110546;2|1224|1236|135623|641|662|1435069,Complete,Folakunmi
bsdb:884/1/1,Study 884,case-control,35863004,10.1128/spectrum.00324-22,NA,"Zhang L, Wang Z, Zhang X, Zhao L, Chu J, Li H, Sun W, Yang C, Wang H, Dai W, Yan S, Chen X , Xu D",Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy,Microbiology spectrum,2022,"composition, diabetic nephropathy, function, gut microbiota, metagenomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetic nephropathy,EFO:0000401,healthy controls (CON),Diabetic nephropathy (DN),"Patients with diabetic nephropathy (DN). DN is a chronic kidney disease (CKD), which is one of the most common complications of diabetic microangiopathy and the primary cause of end-stage renal disease (ESRD).",14,12,Past 1 month,WMS,NA,Illumina,LEfSe,0.05,NA,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,FIG 3 (B),12 March 2024,Rahila,"Rahila,ChiomaBlessing",Differentially abundant taxa identified in the diabetic nephropathy (DN) group compared to the healthy control (CON) group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. 20_3,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MSX73,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. CAG:51",2|976|200643|171549|171550|239759|1470347;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|46506;2|976|200643|171549|2005519|397864|2033407;2|976|200643|171549|2005525|375288|469591;2|976|200643|171549|171552|838|1032506;2|976|200643|171549|2005525|195950|1262979,Complete,ChiomaBlessing
bsdb:884/2/1,Study 884,case-control,35863004,10.1128/spectrum.00324-22,NA,"Zhang L, Wang Z, Zhang X, Zhao L, Chu J, Li H, Sun W, Yang C, Wang H, Dai W, Yan S, Chen X , Xu D",Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy,Microbiology spectrum,2022,"composition, diabetic nephropathy, function, gut microbiota, metagenomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,healthy controls (CON),type 2 diabetes mellitus (T2DM),Patients with type 2 diabetes mellitus (T2DM) without DN,14,12,Past 1 month,WMS,NA,Illumina,LEfSe,0.05,NA,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,FIG 3 (B),12 March 2024,Rahila,"Rahila,ChiomaBlessing",Differentially abundant taxa identified in the Type 2 diabetes mellitus (T2DM) group compared to the healthy control (CON) group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides hominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. PHL 2737,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:715,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. AF19-14,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|976|200643|171549|815|816|2763023;2|976|200643|171549|815|816|2162637;2|1239|186801|186802|31979|1485|1262834;2|1239|91061|186826|33958|2742598|97478;2|976|200643|171549|2005525|375288|2293114;2|976|200643|171549|171552|838|1262936;2|1239|909932|1843489|31977|29465|39778,Complete,ChiomaBlessing
bsdb:884/3/NA,Study 884,case-control,35863004,10.1128/spectrum.00324-22,NA,"Zhang L, Wang Z, Zhang X, Zhao L, Chu J, Li H, Sun W, Yang C, Wang H, Dai W, Yan S, Chen X , Xu D",Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy,Microbiology spectrum,2022,"composition, diabetic nephropathy, function, gut microbiota, metagenomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,type 2 diabetes mellitus (T2DM),Diabetic nephropathy (DN),Patients with diabetic nephropathy (DN).,12,12,Past 1 month,WMS,NA,Illumina,LEfSe,0.05,NA,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:885/1/1,Study 885,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z , Zhao L",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Moderate severity,COVID-19 Patients with moderate severity symptoms.,88,196,NA,WMS,NA,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 2A,9 March 2024,Zheeburg,"Zheeburg,Aleru Divine",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|3118652|2039240;2|976|200643|171549|2005519|397864|487174;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|2719313|208479;2|1239|91061|186826|81852|1350|33945;2|1239|91061|186826|81852|1350|1352;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|1613;2|1239|909932|1843488|909930|33024|33025;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|186802|3082771,Complete,Svetlana up
bsdb:885/1/2,Study 885,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z , Zhao L",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Moderate severity,COVID-19 Patients with moderate severity symptoms.,88,196,NA,WMS,NA,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Fig. 2A,10 March 2024,Zheeburg,"Zheeburg,Aleru Divine",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella|s__Allisonella histaminiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572|216851|853;2|1239|909932|1843489|31977|209879|209880;2|1239|186801|186802|3082771;2|1239|1980693;2|1239|186801|186802|31979|1485;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:885/2/1,Study 885,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z , Zhao L",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,88,12,NA,WMS,NA,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 2A,9 March 2024,Zheeburg,"Zheeburg,Aleru Divine",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|3118652|2039240;2|976|200643|171549|2005519|397864|487174;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|2719313|208479;2|1239|91061|186826|81852|1350|33945;2|1239|91061|186826|81852|1350|1352;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|1613;2|1239|909932|1843488|909930|33024|33025;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|186802|3082771,Complete,Svetlana up
bsdb:885/2/2,Study 885,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z , Zhao L",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,88,12,NA,WMS,NA,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Fig. 2A,10 March 2024,Zheeburg,"Zheeburg,Aleru Divine",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella|s__Allisonella histaminiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572|216851|853;2|1239|909932|1843489|31977|209879|209880;2|1239|186801|186802|3082771;2|1239|1980693;2|1239|186801|186802|31979|1485;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:885/3/1,Study 885,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z , Zhao L",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Moderate severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,196,12,NA,WMS,NA,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 2A,10 March 2024,Zheeburg,"Zheeburg,Aleru Divine",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Candidatus Dorea massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|3085636|3118652|2039240;2|976|200643|171549|2005519|397864|487174;2|1239|186801|3085636|186803|189330|1470355;2|1239|186801|3085636|186803|2719313|208479;2|1239|91061|186826|81852|1350|33945;2|1239|91061|186826|81852|1350|1352;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|1613;2|1239|909932|1843488|909930|33024|33025;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|186802|3082771,Complete,Svetlana up
bsdb:885/3/2,Study 885,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z , Zhao L",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Moderate severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,196,12,NA,WMS,NA,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Fig. 2A,10 March 2024,Zheeburg,"Zheeburg,Aleru Divine",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella|s__Allisonella histaminiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572|216851|853;2|1239|909932|1843489|31977|209879|209880;2|1239|186801|186802|3082771;2|1239|1980693;2|1239|186801|186802|31979|1485;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40518;2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:886/1/1,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 1,Belgium,Sus scrofa domesticus,Colon,UBERON:0001155,Ascariasis,EFO:0007154,Uninfected piglets,Ascaris suum infected piglets,Colon samples from ascariasis infected piglets,4,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 1,Figure 1A,7 March 2024,JimFlashy,"JimFlashy,Scholastica",Differentially abundant microbial signatures in the colon of ascaris suum infected piglets compared to uninfected piglets.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria,k__Bacteria|p__Fibrobacterota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|s__Leuconostocaceae bacterium,k__Bacteria|p__Verrucomicrobiota|c__Opitutia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|201174|1760|2037;2|201174;2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|1224|28216;2|1239|91061|186826|186828;2|1239|186801|186802|31979|1485;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186807|51514;2|1239|526524;2|65842|204430|218872|204431|832;2|65842|204430|218872;2|65842|204430;2|65842;2|32066|203490;2|32066;2|1239|91061|186826|33958|2590211;2|74201|414999;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|203682|203683|112;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|203691|203692;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|186828|82802;2|74201;2|1239|91061|186826|33958|46255,Complete,ChiomaBlessing
bsdb:886/1/2,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 1,Belgium,Sus scrofa domesticus,Colon,UBERON:0001155,Ascariasis,EFO:0007154,Uninfected piglets,Ascaris suum infected piglets,Colon samples from ascariasis infected piglets,4,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 2,Figure 1A,7 March 2024,JimFlashy,"JimFlashy,Scholastica",Differentially abundant microbial signatures in the colon of ascaris suum infected piglets compared to uninfected piglets.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Svetlana up
bsdb:886/2/1,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 2,Belgium,Sus scrofa domesticus,Feces,UBERON:0001988,Ascariasis,EFO:0007154,Uninfected piglets,Ascaris suum infected piglets,Feces samples from ascariasis infected piglets,4,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 1,Figure 1B,7 March 2024,JimFlashy,"JimFlashy,Scholastica",Differentially abundant microbial signatures in the feces of ascaris suum infected piglets compared to uninfected piglets.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1224|1236|91347|543|544;2|1239|186801|3085636|186803;2|544448|31969|2085|2092|2093;2|544448|31969|2085|2092;2|544448|31969|2085;2|1239|186801|3085636|186803|841,Complete,ChiomaBlessing
bsdb:886/2/2,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 2,Belgium,Sus scrofa domesticus,Feces,UBERON:0001988,Ascariasis,EFO:0007154,Uninfected piglets,Ascaris suum infected piglets,Feces samples from ascariasis infected piglets,4,10,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 2,Figure 1B,7 March 2024,JimFlashy,"JimFlashy,Scholastica",Differentially abundant microbial signatures in the feces of ascaris suum infected piglets compared to uninfected piglets.,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,2|1239|909932|1843488|909930|904,Complete,ChiomaBlessing
bsdb:886/3/1,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 3,Belgium,Sus scrofa domesticus,Colon,UBERON:0001155,Ascariasis,EFO:0007154,Uninfected piglets,Low worm burden ascaris suum infected piglets,Colon samples from low worm burden ascariasis infected piglets,4,5,None,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 1,Table 2,11 April 2024,JimFlashy,"JimFlashy,Scholastica",Differences in taxonomic units in the colon of low worm burden ascaris suum infected piglets compared to uninfected piglets.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|1239|909932|909929|1843491|82373;2|1239|526524|526525|128827;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179,Complete,ChiomaBlessing
bsdb:886/3/2,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 3,Belgium,Sus scrofa domesticus,Colon,UBERON:0001155,Ascariasis,EFO:0007154,Uninfected piglets,Low worm burden ascaris suum infected piglets,Colon samples from low worm burden ascariasis infected piglets,4,5,None,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 2,Table 2,11 April 2024,JimFlashy,"JimFlashy,Scholastica",Differences in taxonomic units in the colon of low worm burden ascaris suum infected piglets compared to uninfected piglets.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:886/4/1,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 4,Belgium,Sus scrofa domesticus,Colon,UBERON:0001155,Ascariasis,EFO:0007154,Uninfected piglets,High worm burden ascaris suum infected piglets,Colon samples from high worm burden ascariasis infected piglets,4,5,None,16S,34,Illumina,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 1,Table 2,11 April 2024,JimFlashy,"JimFlashy,Scholastica",Differences in taxonomic units in the colon of high worm burden ascaris suum infected piglets compared to uninfected piglets.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|1239|909932|909929|1843491|82373;2|1239|526524|526525|128827;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:886/4/2,Study 886,laboratory experiment,30738924,https://doi.org/10.1016/j.ijpara.2018.10.007,NA,"Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P , Li RW",Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome,International journal for parasitology,2019,"16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine",Experiment 4,Belgium,Sus scrofa domesticus,Colon,UBERON:0001155,Ascariasis,EFO:0007154,Uninfected piglets,High worm burden ascaris suum infected piglets,Colon samples from high worm burden ascariasis infected piglets,4,5,None,16S,34,Illumina,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 2,Table 2,11 April 2024,JimFlashy,"JimFlashy,Scholastica",Differences in taxonomic units in the colon of high worm burden ascaris suum infected piglets compared to uninfected piglets.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:888/1/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,MagNAPure,"DNA isolation from human fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,5 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|28216|80840|506;2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/1/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,MagNAPure,"DNA isolation from human fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,5 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|1224|1236|135625|712;2|976|200643|171549|171551;2|74201|203494|48461|203557,Complete,NA
bsdb:888/2/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,5 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|909932|1843489|31977;2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/2/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,5 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/3/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,5 April 2024,Aleru002,Aleru002,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/3/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,5 April 2024,Aleru002,Aleru002,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/4/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2D,5 April 2024,Aleru002,Aleru002,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|909932|1843489|31977;2|976|200643|171549|171552,Complete,NA
bsdb:888/4/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2D,5 April 2024,Aleru002,Aleru002,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|74201|203494|48461|203557;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/5/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|74201|203494|48461|203557,Complete,NA
bsdb:888/5/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/6/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,NA
bsdb:888/6/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|74201|203494|48461|203557;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/7/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",2|74201|203494|48461|203557;2|201174|1760|85004|31953,Complete,NA
bsdb:888/7/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/8/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/8/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/9/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 9,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,NA
bsdb:888/9/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 9,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|74201|203494|48461|203557;2|976|200643|171549|171551;2|1224|28216|80840|506,Complete,NA
bsdb:888/10/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 10,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|74201|203494|48461|203557;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/10/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 10,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|976|200643|171549|815;2|201174|1760|85004|31953;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/11/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 11,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,NA
bsdb:888/11/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 11,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|74201|203494|48461|203557;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/12/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 12,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/12/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 12,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|909932|1843489|31977;2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/13/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 13,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/13/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 13,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/14/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 14,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/14/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 14,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/15/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 15,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/15/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 15,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|909932|1843489|31977;2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/16/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 16,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/16/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 16,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/17/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 17,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/17/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 17,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|201174|1760|85004|31953;2|74201|203494|48461|203557,Complete,NA
bsdb:888/18/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 18,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|201174|1760|85004|31953;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/18/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 18,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,2|74201|203494|48461|203557,Complete,NA
bsdb:888/19/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 19,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|74201|203494|48461|203557,Complete,NA
bsdb:888/19/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 19,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/20/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 20,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,NA
bsdb:888/20/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 20,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|74201|203494|48461|203557;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/21/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 21,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,QIAStool,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,NA
bsdb:888/21/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 21,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,QIAStool,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|815;2|74201|203494|48461|203557;2|976|200643|171549|171551;2|1224|28216|80840|506;2|1224|1236|135625|712,Complete,NA
bsdb:888/22/NA,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 22,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,WMS,NA,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:888/23/NA,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 23,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,WMS,NA,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:888/24/NA,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 24,Denmark,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,WMS,NA,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:888/25/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 25,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,MagNAPure,"DNA isolation from pig fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/25/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 25,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,MagNAPure,"DNA isolation from pig fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,2|29547|3031852|213849|72294,Complete,NA
bsdb:888/26/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 26,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,Easy-DNA,"DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/26/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 26,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,Easy-DNA,"DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|31979;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/27/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 27,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/27/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 27,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/28/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 28,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572;2|1239|186801|3085636|186803;2|1239|526524|526525|128827,Complete,NA
bsdb:888/28/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 28,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|1239|186801|186802|31979;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/29/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 29,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/29/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 29,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae",2|1239|186801|3085636|186803;2|29547|3031852|213849|72294,Complete,NA
bsdb:888/30/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 30,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|526524|526525|128827,Complete,NA
bsdb:888/30/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 30,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/31/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 31,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,Easy-DNA,"DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|29547|3031852|213849|72294;2|976|200643|171549|171552,Complete,NA
bsdb:888/31/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 31,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,Easy-DNA,"DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/32/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 32,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|186801|186802|216572;2|1239|186801|186802|31979,Complete,NA
bsdb:888/32/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 32,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|1239|186801|3085636|186803;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/33/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 33,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP)",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572;2|1239|186801|3085636|186803;2|29547|3031852|213849|72294;2|1239|526524|526525|128827,Complete,NA
bsdb:888/33/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 33,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP)",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|186802|31979;2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/34/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 34,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|1239|186801|186802|31979;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/34/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 34,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803;2|1239|186801|186802|216572,Complete,NA
bsdb:888/35/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 35,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|29547|3031852|213849|72294;2|1239|186801|186802|31979,Complete,NA
bsdb:888/35/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 35,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/36/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 36,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/36/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 36,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|29547|3031852|213849|72294;2|1239|526524|526525|128827,Complete,NA
bsdb:888/37/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 37,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/37/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 37,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,NA
bsdb:888/38/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 38,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|29547|3031852|213849|72294;2|1239|526524|526525|128827;2|1239|909932|1843489|31977;2|1239|186801|186802|31979,Complete,NA
bsdb:888/38/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 38,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/39/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 39,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|31979;2|29547|3031852|213849|72294;2|1239|526524|526525|128827,Complete,NA
bsdb:888/39/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 39,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/40/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 40,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572;2|1239|186801|3085636|186803;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/40/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 40,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|976|200643|171549|171552;2|1239|186801|186802|31979,Complete,NA
bsdb:888/41/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 41,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/41/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 41,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/42/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 42,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|29547|3031852|213849|72294;2|1239|526524|526525|128827,Complete,NA
bsdb:888/42/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 42,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,FastDNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/43/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 43,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|1239|186801|186802|31979;2|1239|909932|1843489|31977,Complete,NA
bsdb:888/43/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 43,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572;2|1239|186801|3085636|186803;2|29547|3031852|213849|72294;2|1239|526524|526525|128827,Complete,NA
bsdb:888/44/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 44,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,NA
bsdb:888/44/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 44,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|3085636|186803;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/45/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 45,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,QIAStool,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,NA
bsdb:888/45/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 45,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,QIAStool,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|29547|3031852|213849|72294;2|1239|909932|1843489|31977;2|1239|526524|526525|128827,Complete,NA
bsdb:888/46/NA,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 46,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,Easy-DNA,"DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,WMS,NA,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:888/47/NA,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 47,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,MagNAPure,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,WMS,NA,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:888/48/NA,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 48,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,WMS,NA,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:888/49/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 49,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,MagNAPure,"DNA isolation from sewage samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|2887326|468;2|1224|28216|206351|481;2|74201|203494|48461|203557,Complete,NA
bsdb:888/49/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 49,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,MagNAPure,"DNA isolation from sewage samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1239|186801|3085636|186803;2|74201|414999|415000|134623,Complete,NA
bsdb:888/50/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 50,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|1239|186801|3085636|186803;2|74201|203494|48461|203557,Complete,NA
bsdb:888/50/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 50,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,2|74201|414999|415000|134623,Complete,NA
bsdb:888/51/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 51,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|1224|1236|2887326|468;2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623;2|976|200643|171549|815,Complete,NA
bsdb:888/51/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 51,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/52/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 52,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/52/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 52,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/53/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 53,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/53/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 53,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,NA
bsdb:888/54/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 54,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|1236|2887326|468;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|74201|414999|415000|134623,Complete,NA
bsdb:888/54/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 54,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,InnuPURE,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|29547|3031852|213849|72294;2|1239|186801|3085636|186803;2|74201|203494|48461|203557,Complete,NA
bsdb:888/55/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 55,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/55/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 55,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/56/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 56,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|29547|3031852|213849|72294;2|976|200643|171549|815;2|1239|186801|3085636|186803;2|74201|414999|415000|134623,Complete,NA
bsdb:888/56/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 56,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|2887326|468;2|1239|186801|186802|216572;2|1224|28216|206351|481;2|74201|203494|48461|203557,Complete,NA
bsdb:888/57/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 57,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1239|186801|186802|216572;2|976|200643|171549|815;2|1239|186801|3085636|186803;2|74201|414999|415000|134623,Complete,NA
bsdb:888/57/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 57,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|29547|3031852|213849|72294;2|1224|1236|2887326|468;2|1224|28216|206351|481;2|74201|203494|48461|203557,Complete,NA
bsdb:888/58/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 58,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|815;2|29547|3031852|213849|72294;2|74201|414999|415000|134623;2|1239|186801|186802|216572;2|74201|203494|48461|203557;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/58/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 58,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1224|1236|2887326|468;2|1224|28216|206351|481,Complete,NA
bsdb:888/59/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 59,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1239|186801|3085636|186803;2|74201|414999|415000|134623,Complete,NA
bsdb:888/59/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 59,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,MagNA Pure,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|2887326|468;2|1224|28216|206351|481;2|74201|203494|48461|203557,Complete,NA
bsdb:888/60/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 60,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/60/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 60,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/61/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 61,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/61/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 61,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/62/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 62,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/62/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 62,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/63/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 63,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|28216|206351|481;2|74201|414999|415000|134623,Complete,NA
bsdb:888/63/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 63,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,Easy-DNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1239|186801|3085636|186803;2|74201|203494|48461|203557,Complete,NA
bsdb:888/64/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 64,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,FastDNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|1239|186801|3085636|186803;2|74201|414999|415000|134623,Complete,NA
bsdb:888/64/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 64,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,FastDNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|74201|203494|48461|203557,Complete,NA
bsdb:888/65/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 65,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,FastDNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/65/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 65,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,FastDNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,NA
bsdb:888/66/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 66,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,FastDNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|1236|2887326|468;2|1239|186801|186802|216572;2|1224|28216|206351|481;2|1239|186801|3085636|186803;2|74201|414999|415000|134623,Complete,NA
bsdb:888/66/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 66,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,FastDNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|29547|3031852|213849|72294;2|976|200643|171549|815;2|74201|203494|48461|203557,Complete,NA
bsdb:888/67/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 67,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|976|200643|171549|815;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/67/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 67,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|216572;2|1224|28216|206351|481;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/68/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 68,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|1236|2887326|468;2|29547|3031852|213849|72294;2|1239|186801|3085636|186803,Complete,NA
bsdb:888/68/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 68,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,PowerSoil.HMP,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",2|1239|186801|186802|216572;2|976|200643|171549|815;2|1224|28216|206351|481;2|74201|203494|48461|203557;2|74201|414999|415000|134623,Complete,NA
bsdb:888/69/1,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 69,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,QIAStool,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,NA
bsdb:888/69/2,Study 888,laboratory experiment,27822556,10.1128/mSystems.00095-16,https://journals.asm.org/doi/full/10.1128/msystems.00095-16,"Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM , Pamp SJ",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 69,Denmark,Not specified,NA,NA,Microbiome measurement,EFO:0007882,QIAStool,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,Aleru Divine,The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1224|1236|2887326|468;2|1239|186801|186802|216572;2|976|200643|171549|815;2|29547|3031852|213849|72294;2|74201|203494|48461|203557;2|74201|414999|415000|134623;2|1224|28216|206351|481,Complete,NA
bsdb:889/1/1,Study 889,case-control,37432374,10.3390/nu15092173,NA,"Silvano A, Meriggi N, Renzi S, Seravalli V, Torcia MG, Cavalieri D , Di Tommaso M",Vaginal Microbiome in Pregnant Women with and without Short Cervix,Nutrients,2023,"Gardenerella vaginalis, Lactobacillus, aerobic vaginitis, microbiome, risk in pregnancy, shortened cervix",Experiment 1,Italy,Homo sapiens,Vagina,UBERON:0000996,Cervix erosion,EFO:1000862,Control,Short Cervix Length,Pregnant women of predominantly Caucasian ethnicity with singleton gestation and a cervical length ≤ 25 mm in their second or early third trimester (23–32 weeks’ gestation),29,68,At the time of recruitment,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 2a,6 April 2024,Ayibatari,"Ayibatari,Scholastica",Linear discriminant analysis effect size (LEfSe) showing the significant taxonomic features in short cervix length versus control groups at different taxonomic levels,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Tabrizicola",2|1224|28211;2|1224|28211|204458|76892|41275;2|1224|28211|204458|76892;2|1224|28211|204458;2|201174|1760|85007|1653;2|1224|1236;2|1224|1236|135614|32033;2|1224|1236|135614;2|201174|1760|85007;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224;2|1224|1236|72274|135621|286;2|1224|1236|135614|32033|83618;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1224|28211|204455|31989|1443919,Complete,Svetlana up
bsdb:889/1/2,Study 889,case-control,37432374,10.3390/nu15092173,NA,"Silvano A, Meriggi N, Renzi S, Seravalli V, Torcia MG, Cavalieri D , Di Tommaso M",Vaginal Microbiome in Pregnant Women with and without Short Cervix,Nutrients,2023,"Gardenerella vaginalis, Lactobacillus, aerobic vaginitis, microbiome, risk in pregnancy, shortened cervix",Experiment 1,Italy,Homo sapiens,Vagina,UBERON:0000996,Cervix erosion,EFO:1000862,Control,Short Cervix Length,Pregnant women of predominantly Caucasian ethnicity with singleton gestation and a cervical length ≤ 25 mm in their second or early third trimester (23–32 weeks’ gestation),29,68,At the time of recruitment,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 2a,12 June 2024,Scholastica,Scholastica,Linear discriminant analysis effect size (LEfSe) showing the significant taxonomic features in short cervix length versus control groups at different taxonomic levels,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",2|1224|28211|204455|31989;2|1224|28211|204455;2|201174|1760|2037;2|201174|1760|2037|2049;2|1239|186801;2|1224|28211|204455|31989|265;2|976|200643|171549|171551|836;2|976|200643|171549|171551;2|201174|1760|85006;2|201174|1760|2037|2049|2050,Complete,Svetlana up
bsdb:890/1/1,Study 890,case-control,37608830,10.3389/fmed.2023.1177990,NA,"Vidmar Šimic M, Maver A, Zimani AN, Hočevar K, Peterlin B, Kovanda A , Premru-Sršen T",Oral microbiome and preterm birth,Frontiers in medicine,2023,"16S rDNA, 16S rRNA gene, microbiome, oral microbiome, pregnancy, preterm delivery",Experiment 1,Slovenia,Homo sapiens,Oral cavity,UBERON:0000167,Premature birth,EFO:0003917,Term birth (TB),Preterm birth (PTB),"Spontaneous onset of preterm labor (≤36 6/7 weeks) due to various causes, including spontaneous contractions, preterm premature rupture of membranes (PPROM), intrauterine infection, cervical insufficiency, and others",91,61,Week before inclusion,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4,6 April 2024,Ayibatari,"Ayibatari,Scholastica",Differential relative abundance of oral bacteria in term vs. preterm delivery groups,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella massiliensis",2|976|117743|200644|49546|1016;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|1936062,Complete,Svetlana up
bsdb:890/1/2,Study 890,case-control,37608830,10.3389/fmed.2023.1177990,NA,"Vidmar Šimic M, Maver A, Zimani AN, Hočevar K, Peterlin B, Kovanda A , Premru-Sršen T",Oral microbiome and preterm birth,Frontiers in medicine,2023,"16S rDNA, 16S rRNA gene, microbiome, oral microbiome, pregnancy, preterm delivery",Experiment 1,Slovenia,Homo sapiens,Oral cavity,UBERON:0000167,Premature birth,EFO:0003917,Term birth (TB),Preterm birth (PTB),"Spontaneous onset of preterm labor (≤36 6/7 weeks) due to various causes, including spontaneous contractions, preterm premature rupture of membranes (PPROM), intrauterine infection, cervical insufficiency, and others",91,61,Week before inclusion,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 4,11 June 2024,Scholastica,Scholastica,Differential relative abundance of oral bacteria in term vs. preterm delivery groups,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 848,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus",2|201174|1760|85007|1653|1716;2|201174|1760|2037|2049|1654;2|1239|186801|3085636|186803|1164882;2|201174|1760|2037|2049|1654|649739;2|29547|3031852|213849|72294|194;2|976|200643|171549|171552|1283313;2|976|200643|171549|171551|836;2|1239|186801|3085636|186803|43996;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2047;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1305;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|1239|91061|186826|1300|1301|45634;2|1239|91061|1385|539738|1378|84135;2|32066|203490|203491|1129771|32067|157687;2|1224|1236|135625|712|724|1078480;2|32066|203490|203491|1129771|32067|109328;2|1239|186801|3085636|186803|1164882|467210;2|29547|3031852|213849|72294|194|824;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|257758;2|1224|28216|206351|481|482|1107316;2|1224|28216|206351|481|482|483;2|1224|28216|206351|481|482|487;2|1224|28216|206351|481|482|28449;2|1224|28216|206351|481|482|488;2|201174|1760|85006|1268|32207|43675;2|1224|1236|135625|712|724|726,Complete,Svetlana up
bsdb:891/1/1,Study 891,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B , Pandey R",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 1,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,mild,moderate,patients showing breathing difficulty with SpO2 levels ranging between 91% and 93%.,24,36,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3i-j,8 March 2024,Leenaa,Leenaa,Differentially abundant bacterial species between mild group and moderate group,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas|s__Halomonas sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri",2|1224|1236|135619|28256|2745|1486246;2|201174|1760|2037|2049|2529408|52773,Complete,Folakunmi
bsdb:891/2/1,Study 891,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B , Pandey R",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 2,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,mild,mortality,patients who succumbed to COVID-19 during hospital stay,24,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3e,10 March 2024,Leenaa,Leenaa,Differentially abundant bacterial species between mild group and mortality group,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter xylosoxidans,2|1224|28216|80840|506|222|85698,Complete,Folakunmi
bsdb:891/3/1,Study 891,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B , Pandey R",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 3,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,moderate,severe,patients showing respiratory distress with respiratory support requirement and SpO2 levels < 90%,36,14,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,10 March 2024,Leenaa,Leenaa,Differentially abundant bacterial species between moderate group and severe group,increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,2|32066|203490|203491|1129771|32067|40542,Complete,Folakunmi
bsdb:891/4/1,Study 891,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B , Pandey R",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 4,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,moderate,mortality,patients who succumbed to COVID-19 during hospital stay,36,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3f,10 March 2024,Leenaa,Leenaa,Differentially abundant bacterial species between moderate group and mortality group,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,2|1239|91061|1385|186817|1386|1396,Complete,Folakunmi
bsdb:891/4/2,Study 891,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B , Pandey R",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 4,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,moderate,mortality,patients who succumbed to COVID-19 during hospital stay,36,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3h,10 March 2024,Leenaa,Leenaa,Differentially abundant bacterial species between moderate group and mortality group,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,2|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:891/5/1,Study 891,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B , Pandey R",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 5,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,severe,mortality,patients who succumbed to COVID-19 during hospital stay,14,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,10 March 2024,Leenaa,Leenaa,Differentially abundant bacterial species between severe group and mortality group,decreased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,2|32066|203490|203491|1129771|32067|40542,Complete,Folakunmi
bsdb:892/1/1,Study 892,case-control,37805557,https://doi.org/10.1186/s40168-023-01657-0,NA,"Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F , Wei F","PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation",Microbiome,2023,"Adaptive evolution, Conservation, Diversity, Giant panda, Gut microbiome, Wild mammal",Experiment 1,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Diet,EFO:0002755,Pandas in shoot-eating season,Pandas in leaf-eating season,Pandas in leaf-eating season from the Qinling cohort of wild pandas,24,33,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,15 March 2024,Svetlana up,"Svetlana up,Omojokunoluwatomisin",A very challenging figure to interpret: Significantly differentially abundant taxa between diet seasons. Increased abundance in pandas leaf-eating season.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,2|1239|186801|186802|31979|1485|1506,Complete,Svetlana up
bsdb:892/2/NA,Study 892,case-control,37805557,https://doi.org/10.1186/s40168-023-01657-0,NA,"Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F , Wei F","PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation",Microbiome,2023,"Adaptive evolution, Conservation, Diversity, Giant panda, Gut microbiome, Wild mammal",Experiment 2,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Diet,EFO:0002755,MIN wild pandas,QXL wild pandas,"Only 1864 wild giant pandas are extant and are distributed in six mountain ranges including the Qinling (QIN), Minshan (MIN), Qionglai (QIO), Daxiangling (DXL), Xiaoxiangling (XXL), and Liangshan (LSH) mountains that can be classified into three genetic populations including the QIN, MIN, and QIO-DXL-XXL-LSH (QXL) populations",7,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:892/3/NA,Study 892,case-control,37805557,https://doi.org/10.1186/s40168-023-01657-0,NA,"Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F , Wei F","PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation",Microbiome,2023,"Adaptive evolution, Conservation, Diversity, Giant panda, Gut microbiome, Wild mammal",Experiment 3,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Diet,EFO:0002755,QIN wild pandas,QXL wild pandas,"Only 1864 wild giant pandas are extant and are distributed in six mountain ranges including the Qinling (QIN), Minshan (MIN), Qionglai (QIO), Daxiangling (DXL), Xiaoxiangling (XXL), and Liangshan (LSH) mountains that can be classified into three genetic populations including the QIN, MIN, and QIO-DXL-XXL-LSH (QXL) populations",31,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:893/1/1,Study 893,"cross-sectional observational, not case-control",35865814,10.3389/fcimb.2022.894777,NA,"Sarkar P, Malik S, Banerjee A, Datta C, Pal DK, Ghosh A , Saha A",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer,Frontiers in cellular and infection microbiology,2022,"EBV, HPV, benign prostate hyperplasia, microbiome, prostate cancer",Experiment 1,India,Homo sapiens,Prostate gland,UBERON:0002367,Prostate carcinoma,EFO:0001663,"Benign prostatic hyperplasia (BPH),  Cohort-1 (Discovery Cohort)","Prostate Cancer (PCa),  Cohort-1 (Discovery Cohort)",Patients who are diagnosed with Prostate Cancer (PCa),13,33,None,16S,23456789,Ion Torrent,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,"Fig 2D, Supp. Fig 1E",6 April 2024,Ayibatari,"Ayibatari,Scholastica",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia versus Prostate Cancer.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia adecarboxylata,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter segnis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus basilensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium cytisi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas vancanneytii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium organophilum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus taiwanensis",2|1224|28211|356|41294|374;2|1224|28216|206351|481|482|495;2|1224|1236|91347|543|83654|83655;2|1224|28211|204458|76892|75|88688;2|1224|28216|80840|119060|106589|68895;2|1224|28211|356|41294|374|515489;2|1224|1236|2887326|468|469|40215;2|1224|28216|206351|481|482|484;2|1224|28211|204458|76892|41275|1325724;2|1224|28211|356|119045|407|410;2|1224|28216|80840|119060|106589|164546,Complete,Svetlana up
bsdb:893/1/2,Study 893,"cross-sectional observational, not case-control",35865814,10.3389/fcimb.2022.894777,NA,"Sarkar P, Malik S, Banerjee A, Datta C, Pal DK, Ghosh A , Saha A",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer,Frontiers in cellular and infection microbiology,2022,"EBV, HPV, benign prostate hyperplasia, microbiome, prostate cancer",Experiment 1,India,Homo sapiens,Prostate gland,UBERON:0002367,Prostate carcinoma,EFO:0001663,"Benign prostatic hyperplasia (BPH),  Cohort-1 (Discovery Cohort)","Prostate Cancer (PCa),  Cohort-1 (Discovery Cohort)",Patients who are diagnosed with Prostate Cancer (PCa),13,33,None,16S,23456789,Ion Torrent,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Fig 2D, Supp. Fig 1E",6 April 2024,Ayibatari,"Ayibatari,Scholastica",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia versus Prostate Cancer.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Aeromicrobium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Serinicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio|s__Cellvibrio mixtus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium paraconglomeratum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus arlettae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius",2|201174|1760|85009|85015|2040;2|1239|1737404|1737405|1570339|165779;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1224|1236|1706369|1706371|10;2|976|117743|200644|2762318|59732;2|1224|28216|80840|80864|283;2|201174|1760|85007|1653|1716;2|976|117743|200644|2762318|59734;2|201174|1760|85006|1268|57493;2|1224|1236|135614|32033|68;2|1224|28211|356|119045|186650;2|1224|28211|204455|31989|265;2|1224|1236|72274|135621|286;2|1224|1236|135614|32033|83618;2|1224|28211|204455|31989|1060;2|201174|1760|85006|2805590|265976;2|1239|91061|1385|90964|1279;2|1224|1236|135614|32033|40323;2|201174|1760|85006|1268|57493|71999;2|1224|1236|1706369|1706371|10|39650;2|1224|1236|72274|135621|2901164|316;2|1239|91061|1385|90964|1279|1290;2|201174|1760|85007|1653|1716|38304;2|201174|1760|85006|85020|43668|173362;2|1239|91061|1385|90964|1279|29378;2|1239|91061|1385|90964|1279|29382;2|1239|1737404|1737405|1570339|165779|54007,Complete,Svetlana up
bsdb:894/1/1,Study 894,time series / longitudinal observational,36197290,10.1128/spectrum.01899-22,NA,"Jiang CH, Fang X, Huang W, Guo JY, Chen JY, Wu HY, Li ZS, Zou WB , Liao Z",Alterations in the Gut Microbiota and Metabolomics of Seafarers after a Six-Month Sea Voyage,Microbiology spectrum,2022,"16S rRNA gene sequencing, gut microbiota, metabolic pathways, sea voyage, seafarers’ health care, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Seasonal gut microbiome measurement,EFO:0007753,Day 0,Day 180,Seafarers at the end (day 180) of the 6-month voyage,30,30,None,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Fig. 1c, Fig. 1d",31 March 2024,Scholastica,"Scholastica,Welile","Differential relative abundances of bacterial genera between day 0 and day 180 of the voyage. *, P , 0.05; **, P , 0.01. (Wilcoxon rank sum test and LeFse)",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ramlibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|s__Rhodobacteraceae bacterium HIMB11,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|526524|526525|128827|174708;2|1239|186801|3085636|186803|43996;2|1239|1737404|1737405|1570339|150022;2|1239|526524|526525|128827|1573535;2|1224|1236|91347|543|702;2|1224|28216|80840|80864|174951;2|1224|28211|204455|31989|1366046;2|1239|91061|186826|33958|46255;2|1239|91061|186826|33958,Complete,Svetlana up
bsdb:894/1/2,Study 894,time series / longitudinal observational,36197290,10.1128/spectrum.01899-22,NA,"Jiang CH, Fang X, Huang W, Guo JY, Chen JY, Wu HY, Li ZS, Zou WB , Liao Z",Alterations in the Gut Microbiota and Metabolomics of Seafarers after a Six-Month Sea Voyage,Microbiology spectrum,2022,"16S rRNA gene sequencing, gut microbiota, metabolic pathways, sea voyage, seafarers’ health care, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Seasonal gut microbiome measurement,EFO:0007753,Day 0,Day 180,Seafarers at the end (day 180) of the 6-month voyage,30,30,None,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Fig. 1c, Fig. 1d",31 March 2024,Scholastica,"Scholastica,Welile","Differential relative abundances of bacterial genera between day 0 and day 180 of the voyage. *, P , 0.05; **, P , 0.01. (Wilcoxon rank sum test and LeFse)",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",2|1239|526524|526525|2810280|3025755;2|200940|3031449|213115|194924|35832;2|1239|526524|526525|128827|1573534;2|1239|186801|3085636|186803|1506553;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930;2|28221;2|201174|1760|85007;2|200940|3031449|213115|194924;2|200940|3031449|213115,Complete,Svetlana up
bsdb:895/1/1,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Post sleep deprivation samples (7d-SD),Samples collected from rats after being subjected to 7 days of sleep deprivation (7d-SD).,30,29,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Fig.3d,18 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 7 days of sleep deprivation (7d-SD) samples.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",2|201174|84998|1643822|1643826|447020|446660;2|976|200643|171549|815|816|820;2|201174|1760|85004|31953|1678|1694;2|200940|3031449|213115|194924|2049043;2|1224|1236|91347|543|561|562;2|1224|28216|80840|506|90243|90244;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|838|2033406;2|1239|91061|186826|1300|1301|1337;2|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:895/1/2,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Post sleep deprivation samples (7d-SD),Samples collected from rats after being subjected to 7 days of sleep deprivation (7d-SD).,30,29,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Fig.3d,18 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 7 days of sleep deprivation (7d-SD) samples.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii",2|1239|91061|186826|186827|2053495;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|818;2|201174|1760|85007|1653|1716|1705;2|1239|91061|186826|33958|1578|33959;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|671267;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|2024224;2|1224|1236|2887326|468|497|1945520,Complete,Svetlana up
bsdb:895/2/1,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,30,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 14 days of saline supplementation (21d-SA) samples,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",2|201174|84998|1643822|1643826|447020|446660;2|1239|91061|186826|186827|2053495;2|201174|1760|85004|31953|1678|1694;2|201174|1760|85007|1653|1716|1705;2|200940|3031449|213115|194924|2049043;2|1224|28216|80840|506|90243|90244;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|2033406;2|976|200643|171549|171552|838|2024224;2|1239|91061|186826|1300|1301|1337;2|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:895/2/2,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,30,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 14 days of saline supplementation (21d-SA) samples,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|201174|1760|85004|31953|1678|1694;2|1224|1236|91347|543|561|562;2|1239|91061|186826|33958|1578|33959;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|671267;2|976|200643|171549|815|909656|821;2|1224|1236|2887326|468|497|1945520;2|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:895/3/1,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,30,14,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 14 days of multi-probiotic supplementation (21d-MP) samples.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",2|201174|84998|1643822|1643826|447020|446660;2|1239|91061|186826|186827|2053495;2|201174|1760|85004|31953|1678|1694;2|201174|1760|85007|1653|1716|1705;2|1224|1236|91347|543|561|562;2|1239|91061|186826|33958|1578|33959;2|1224|28216|80840|506|90243|90244;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|2033406;2|976|200643|171549|171552|838|2024224;2|1224|1236|2887326|468|497|1945520;2|1239|91061|186826|1300|1301|1337;2|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:895/3/2,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,30,14,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 14 days of multi-probiotic supplementation (21d-MP) samples.,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|200940|3031449|213115|194924|2049043;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|671267;2|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:895/4/1,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,29,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of saline supplementation (21d-SA) samples,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis",2|1239|91061|186826|186827|2053495;2|201174|1760|85007|1653|1716|1705;2|1239|91061|186826|33958|1578|33959;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|2033406;2|976|200643|171549|171552|838|2024224;2|1239|91061|186826|1300|1301|1337,Complete,Svetlana up
bsdb:895/4/2,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,29,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of saline supplementation (21d-SA) samples,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",2|201174|84998|1643822|1643826|447020|446660;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|201174|1760|85004|31953|1678|1694;2|200940|3031449|213115|194924|2049043;2|1224|1236|91347|543|561|562;2|1224|28216|80840|506|90243|90244;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|671267;2|976|200643|171549|815|909656|821;2|1224|1236|2887326|468|497|1945520;2|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:895/5/1,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,29,14,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of multi-probiotic supplementation (21d-MP) samples,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",2|201174|84998|1643822|1643826|447020|446660;2|1239|91061|186826|186827|2053495;2|201174|1760|85007|1653|1716|1705;2|1239|91061|186826|33958|1578|33959;2|1224|28216|80840|506|90243|90244;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|2033406;2|976|200643|171549|171552|838|2024224;2|1224|1236|2887326|468|497|1945520;2|1239|91061|186826|1300|1301|1337;2|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:895/5/2,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,29,14,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of multi-probiotic supplementation (21d-MP) samples,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|201174|1760|85004|31953|1678|1694;2|200940|3031449|213115|194924|2049043;2|1224|1236|91347|543|561|562;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|671267;2|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:895/6/1,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Saline supplementation - SA (21d-SA),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,15,14,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in 14 days of saline supplementation (21d-SA)  versus 14 days of multi-probiotic supplementation (21d-MP) samples,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",2|201174|84998|1643822|1643826|447020|446660;2|1239|91061|186826|186827|2053495;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|818;2|201174|1760|85004|31953|1678|1694;2|201174|1760|85007|1653|1716|1705;2|1224|1236|91347|543|561|562;2|1239|91061|186826|33958|1578|33959;2|1224|28216|80840|506|90243|90244;2|1224|1236|2887326|468|497|1945520;2|1239|91061|186826|1300|1301|1337;2|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:895/6/2,Study 895,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y , Wang Z",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Saline supplementation - SA (21d-SA),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,15,14,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica",LEfSe analysis identified bacteria species that significantly differed in 14 days of saline supplementation (21d-SA)  versus 14 days of multi-probiotic supplementation (21d-MP) samples,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|820;2|200940|3031449|213115|194924|2049043;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|671267;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|838|1262917;2|976|200643|171549|171552|838|2033406;2|976|200643|171549|171552|838|2024224,Complete,Svetlana up
bsdb:896/1/1,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 1 participants,Day 7 participants,The day participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Fig 5a (3rd Cladogram),6 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in participants at Day 7 after a course of Omeprazole (20 mg) compared to Day 1,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia amnigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter ludwigii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",2|1239|91061;2|1239|186801|3085636|186803|43994;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|187328;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|33958|2767887|1624;2|1224|1236|91347|543|1330545|61646;2|1224|1236|91347|543|547|299767;2|1224|1236|91347|543|547;2|1224|1236|135625|712|724|729;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|909932|1843489|31977|29465|419208;2|1239|186801|3085636|186803|43994|43995;2|976|200643|171549|171552|838|28125,Complete,ChiomaBlessing
bsdb:896/1/2,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 1 participants,Day 7 participants,The day participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Fig 5a (3rd Cladogram),6 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in participants at Day 7 after a course of Omeprazole (20 mg) compared to Day 1,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|201174|84998|84999|84107|102106|626935;2|1239|186801|68295;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236,Complete,ChiomaBlessing
bsdb:896/3/1,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 7,Day 14,The day that marked the 7th day after participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5a (2nd Cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in participants at Day 14 after they stopped the course of Omeprazole (20 mg) compared to Day 7,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|244127|169435;2|976|200643|171549;2|976|200643;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281,Complete,ChiomaBlessing
bsdb:896/3/2,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 7,Day 14,The day that marked the 7th day after participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig 5a (2nd cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in participants at Day 14 after they stopped the course of Omeprazole (20 mg) compared to Day 7,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia billingiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia amnigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales,k__Bacteria|p__Chloroflexota|c__Anaerolineae,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea|s__Caldilinea tarbellica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia caviae",2|1239|91061;2|1224|1236|91347|543|547;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|1903409|551;2|1224|1236|91347|1903409|551|182337;2|1224|1236;2|1224|1236|135625|712|724|729;2|1239|91061|186826;2|1224|1236|91347|543|1330545|61646;2|1224|1236|135625|712|75984;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|419208;2|1239|909932|1843489|31977|29465|187328;2|200795|475962|475963|475964;2|200795|475962|475963|475964|233191;2|200795|475962|475963;2|200795|292625;2|200795|475962|475963|475964|233191|859243;2|1239|91061|186826|33958|2767887|1624;2|1239|186801|3085636|186803|43994|43995;2|1239|186801|3085636|186803|43994;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2|1224|1236|91347|543|547|885040;2|1224|1236|135625|712|724;2|1224|1236|135625|712|75984|879276,Complete,ChiomaBlessing
bsdb:896/4/1,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 4,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Chinese participants,Indian participants,Participants who belong to the Indian ethnic group,12,10,1 month,16S,34,Illumina,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5b (1st cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in participants of Indian descent compared to participants of Chinese descent,increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,2|1239|526524|526525|128827|1647,Complete,ChiomaBlessing
bsdb:896/4/2,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 4,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Chinese participants,Indian participants,Participants who belong to the Indian ethnic group,12,10,1 month,16S,34,Illumina,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig 5b (1st cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in participants of Indian descent compared to participants of Chinese descent,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme",2|1239|186801|186802|216572|244127|169435;2|74201|203494|48461|203557;2|74201|203494|48461|1647988|239934|239935;2|74201|203494|48461;2|32066|203490|203491|203492|848|77917,Complete,ChiomaBlessing
bsdb:896/6/1,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 6,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Indian participants,Malay participants,Participants who belong to the Malay ethnic group,10,12,1 month,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5b (1st cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in participants of Malay descent compared to participants of Indian descent,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella granulomatis",2|1224|28216|80840|995019|40544|234908;2|1224|1236|91347|543|570|39824,Complete,ChiomaBlessing
bsdb:896/7/1,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 7,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Male participants,Female participants,Participants who identify with the female gender,16,18,1 month,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5c,7 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in Female participants compared to Male participants,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium shayense",2|1239|909932|1843488|909930|904|187327;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|371601;2|976|200643|171549|171552|2974257|28127;2|976|117747|200666|84566;2|976|117747|200666;2|976|117747;2|976|117747|200666|84566|28453;2|976|117747|200666|84566|28453|626343,Complete,ChiomaBlessing
bsdb:896/7/2,Study 896,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD , Ang TL",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 7,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Male participants,Female participants,Participants who identify with the female gender,16,18,1 month,16S,34,Illumina,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig 5c,7 March 2024,Deacme,"Deacme,ChiomaBlessing",Significant taxa abundance in Female participants compared to Male participants,decreased,"k__Bacteria|p__Chloroflexota|c__Anaerolineae,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea|s__Caldilinea tarbellica,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae,k__Bacteria|p__Chloroflexota|c__Caldilineae|o__Caldilineales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme",2|200795|292625;2|200795|475962|475963|475964|233191;2|200795|475962|475963|475964|233191|859243;2|200795|475962|475963|475964;2|200795|475962|475963;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|265975|237576;2|32066|203490|203491|203492|848|77917,Complete,ChiomaBlessing
bsdb:897/1/1,Study 897,laboratory experiment,37060097,https://doi.org/10.1186/s40168-023-01527-9,NA,"Maidment TI, Bryan ER, Pyne M, Barnes M, Eccleston S, Cunningham S, Whitlock E, Redman K, Nicolson V, Beagley KW , Pelzer E",Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality,Microbiome,2023,"Dysbiosis, Endangered species, Enterobacteriaceae, Klebsiella pneumoniae, Koala, Marsupial, Muribaculaceae, Phascolarctos cinereus, Pluralibacter gergoviae, Pouch, Reproduction",Experiment 1,Australia,Phascolarctos cinereus,Marsupium,UBERON:0009118,Neonatal death,HP:0003811,Successful breeders,Unsuccessful breeders,Captive Koalas who lost their pouch young during lactation.,10,7,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,supplementary Table 11,7 March 2024,Ehi,"Ehi,Folakunmi",Differentially abundant genera in the pouch microbiota of successful vs. unsuccessful breeding koalas during early lactation.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Lonepinella",2|1239|909932|1843488|909930|33024|33025;2|1224|1236|72274|135621|286;2|1224|1236|91347|543|1940338;2|1224|1236|91347|543|570;2|1224|1236|91347|543|1330546;2|1224|1236|135625|712|53416,Complete,Folakunmi
bsdb:897/1/2,Study 897,laboratory experiment,37060097,https://doi.org/10.1186/s40168-023-01527-9,NA,"Maidment TI, Bryan ER, Pyne M, Barnes M, Eccleston S, Cunningham S, Whitlock E, Redman K, Nicolson V, Beagley KW , Pelzer E",Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality,Microbiome,2023,"Dysbiosis, Endangered species, Enterobacteriaceae, Klebsiella pneumoniae, Koala, Marsupial, Muribaculaceae, Phascolarctos cinereus, Pluralibacter gergoviae, Pouch, Reproduction",Experiment 1,Australia,Phascolarctos cinereus,Marsupium,UBERON:0009118,Neonatal death,HP:0003811,Successful breeders,Unsuccessful breeders,Captive Koalas who lost their pouch young during lactation.,10,7,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,supplementary Table 11,7 March 2024,Ehi,"Ehi,Folakunmi",Differentially abundant genera in the pouch microbiota of successful vs. unsuccessful breeding koalas during early lactation.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",2|976|200643|171549|2005473|1918540;2|1239|909932|1843488|909930|33024|33025,Complete,Folakunmi
bsdb:898/1/1,Study 898,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, Zhong J , Zeng J",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Bladder carcinoma,MONDO:0004986,Non-neoplastic (controls),Bladder cancer,Male patients with bladder cancer,18,31,1 month,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica",Microbial taxa associated with bladder cancer (red) versus non-cancer group (green),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baylyi,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Candidatus Limnoluna,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacteria|p__Actinomycetota|c__Rubrobacteria,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|202950;2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|186828|292480;2|201174|1760|85006|85023|507002;2|1239|91061|186826|186828;2|1239|91061|1385|186817|129337;2|1224|28211|766;2759|33090|35493|3398|72025|3803|3814|508215;2|201174|84995|84996|84997|42255;2|201174|84995|84996|84997;2|201174|84995|84996;2|201174|84995;2|976|117747|200666|84566;2|976|117747|200666|84566|28453,Complete,Svetlana up
bsdb:898/1/2,Study 898,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, Zhong J , Zeng J",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Bladder carcinoma,MONDO:0004986,Non-neoplastic (controls),Bladder cancer,Male patients with bladder cancer,18,31,1 month,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica",Microbial taxa associated with bladder cancer (red) versus non-cancer group (green),decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1224|28211|204441|433;2|976|200643;2|1224|28216|80840|119060;2|1239|186801|186802|186806|1730|39497;2|1224|1236|91347|1903414|583;2|1224|28211|204441;2|1224|28211|204441|433|125216;2|1224|1236|91347|1903411|613;2|976|200643|171549|2005473,Complete,Svetlana up
bsdb:898/2/1,Study 898,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, Zhong J , Zeng J",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 2,China,Homo sapiens,Urine,UBERON:0001088,Disease recurrence,EFO:0004952,Lower risk of recurrence (LER),Higher risk of recurrence (HER),"Male bladder cancer patients stratified into the higher risk of recurrence group (HER, recurrence score of EORTC ≥ 5) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",16,10,1 month,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Supplementary Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica","Microbial taxa associated with high risk of recurrence (HER, red) versus low risk of recurrence (LER, green)",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter",2|1224|1236|135624|84642;2|1224|1236|135624;2|1224|1236|135624|84642|642;2|976|200643|171549|815;2|976|200643|171549|815|816;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|200795|32061|32064;2|200795|32061;2|201174|1760|85006|85020;2|29547|3031852;2|1224|28211|204457|335929;2|1239|186801|186802|216572|216851;2|1239|91061|1385|539738|1378;2|1224|28216|80840|75682|963;2|201174|1760|85009|85015;2|1224|28211|204457|335929|1111,Complete,Svetlana up
bsdb:898/2/2,Study 898,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, Zhong J , Zeng J",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 2,China,Homo sapiens,Urine,UBERON:0001088,Disease recurrence,EFO:0004952,Lower risk of recurrence (LER),Higher risk of recurrence (HER),"Male bladder cancer patients stratified into the higher risk of recurrence group (HER, recurrence score of EORTC ≥ 5) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",16,10,1 month,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Supplementary Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica","Microbial taxa associated with high risk of recurrence (HER, red) versus low risk of recurrence (LER, green)",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,2|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:898/3/1,Study 898,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, Zhong J , Zeng J",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 3,China,Homo sapiens,Urine,UBERON:0001088,Disease progression measurement,EFO:0008336,Lower risk of progression (LEP),Higher risk of progression (HEP),"Male bladder cancer patients stratified into the higher risk of progression group (HEP, progression score of EORTC ≥ 7) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",15,11,1 month,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Supplementary Figure 5B,7 April 2024,Ayibatari,"Ayibatari,Scholastica","Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter",2|976|200643|171549|815;2|976|200643|171549|815|816;2|200795|32061|32064;2|201174|1760|85006|85020;2|1224|28211|204457|335929;2|201174|1760|85009|85015|86795;2|201174|1760|85006|1268;2|201174|1760|85009|85015;2|1224|28211|204457|335929|1111,Complete,Svetlana up
bsdb:898/3/2,Study 898,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, Zhong J , Zeng J",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 3,China,Homo sapiens,Urine,UBERON:0001088,Disease progression measurement,EFO:0008336,Lower risk of progression (LEP),Higher risk of progression (HEP),"Male bladder cancer patients stratified into the higher risk of progression group (HEP, progression score of EORTC ≥ 7) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",15,11,1 month,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Supplementary Figure 5B,7 April 2024,Ayibatari,"Ayibatari,Scholastica","Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)",decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__uncultured Corynebacterium sp.",2|1239|91061;2|1239;2|1117;2|1239|91061|186826;2|201174|1760|85007|1653|1716|159447,Complete,Svetlana up
bsdb:899/1/1,Study 899,"cross-sectional observational, not case-control",34264502,https://doi.org/10.1007/s42770-021-00539-7,NA,"de Oliveira Scoaris D, Hughes FM, Silveira MA, Evans JD, Pettis JS, Bastos EMAF , Rosa CA",Microbial communities associated with honey bees in Brazil and in the United States,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2021,"Apis mellifera, Bacteria, Diversity, Environment, Microorganisms, Yeasts",Experiment 1,"Brazil,United States of America",Not specified,Intestinal mucosa,UBERON:0001242,Restricted to specific location,MONDO:0045042,Brazilian hive microenvironment,North American hive microenvironments,North American samples were collected from four hives of honey bees,5,4,2 weeks,ITS / ITS2,NA,RT-qPCR,NA,NA,NA,NA,NA,physical activity,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,7 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Rahila","Frequency of occurrence (fi) and density (ρ, in log CFU g−1 or CFU individual bee−1) of bacteria associated with honey bee substrates from the United States and Brazil",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia aryabhattai",2|1239|91061|1385|186817|1386|1402;2|1239|91061|1385|186817|1386|1409;2|1239|91061|1385|186817|2800373|1404;2|1239|91061|1385|186817|2800373|412384,Complete,NA
bsdb:899/1/2,Study 899,"cross-sectional observational, not case-control",34264502,https://doi.org/10.1007/s42770-021-00539-7,NA,"de Oliveira Scoaris D, Hughes FM, Silveira MA, Evans JD, Pettis JS, Bastos EMAF , Rosa CA",Microbial communities associated with honey bees in Brazil and in the United States,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2021,"Apis mellifera, Bacteria, Diversity, Environment, Microorganisms, Yeasts",Experiment 1,"Brazil,United States of America",Not specified,Intestinal mucosa,UBERON:0001242,Restricted to specific location,MONDO:0045042,Brazilian hive microenvironment,North American hive microenvironments,North American samples were collected from four hives of honey bees,5,4,2 weeks,ITS / ITS2,NA,RT-qPCR,NA,NA,NA,NA,NA,physical activity,NA,NA,NA,NA,NA,NA,Signature 2,Table 5,7 March 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,"Frequency of occurrence (fi) and density (ρ, in log CFU g−1 or CFU individual bee−1) of bacteria associated with honey bee substrates from the United States and Brazil",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus fusiformis",2|1239|91061|1385|186817|1386|1423;2|1239|91061|186826|33958|1578|1591;2|1239|91061|1385|186817|400634|28031,Complete,NA
bsdb:900/3/1,Study 900,laboratory experiment,32987006,https://doi.org/10.1016/j.envres.2020.110245,NA,"Gust KA, Indest KJ, Lotufo G, Everman SJ, Jung CM, Ballentine ML, Hoke AV, Sowe B, Gautam A, Hammamieh R, Ji Q , Barker ND",Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles,Environmental research,2021,"Amphibian health, Amphibian skin microbiome, Aquatic ecotoxicology, Munitions constituents, Transcript expression",Experiment 3,United States of America,Rana pipiens,Tadpole,UBERON:0002547,Environmental exposure measurement,EFO:0008360,Control group,Tadpoles exposed to 3560 mg/L Nitroguanidine (NQ),Tadpoles were exposed to the concentration of 3560 mg/L of Nitroguanidine (NQ) for 96 hours.,4,4,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,7 March 2024,Victoria,"Victoria,ChiomaBlessing",LEfSe-identified significant taxa in the NQ exposed group compared to the control group,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae",2|1224|1236|135624|84642;2|1224|1236|135624;2|1224|28216|80840|80864;2|1224|1236;2|1224|1236|72274|135621;2|1224|1236|135622|267890,Complete,ChiomaBlessing
bsdb:900/3/2,Study 900,laboratory experiment,32987006,https://doi.org/10.1016/j.envres.2020.110245,NA,"Gust KA, Indest KJ, Lotufo G, Everman SJ, Jung CM, Ballentine ML, Hoke AV, Sowe B, Gautam A, Hammamieh R, Ji Q , Barker ND",Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles,Environmental research,2021,"Amphibian health, Amphibian skin microbiome, Aquatic ecotoxicology, Munitions constituents, Transcript expression",Experiment 3,United States of America,Rana pipiens,Tadpole,UBERON:0002547,Environmental exposure measurement,EFO:0008360,Control group,Tadpoles exposed to 3560 mg/L Nitroguanidine (NQ),Tadpoles were exposed to the concentration of 3560 mg/L of Nitroguanidine (NQ) for 96 hours.,4,4,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,7 March 2024,Victoria,"Victoria,ChiomaBlessing",LEfSe-identified significant taxa in the NQ exposed group compared to the control group,decreased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales|f__Chthoniobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Solibacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Terriglobales,k__Bacteria|p__Acidobacteriota|c__Terriglobia,k__Bacteria|p__Actinomycetota|c__Thermoleophilia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",2|57723;2|201174;2|1224|28211;2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061;2|1239;2|57723|204432|332160;2|1224|28216|80840;2|200795;2|74201|134549|1836787|1836792;2|1224|28211|356|45401;2|1224|28211|356;2|1224|28216|80840|75682;2|203682;2|1224|28211|204441;2|57723|204432|332160|332161;2|74201|134549;2|1224|28211|204457|41297;2|1224|28211|204457;2|57723|204432|204433;2|57723|204432;2|201174|1497346;2|74201;2|74201|134549|1836787;2|1224|28216|80840|119060,Complete,ChiomaBlessing
bsdb:901/1/1,Study 901,case-control,37700874,10.2147/JAA.S422537,NA,"Wan J, Song J, Lv Q, Zhang H, Xiang Q, Dai H, Zheng H, Lin X , Zhang W",Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing,Journal of asthma and allergy,2023,"allergic asthma, allergic rhinitis, childhood, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Allergic asthma,MONDO:0004784,Healthy control,Allergic asthma,Children with allergic asthma,19,23,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,NA,increased,NA,NA,Signature 1,"FIG 4A, 4B",8 April 2024,Rahila,"Rahila,Scholastica",Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in allergic asthma versus healthy groups,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus macedonicus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales",2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|216572|1263|457412;2|1239|91061|186826|1300|1301|1304;2|201174|1760|2037|2049|1654|55565;2|201174|1760|2037|2049|2529408|1660;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|84998|1643822|1643826|84111|84112;2|201174|84998|1643822|1643826|84111;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|91061|1385|539738|1378|1379;2|1239|91061|186826|1300|1301|59310;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|909932|1843489|31977|906|907;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|3239874|2916678|766764|5475;2759|4751|4890|4891|4892,Complete,Svetlana up
bsdb:901/1/2,Study 901,case-control,37700874,10.2147/JAA.S422537,NA,"Wan J, Song J, Lv Q, Zhang H, Xiang Q, Dai H, Zheng H, Lin X , Zhang W",Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing,Journal of asthma and allergy,2023,"allergic asthma, allergic rhinitis, childhood, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Allergic asthma,MONDO:0004784,Healthy control,Allergic asthma,Children with allergic asthma,19,23,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,NA,increased,NA,NA,Signature 2,"FIG 4A, 4B",9 June 2024,Scholastica,Scholastica,Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in allergic asthma versus healthy groups,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae",2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|818;2|976|200643|171549|2005519|397864|487174;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|821;2|1239|909932|1843489|31977|906;2|976|200643|171549|815|816;2|976|200643|171549|815;2|976|200643|171549|2005519|1348911|1099853;2|976|200643|171549|2005519|1348911;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759;2|976|200643|171549|171550;2|976|200643|171549;2|1239|91061|186826|33958|2742598|1613;2|1239|909932|1843488|909930|904;2|1239|909932|1843488|909930,Complete,Svetlana up
bsdb:901/2/1,Study 901,case-control,37700874,10.2147/JAA.S422537,NA,"Wan J, Song J, Lv Q, Zhang H, Xiang Q, Dai H, Zheng H, Lin X , Zhang W",Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing,Journal of asthma and allergy,2023,"allergic asthma, allergic rhinitis, childhood, gut microbiome, metagenomic sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Allergic rhinitis,EFO:0005854,Healthy control,Allergic rhinitis,Children with allergic rhinitis,19,18,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,NA,increased,NA,NA,Signature 1,"FIG 4A, 4C",8 April 2024,Rahila,"Rahila,Scholastica",Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in allergic rhinitis versus healthy groups,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis",2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|28026;2|1224|28216|80840|469610;2|1239|186801|3085636|186803|189330|88431;2|1224|1236|91347|543|561|562;2|1239|91061|1385|539738|1378|1379;2|1239|91061|186826|1300|1301|1304;2|1224|1236|91347|543|561;2|1239|91061|1385|539738|1378;2|1239|91061|186826|33958|1578|1584;2|1239|91061|186826|1300|1301|45634;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|265975|237576;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803;2|1224|1236|91347|1903414|583|584,Complete,Svetlana up
bsdb:901/2/2,Study 901,case-control,37700874,10.2147/JAA.S422537,NA,"Wan J, Song J, Lv Q, Zhang H, Xiang Q, Dai H, Zheng H, Lin X , Zhang W",Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing,Journal of asthma and allergy,2023,"allergic asthma, allergic rhinitis, childhood, gut microbiome, metagenomic sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Allergic rhinitis,EFO:0005854,Healthy control,Allergic rhinitis,Children with allergic rhinitis,19,18,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,NA,increased,NA,NA,Signature 2,"FIG 4A, 4C",9 June 2024,Scholastica,Scholastica,Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in allergic rhinitis versus healthy groups,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|46506;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|815|909656|310298;2|1239|909932|1843489|31977|906;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816;2|976|200643|171549|815;2|976|200643|171549|2005519|1348911|1099853;2|976|200643|171549|2005519|1348911;2|976|200643|171549|171550|239759;2|976|200643|171549|171550;2|976|200643|171549;2|1239|91061|186826|33958|2742598|1613;2|1239|909932|1843488|909930|904;2|1239|909932|1843488|909930,Complete,Svetlana up
bsdb:902/1/1,Study 902,case-control,NA,https://doi.org/10.1186/s12866-021-02221-2,NA,"Chen Li, Hesong Wang, Jianhua Zhen, Li Wang, Lu Zhao, Pengfei Zhao, Yini Li",Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome,BMC microbiology,2021,Fecal-associated microbiome SAPHO syndrome Biomarkers,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,SAPHO syndrome,EFO:1001164,Healthy control group,SAPHO syndrome Patients,"SAPHO (synovitis, acne, pustulosis, hyperostosis and osteosis) syndrome, The main features of SAPHO syndrome consist of cutaneous and osteoarticular manifestations, the latter more often affects the anterior chest wall and has a typical radiologic finding called the “bull’s head sign”",14,17,3months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,8 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Peace Sandy","Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1239|91061|1385;2|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:902/1/2,Study 902,case-control,NA,https://doi.org/10.1186/s12866-021-02221-2,NA,"Chen Li, Hesong Wang, Jianhua Zhen, Li Wang, Lu Zhao, Pengfei Zhao, Yini Li",Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome,BMC microbiology,2021,Fecal-associated microbiome SAPHO syndrome Biomarkers,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,SAPHO syndrome,EFO:1001164,Healthy control group,SAPHO syndrome Patients,"SAPHO (synovitis, acne, pustulosis, hyperostosis and osteosis) syndrome, The main features of SAPHO syndrome consist of cutaneous and osteoarticular manifestations, the latter more often affects the anterior chest wall and has a typical radiologic finding called the “bull’s head sign”",14,17,3months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3,9 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Peace Sandy","Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|1239|186801|186802|216572;2|1239|186801|186802|216572|1508657,Complete,Peace Sandy
bsdb:903/1/1,Study 903,case-control,36523636,https://doi.org/10.3389/fcimb.2022.943609,https://www.frontiersin.org/articles/10.3389/fcimb.2022.943609/full,"Morales C, Rojas G, Rebolledo C, Rojas-Herrera M, Arias-Carrasco R, Cuadros-Orellana S, Maracaja-Coutinho V, Saavedra K, Leal P, Lanas F, Salazar LA , Saavedra N",Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects,Frontiers in cellular and infection microbiology,2022,"16S rRNA sequencing, LDL cholesterol, LEfSe analysis, gut microbiota, microbial signature",Experiment 1,Chile,Homo sapiens,Feces,UBERON:0001988,Hypercholesterolemia,HP:0003124,normocholesterolemic individuals (controls),hypercholesterolemic (cases),Patients with hypercholesterolemia (concentration of LDL-C greater than 4.16mmol/L),30,27,6 Months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,8 March 2024,Abiola-Salako,"Abiola-Salako,Folakunmi",Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",2|1239|186801|186802|216572|216851;2|1239|909932|909929|1843491|970;2|256845|1313211|278082|255528|172900,Complete,Folakunmi
bsdb:903/1/2,Study 903,case-control,36523636,https://doi.org/10.3389/fcimb.2022.943609,https://www.frontiersin.org/articles/10.3389/fcimb.2022.943609/full,"Morales C, Rojas G, Rebolledo C, Rojas-Herrera M, Arias-Carrasco R, Cuadros-Orellana S, Maracaja-Coutinho V, Saavedra K, Leal P, Lanas F, Salazar LA , Saavedra N",Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects,Frontiers in cellular and infection microbiology,2022,"16S rRNA sequencing, LDL cholesterol, LEfSe analysis, gut microbiota, microbial signature",Experiment 1,Chile,Homo sapiens,Feces,UBERON:0001988,Hypercholesterolemia,HP:0003124,normocholesterolemic individuals (controls),hypercholesterolemic (cases),Patients with hypercholesterolemia (concentration of LDL-C greater than 4.16mmol/L),30,27,6 Months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,8 March 2024,Abiola-Salako,"Abiola-Salako,Folakunmi",Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|1239|91061|1385|186817;2|1224|1236|135613;2|201174|84998|84999|84107;2|1239|186801|186802;2157|28890|183925|2158|2159|2316;2759|33090|35493|3398|72025|3803|3814|508215,Complete,Folakunmi
bsdb:904/1/1,Study 904,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V, Bruno JS, Knebel FH, de Molla VC, Miranda-Silva W, Asprino PF, Tucunduva L, Rocha V, Novis Y, Arrais-Rodrigues C, Fregnani ER , Camargo AA",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 1,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Preconditioning (Patients Before Allogeneic Hematopoietic Stem Cell Transplantation),Engraftment (Patients After Allogeneic Hematopoietic Stem Cell Transplantation),"Patients at the final phase of Allogeneic Hematopoietic Stem Cell transplant, when the new transplanted stem cells start to grow and produce new blood cells.",30,27,No,16S,34,Illumina,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 1C,8 March 2024,Joan Chuks,"Joan Chuks,ChiomaBlessing",Significant genera relative abundance in the engraftment (After transplantation) group compared to the preconditioning (Before transplantation) group according to ANCOM test (W > 0.7).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1243;2|544448|31969|2085|2092|2093;2|1239|91061|1385|90964|1279,Complete,ChiomaBlessing
bsdb:904/1/2,Study 904,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V, Bruno JS, Knebel FH, de Molla VC, Miranda-Silva W, Asprino PF, Tucunduva L, Rocha V, Novis Y, Arrais-Rodrigues C, Fregnani ER , Camargo AA",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 1,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Preconditioning (Patients Before Allogeneic Hematopoietic Stem Cell Transplantation),Engraftment (Patients After Allogeneic Hematopoietic Stem Cell Transplantation),"Patients at the final phase of Allogeneic Hematopoietic Stem Cell transplant, when the new transplanted stem cells start to grow and produce new blood cells.",30,27,No,16S,34,Illumina,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 1C,8 March 2024,Joan Chuks,"Joan Chuks,ChiomaBlessing",Significant genera relative abundance in the engraftment (After transplantation) group compared to the preconditioning (Before transplantation) group according to ANCOM test (W > 0.7).,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|1239|91061|1385|539738|1378;2|1239|186801|3085636|186803|1164882;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:904/2/NA,Study 904,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V, Bruno JS, Knebel FH, de Molla VC, Miranda-Silva W, Asprino PF, Tucunduva L, Rocha V, Novis Y, Arrais-Rodrigues C, Fregnani ER , Camargo AA",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 2,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Preconditioning (Patients Before Allogeneic Hematopoietic Stem Cell Transplantation),Aplasia group,"Patients after the conditioning regimen, when the patient's bone marrow is intentionally depleted of cells, necessary for the success of the transplant",30,30,No,16S,34,Illumina,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:904/3/NA,Study 904,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V, Bruno JS, Knebel FH, de Molla VC, Miranda-Silva W, Asprino PF, Tucunduva L, Rocha V, Novis Y, Arrais-Rodrigues C, Fregnani ER , Camargo AA",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 3,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Aplasia group,Engraftment group,"Patients at the final phase of Allogeneic Hematopoietic Stem Cell transplant, when the new transplanted stem cells start to grow and produce new blood cells.",30,27,No,16S,34,Illumina,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:905/1/1,Study 905,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R , Payami H",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease by a movement disorder specialist according to the modified UK Brain Bank criteria.,130,197,NA,16S,NA,Illumina,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Table 2,17 April 2024,Aleru Divine,"Aleru Divine,Peace Sandy",Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|41200;2|1239|186801|3082768|990719;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1737406;2|74201|203494|48461|203557;2|1239|186801|3082768|990719;2|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:905/1/2,Study 905,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R , Payami H",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease by a movement disorder specialist according to the modified UK Brain Bank criteria.,130,197,NA,16S,NA,Illumina,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Table 2,18 April 2024,Aleru Divine,Aleru Divine,Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1224|1236|135625|712;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:905/2/1,Study 905,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R , Payami H",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease who were not on catechol-o-methyl-transferase (COMT) inhibitors or anticholinergic drugs (AC).,130,141,NA,16S,NA,Illumina,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Table 2,18 April 2024,Aleru Divine,Aleru Divine,Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|41200;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572;2|1239|186801|3082768|990719;2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953;2|1239|91061|186826|33958;2|1239|1737404|1737405|1737406;2|1239|186801|3082768|990719;2|74201|203494|48461|203557,Complete,Peace Sandy
bsdb:905/2/2,Study 905,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R , Payami H",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease who were not on catechol-o-methyl-transferase (COMT) inhibitors or anticholinergic drugs (AC).,130,141,NA,16S,NA,Illumina,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Table 2,18 April 2024,Aleru Divine,Aleru Divine,Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|1955243;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1224|1236|135625|712;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:906/1/1,Study 906,laboratory experiment,NA,10.1038/s41598-019-43280-w,https://doi.org/10.1038/s41598-019-43280-w,"Choi In-Soo, La Tae-Min, Lee Hong-Jae, Lee Joong-Bok, Lee Sangwon, Park Seung-Yong, Song Chang-Seon",Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota,Scientific reports,2019,"Metagenomics, Metagenomics",Experiment 1,South Korea,Gallus gallus,Oviduct,UBERON:0000993,Developmental stage,EFO:0000399,Immature hen magnum sample (23 weeks-old),Mature hen magnum sample,Magnum samples of 34 weeks-old laying SPF hens,8,16,NA,16S,23456789,Ion Torrent,ANCOM,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2.,11 March 2024,KwennB,"KwennB,Ayibatari,Rahila,Folakunmi",ANCOM differential abundance mature and immature hen magnum groups.,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|976|117743|200644|49546|237;2|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:906/1/2,Study 906,laboratory experiment,NA,10.1038/s41598-019-43280-w,https://doi.org/10.1038/s41598-019-43280-w,"Choi In-Soo, La Tae-Min, Lee Hong-Jae, Lee Joong-Bok, Lee Sangwon, Park Seung-Yong, Song Chang-Seon",Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota,Scientific reports,2019,"Metagenomics, Metagenomics",Experiment 1,South Korea,Gallus gallus,Oviduct,UBERON:0000993,Developmental stage,EFO:0000399,Immature hen magnum sample (23 weeks-old),Mature hen magnum sample,Magnum samples of 34 weeks-old laying SPF hens,8,16,NA,16S,23456789,Ion Torrent,ANCOM,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2.,13 March 2024,KwennB,"KwennB,Ayibatari,Rahila,Folakunmi",ANCOM differential abundance between the mature and immature hen magnum groups.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae",2|1224|28211|356|41294|374;2|1224|28211|356|41294;2|201174|1760|85007|85025,Complete,Folakunmi
bsdb:907/1/1,Study 907,case-control,36453905,https://doi.org/10.1128/spectrum.01593-22,https://journals.asm.org/doi/10.1128/spectrum.01593-22,"Han S, Zhuang J, Pan Y, Wu W , Ding K",Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis,Microbiology spectrum,2022,"SNP, artificial intelligence, colorectal cancer, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Adenoma Patients,Colorectal Cancer Patients,Patients with fully  developed Colorectal cancer,26,26,2 Months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2 G and H,7 March 2024,Imaspecial,"Imaspecial,Peace Sandy",LEfSe analysis filtered out the biomarkers of the microbial community between AA and CRC patients. and cladogram plot of LEfSe analysis (G) and histogram of LDA analysis (H) of bacteria.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae|g__Acidihalobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Kushneria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|1224|1236|135613|72276|1765964;2|1224|1236|135619|28256|504090;2|1224|1236|91347|543|1330545;2|1239|1737404|1737405|1570339|543311,Complete,Peace Sandy
bsdb:907/1/2,Study 907,case-control,36453905,https://doi.org/10.1128/spectrum.01593-22,https://journals.asm.org/doi/10.1128/spectrum.01593-22,"Han S, Zhuang J, Pan Y, Wu W , Ding K",Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis,Microbiology spectrum,2022,"SNP, artificial intelligence, colorectal cancer, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Adenoma Patients,Colorectal Cancer Patients,Patients with fully  developed Colorectal cancer,26,26,2 Months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2 G and H,7 March 2024,Imaspecial,"Imaspecial,Peace Sandy",LEfSe analysis filtered out the biomarkers of the microbial community between AA and CRC patients. and cladogram plot of LEfSe analysis (G) and histogram of LDA analysis (H) of bacteria.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Merdibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Levyella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fournierella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239;2|1239|186801|186802;2|1239|186801;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|841;2|1239|526524|526525|128827;2|1239|526524;2|1239|526524|526525;2|1239|186801|3085636|186803|1407607;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572;2|1239|186801|186802|216572|459786;2|1239|1980693;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|1935176;2|1239|186801|3082768|990719|990721;2|1239|186801|3082768|990719;2|1239|186801|3085636|186803|2005359;2|1239|186801|3085636|186803|2023266;2|1239|186801|186802|1392389;2|1239|186801|186802|31979|1935927;2|1239|186801|3085636|186803|207244;2|1239|526524|526525|128827|1935200;2|1239|526524|526525|128827|61170;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|35829;2|1239|186801|186802|1715798;2|1239|186801|3085636|186803|1164882;2|1224|28216|80840|995019;2|1239|186801|186802|216572|1940255;2|1239|186801|186802|216572|244127;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803|588605;2|1239|186801|3085636|186803|1213720,Complete,Peace Sandy
bsdb:908/1/1,Study 908,case-control,34650681,NA,NA,"Wu R, Ruan XL, Ruan DD, Zhang JH, Wang HL, Zeng QZ, Lu T, Gan YM, Luo JW , Wu JB",Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease,American journal of translational research,2021,"16S rDNA sequencing, Chronic kidney disease stages 4-5, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic kidney disease,Diagnosed with stage 4-5 Chronic Kidney Disease (CKD) based on established medical criteria and diagnostic assessments conducted by nephrology experts.,40,39,4 weeks,16S,34,MGISEQ-2000,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4,26 March 2024,Sneha6003,"Sneha6003,Peace Sandy","LEfSe analysis was used to statistically resolve the microbiota with 
significant effects in the different groups. The LDA threshold was set as 2. (A) 
The stage 4-5 CKD group and (B) the control group.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826|186827|46123;2|1224|1236|2887326|468|469;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|1239|91061|186826|186827;2|201174|84998|84999|1643824|1380;2|1239|91061|1385;2|1239|91061;2|1224|28216;2|1224|28216|80840;2|95818;2|95818;2|1239|91061|186826|186828;2|1239|186801|3082768|990719|990721;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|526524|526525|2810280|100883;2|976|200643|171549|2005519|1348911;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|526524|526525|128827;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1224|1236;2|1239|186801|186802|204475;2|1239|91061|186826|186828|117563;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|32066|203490|203491|1129771|32067;2|201174|1760|85006|1268;2|1224|1236|2887326|468;2|1224|1236|91347|1903414|581;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|201174|84998|84999|1643824|133925;2|976|200643|171549|171552|577309;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224;2|1224|1236|72274|135621|286;2|508458|649775|649776|3029088|638847;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|1263;2|201174|1760|85004|31953|196081;2|1239|186801|3085636|186803|177971;2|1239|526524|526525|128827|123375;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:908/1/2,Study 908,case-control,34650681,NA,NA,"Wu R, Ruan XL, Ruan DD, Zhang JH, Wang HL, Zeng QZ, Lu T, Gan YM, Luo JW , Wu JB",Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease,American journal of translational research,2021,"16S rDNA sequencing, Chronic kidney disease stages 4-5, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic kidney disease,Diagnosed with stage 4-5 Chronic Kidney Disease (CKD) based on established medical criteria and diagnostic assessments conducted by nephrology experts.,40,39,4 weeks,16S,34,MGISEQ-2000,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4,27 March 2024,Peace Sandy,Peace Sandy,LEfSe analysis was used to statistically resolve the microbiota with significant effects in the different groups. The LDA threshold was set as 2. (A) The stage 4-5 CKD group and (B) the control group.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella",2|1239|186801;2|1239|186801|186802;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|909932|909929;2|1239|909932;2|1239|186801|3085636|186803;2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|459786;2|1224|28216|80840|995019;2|1224|28216|80840|995019|577310;2|1224|28211|204441|41295;2|1224|28211|204441;2|201174|84998|1643822|1643826|553372;2|1224|1236|135625|712|724;2|1224|28216|80840|75682;2|1239|186801|186802|3085642|580596;2|1224|28216|80840|75682|846;2|201174|84998|1643822|1643826|84108;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1407607;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|31979|1485;2|976|200643|171549|2005519|397864;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|207244;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|283168;2|1239|909932|1843488|909930|904;2|1239|909932|1843489|31977|209879,Complete,Peace Sandy
bsdb:909/1/1,Study 909,case-control,34884399,https://doi.org/10.3390/jcm10235698,NA,"Zapała B, Stefura T, Wójcik-Pędziwiatr M, Kabut R, Bałajewicz-Nowak M, Milewicz T, Dudek A, Stój A , Rudzińska-Bar M",Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study,Journal of clinical medicine,2021,"Parkinson’s disease, gut microbiome, microbiota",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Hospitalized Patients diagnosed with Parkinson's disease with well-controlled symptoms.,44,27,3 weeks,16S,34,"Illumina,MGISEQ-2000",LEfSe,0.05,FALSE,2,age,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 6 , Figure 7",7 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Peace Sandy","Bacterial species are more abundant in the PD than in the control group, according to the LefSE analysis.

Cladogram generated by LEfSe shows the taxa differences between PD patients (2) and healthy controls (1).",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter|s__Acidaminobacter hydrogenoformans,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella timonensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella|s__Robinsoniella peoriensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Synergistota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|3082720|3118653|65402|65403;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|47678;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|3082768|990719|990721|1816678;2|201174|84998;2|28221;2|1239|526524;2|976|117743;2|1239|186801|186802|216572|946234|292800;2|1224|1236;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|3085636|186803|1649459|154046;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|815|909656|204516;2|1239|186801|186802|31979|1485|84032;2|1224;2|1239|186801|3085636|186803|588605|180332;2|1239|186801|186802|216572|1263|438033;2|1239|91061|186826|1300|1301|1309;2|508458;2|74201|203494;2|74201;2|1239|186801|186802|216572|47246;2|1239|186801|3085636|186803|2316020|33039,Complete,Peace Sandy
bsdb:909/1/2,Study 909,case-control,34884399,https://doi.org/10.3390/jcm10235698,NA,"Zapała B, Stefura T, Wójcik-Pędziwiatr M, Kabut R, Bałajewicz-Nowak M, Milewicz T, Dudek A, Stój A , Rudzińska-Bar M",Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study,Journal of clinical medicine,2021,"Parkinson’s disease, gut microbiome, microbiota",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Hospitalized Patients diagnosed with Parkinson's disease with well-controlled symptoms.,44,27,3 weeks,16S,34,"Illumina,MGISEQ-2000",LEfSe,0.05,FALSE,2,age,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 6 , Figure 7",8 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Peace Sandy","Bacterial species are more abundant in the PD than in the control group, according to the LefSE analysis.

Cladogram generated by LEfSe shows the taxa differences between PD patients (2) and
healthy controls (1).",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes butyraticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Intestinibacillus|s__Intestinibacillus massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244|645466;2|201174|1760|85004|31953|1678|216816;2|1239|186801|3085636|186803|572511|871665;2|1239|186801|3085636|186803|572511|40520;2|1239|91061|186826|81852|1350|1351;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|3085642|1928820|1871029;2|1239|186801|3085636|186803|28050|39485;2|1239|909932|909929|1843491|158846|437897;2|1239|186801|186802|216572|1263|1264;2|1239|186801;2|1239;2|32066|203490,Complete,Peace Sandy
bsdb:910/1/1,Study 910,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R , Mazmanian SK",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Wild-type (WT) mice with fecal microbes from healthy controls (HC),Wild-type (WT) mice with fecal microbes from Parkinson’s disease patients (PD),Germ-free wild-type (WT) mice colonized with fecal microbes from Parkinson’s disease patients (PD),6,6,NA,16S,4,Illumina,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6E,20 March 2024,Toyosiolann,"Toyosiolann,Svetlana up",Differentially abundant taxon in the WT mice with HC fecal transfer and the WT mice with PD fecal transfer.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter",2|1239|91061|186826|81852|1350;2|1239|186801|186802|186806|113286,Complete,Svetlana up
bsdb:910/1/2,Study 910,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R , Mazmanian SK",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Wild-type (WT) mice with fecal microbes from healthy controls (HC),Wild-type (WT) mice with fecal microbes from Parkinson’s disease patients (PD),Germ-free wild-type (WT) mice colonized with fecal microbes from Parkinson’s disease patients (PD),6,6,NA,16S,4,Illumina,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6E,20 March 2024,Toyosiolann,"Toyosiolann,Svetlana up",Differentially abundant taxon in the WT mice with HC fecal transfer and the WT mice with PD fecal transfer.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|1853231|574697;2|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:910/2/1,Study 910,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R , Mazmanian SK",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,ASO mice with fecal microbes from healthy controls (HC),ASO mice with fecal microbes from Parkinson’s disease patients (PD),"Germ-free mice, Thy1-α-synuclein genotype (ASO) colonized with fecal microbes from Parkinson’s disease patients (PD)",6,6,NA,16S,4,Illumina,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6E,2 April 2024,Svetlana up,Svetlana up,Differentially abundant taxon in the ASO mice with HC fecal transfer and the ASO mice with PD fecal transfer.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter",2|976|200643|171549|815|816;2|200940|3031449|213115|194924|35832;2|1239|91061|186826|81852|1350;2|1224|1236|91347|1903414|583;2|1239|186801|186802|186806|113286,Complete,Svetlana up
bsdb:910/2/2,Study 910,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R , Mazmanian SK",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,ASO mice with fecal microbes from healthy controls (HC),ASO mice with fecal microbes from Parkinson’s disease patients (PD),"Germ-free mice, Thy1-α-synuclein genotype (ASO) colonized with fecal microbes from Parkinson’s disease patients (PD)",6,6,NA,16S,4,Illumina,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6E,2 April 2024,Svetlana up,Svetlana up,Differentially abundant taxon in the ASO mice with HC fecal transfer and the ASO mice with PD fecal transfer.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:911/1/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 1,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Early pregnancy glucocorticoid(Early-preGC) exposure in 4.7years (mean age),Early pregnancy glucocorticoid (Early-preGC) exposure in 2.3years (mean age -1SD),"Assamese macaques aged 2.3 years (roughly equivalent to infants age class), who were exposed to prenatal, maternal glucocorticoid in early pregnancy/gestation (Early-preGC) during the Rich season(periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,decreased,Signature 1,Figure 4A,20 March 2024,Ikehdarlington,"Ikehdarlington,Joan Chuks","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Caldicoprobacteraceae|g__Caldicoprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Entomoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|3118652|2039240;2|201174|1760|85004|31953|1678;2|976|200643|171549|1853231|574697;2|1239|186801|186802|715221|715222;2|1239|186801|186802|1980681;2|201174|84998|84999|84107|102106;2|74152|641853|641854|641876|423604;2|544448|31969|186328|33925|46238;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|946234;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|1392389;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572|119852;2|1239|909932|1843488|909930|33024;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827|123375;2|1224|1236|135624|83763|83770;2|1239|186801|186802|216572|39492;2|1239|186801|186802|216572|35829;2|201174|84998|84999|1643824;2|1239|91061;2|1798710|1906119;2|1239|526524|526525|128827;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|1224|28211|204441;2|1239|186801|186802|68298;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/1/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 1,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Early pregnancy glucocorticoid(Early-preGC) exposure in 4.7years (mean age),Early pregnancy glucocorticoid (Early-preGC) exposure in 2.3years (mean age -1SD),"Assamese macaques aged 2.3 years (roughly equivalent to infants age class), who were exposed to prenatal, maternal glucocorticoid in early pregnancy/gestation (Early-preGC) during the Rich season(periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,decreased,Signature 2,Figure 4A,20 March 2024,Ikehdarlington,"Ikehdarlington,Joan Chuks","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|201174|1760|85004|31953|419014;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|216851;2|65842|204430|218872|204431|832;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|1410626;2|1239|186801|186802|216572|459786;2|1224|1236|135625|712|1960084;2|1239|186801|3085636|186803|1506577;2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|201174|84998|84999;2|201174|84998|1643822|1643826;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|976|200643|171549|2005473;2|1224|28211|204441;2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|297314;2|976|200643|171549,Complete,Svetlana up
bsdb:911/2/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 2,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Early pregnancy glucocorticoid(Early-preGC)  exposure in 4.7years old(mean age),Early pregnancy glucocorticoid (Early-preGC) exposure in 7.1years old(mean age +1SD),"Assamese macaques aged 7.1years (equivalent to Adult age class), who were exposed to prenatal, maternal glucocorticoid in early pregnancy/gestation (Early-preGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,decreased,Signature 1,Figure 4A,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD-equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age: equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|201174|1760|85004|31953|419014;2|976|200643|171549|1853231|574697;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|216851;2|65842|204430|218872|204431|832;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|1410626;2|1239|186801|186802|216572|459786;2|1224|1236|135625|712|1960084;2|1239|186801|3085636|186803|1506577;2|201174|84998|84999;2|201174|84998|1643822|1643826;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1224|28211|204441;2|976|200643|171549;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/2/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 2,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Early pregnancy glucocorticoid(Early-preGC)  exposure in 4.7years old(mean age),Early pregnancy glucocorticoid (Early-preGC) exposure in 7.1years old(mean age +1SD),"Assamese macaques aged 7.1years (equivalent to Adult age class), who were exposed to prenatal, maternal glucocorticoid in early pregnancy/gestation (Early-preGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,decreased,Signature 2,Figure 4A,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old   Assamese macaques (mean age +1SD-equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age: equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Caldicoprobacteraceae|g__Caldicoprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Entomoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|3118652|2039240;2|201174|1760|85004|31953|1678;2|1239|186801|186802|715221|715222;2|1239|186801|186802|1980681;2|201174|84998|84999|84107|102106;2|74152|641853|641854|641876|423604;2|544448|31969|186328|33925|46238;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|946234;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|1392389;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572|119852;2|1239|909932|1843488|909930|33024;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827|123375;2|1224|1236|135624|83763|83770;2|1239|186801|186802|216572|39492;2|1239|186801|186802|216572|35829;2|201174|84998|84999|1643824;2|1239|91061;2|1798710|1906119;2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|1239|526524|526525|128827;2|976|200643|171549|2005473;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|1224|28211|204441;2|1239|186801|186802|68298;2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/3/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 3,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Late pregnancy glucocorticoid (Late-preGC) exposure in 4.7years old (mean age),Late pregnancy glucocorticoid (Late-preGC) exposure in 2.3years old (mean age -1SD),"Assamese macaques aged 2.3 years (equivalent to infant age class), who were exposed to prenatal, maternal glucocorticoid in late pregnancy/gestation (Late-preGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 4B,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD = equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age =equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.",increased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.",2|544448|31969|186332|186333|2152;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|74152|641853|641854|641876|423604;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|877406;2|1239|186801|3085656|3085657|2039302;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|1929305;2|201174|84998|84999|84107|1473205;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827|123375;2|1239|91061|186826|1300|1301;2|1224|1236|135624|83763|83770;2|203691|203692|136|2845253|157;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|216572|84026;2|1239|186801|186802|216572|35829;2|201174|84998|84999|1643824;2|1239|91061;2|201174|1760|85004|31953;2|1239|186801|186802|3085642;2|1798710|1906119;2|544448|1912503|2975519;2|1239|186801|186802|31979;2|1224|28216|80840|80864;2|201174|84998|1643822|1643826;2|1224|1236|91347|543;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|201174|1760|85008|28056;2|976|200643|171549|2005473;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|74201|414999|415001|415002;2|1224|28211|356|82115;2|1224|28216|206389|75787;2|1224|28211|204441;2|1224|28211|204457|41297;2|1224|28211|356|335928;2|1239|526524|526525|128827|331630;2|976|200643|171549|171552|838|159272,Complete,Svetlana up
bsdb:911/3/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 3,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Late pregnancy glucocorticoid (Late-preGC) exposure in 4.7years old (mean age),Late pregnancy glucocorticoid (Late-preGC) exposure in 2.3years old (mean age -1SD),"Assamese macaques aged 2.3 years (equivalent to infant age class), who were exposed to prenatal, maternal glucocorticoid in late pregnancy/gestation (Late-preGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 4B,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD = equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age = equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fournierella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,s__gut metagenome,k__Bacteria|c__Deltaproteobacteria|o__Bradymonadales,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|976|200643|171549|1853231|574697;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|1940255;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|1960084;2|1239|186801|186802|216572|1263|438033;749906;2|28221|1779134;2|544448|1912503|2975519;2|1224|1236|1706369|1706371;2|1239|186801|186802|216572|596767;2|1224|1236|72274|135621;2|203691|203692|136|137;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/4/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 4,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Late pregnancy glucocorticoid(Late-preGC) exposure in 4.7years old(mean age),Late pregnancy glucocorticoid (Late-preGC) exposure in 7.1years old(mean age +1SD),"Assamese macaques aged 7.1 years (equivalent to Adult age class), who were exposed to prenatal, maternal glucocorticoid in late pregnancy/gestation (Late-preGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 4B,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD-equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age: equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fournierella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,s__gut metagenome,k__Bacteria|c__Deltaproteobacteria|o__Bradymonadales,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|976|200643|171549|1853231|574697;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|1940255;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|1960084;2|1239|186801|186802|216572|1263|438033;749906;2|28221|1779134;2|544448|1912503|2975519;2|1224|1236|1706369|1706371;2|1239|186801|186802|216572|596767;2|1224|1236|72274|135621;2|203691|203692|136|137;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/4/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 4,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Late pregnancy glucocorticoid(Late-preGC) exposure in 4.7years old(mean age),Late pregnancy glucocorticoid (Late-preGC) exposure in 7.1years old(mean age +1SD),"Assamese macaques aged 7.1 years (equivalent to Adult age class), who were exposed to prenatal, maternal glucocorticoid in late pregnancy/gestation (Late-preGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 4B,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.",decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.",2|544448|31969|186332|186333|2152;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|74152|641853|641854|641876|423604;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|877406;2|1239|186801|3085656|3085657|2039302;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|1929305;2|201174|84998|84999|84107|1473205;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827|123375;2|1239|91061|186826|1300|1301;2|1224|1236|135624|83763|83770;2|203691|203692|136|2845253|157;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|216572|84026;2|1239|186801|186802|216572|35829;2|201174|84998|84999|1643824;2|1239|91061;2|201174|1760|85004|31953;2|1239|186801|186802|3085642;2|1798710|1906119;2|544448|1912503|2975519;2|1239|186801|186802|31979;2|1224|28216|80840|80864;2|201174|84998|1643822|1643826;2|1224|1236|91347|543;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|201174|1760|85008|28056;2|976|200643|171549|2005473;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|74201|414999|415001|415002;2|1224|28211|356|82115;2|1224|28216|206389|75787;2|1224|28211|204441;2|1224|28211|204457|41297;2|1224|28211|356|335928;2|1239|526524|526525|128827|331630;2|976|200643|171549|171552|838|159272,Complete,Svetlana up
bsdb:911/5/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 5,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Post-pregnancy glucocorticoid(PostGC) exposure in 4.7years old(mean age),Post-pregnancy glucocorticoid (PostGC) exposure in 2.3years old(mean age -1SD),"Assamese macaques aged 2.3 years (equivalent to infant age class), who were exposed to postnatal, maternal glucocorticoid in post pregnancy/lactation (PostGC) for the first 6 months of life during the Rich season (periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 4C,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Caldicoprobacteraceae|g__Caldicoprobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Entomoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,s__gut metagenome,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|186803|653683;2|1239|186801|3082720|3030910;2|1239|186801|3082720|3030910|109326;2|976|200643|171549|1853231|574697;2|1239|186801|186802|715221|715222;2|200940|3031449|213115|194924|872;2|74152|641853|641854|641876|423604;2|544448|31969|186328|33925|46238;2|1239|186801|186802|186806|1730|290054;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803|1649471;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1929305;2|1239|186801|186802|216572|1263|438033;2|1239|909932|909929|1843491|970;2|203691|203692|136|2791015|399320;749906;2|1239|186801|186802|216572|35829;2|201174|84998|84999|1643824;2|1239|91061;2|1798710|1906119;2|1239|186801;2|1239|186801|186802|31979;2|1239|526524|526525|128827;2|1239|186801|186802|216572;2|74201|414999|415001|415002;2|1224|28211|204441;2|1239|186801|186802|68298;2|976|200643|171549|2005525;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/5/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 5,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Post-pregnancy glucocorticoid(PostGC) exposure in 4.7years old(mean age),Post-pregnancy glucocorticoid (PostGC) exposure in 2.3years old(mean age -1SD),"Assamese macaques aged 2.3 years (equivalent to infant age class), who were exposed to postnatal, maternal glucocorticoid in post pregnancy/lactation (PostGC) for the first 6 months of life during the Rich season (periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 4C,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.",decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacteria|c__Deltaproteobacteria|o__Bradymonadales,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|29547|3031852|213849|72294|194;2|1239|186801|3085636|186803|189330;2|29547|3031852|213849|72293|209;2|1239|91061|186826|33958|2767887;2|1239|909932|1843489|31977|906;2|201174|84998|1643822|1643826|84108;2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|84026;2|28221|1779134;2|544448|1912503|2975519;2|1239|186801;2|1224|28216|80840|80864;2|201174|84998|84999;2|201174|84998|1643822|1643826;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|201174|1760|85008|28056;2|1224|28211|356|82115;2|1224|28211|204457|41297;2|1239|91061|1385|90964;2|1239|91061|186826|1300,Complete,Svetlana up
bsdb:911/6/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 6,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Post-pregnancy glucocorticoid(PostGC) exposure in 4.7years old(mean age),Post-pregnancy glucocorticoid (PostGC) exposure in 7.1years old(mean age +1SD),"Assamese macaques aged 7.1 years (equivalent toAdult age class), who were exposed to postnatal, maternal glucocorticoid in post pregnancy/lactation (PostGC) for the first 6 months of life during the Rich season (periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 4C,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|c__Deltaproteobacteria|o__Bradymonadales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|29547|3031852|213849|72294|194;2|74152|641853|641854|641876|423604;2|1239|186801|186802|186806|1730|290054;2|29547|3031852|213849|72293|209;2|1239|909932|1843489|31977|906;2|201174|84998|1643822|1643826|84108;2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|84026;2|1239|186801|186802|216572|35829;2|201174|84998|84999|1643824;2|28221|1779134;2|1239|186801;2|1239|186801|186802|31979;2|1224|28216|80840|80864;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|201174|1760|85008|28056;2|1224|28211|356|82115;2|1224|28211|204457|41297;2|1239|91061|1385|90964;2|1239|91061|186826|1300,Complete,Svetlana up
bsdb:911/6/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 6,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Post-pregnancy glucocorticoid(PostGC) exposure in 4.7years old(mean age),Post-pregnancy glucocorticoid (PostGC) exposure in 7.1years old(mean age +1SD),"Assamese macaques aged 7.1 years (equivalent toAdult age class), who were exposed to postnatal, maternal glucocorticoid in post pregnancy/lactation (PostGC) for the first 6 months of life during the Rich season (periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 4C,21 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Caldicoprobacteraceae|g__Caldicoprobacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Entomoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,s__gut metagenome,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|186803|653683;2|1239|186801|3082720|3030910;2|1239|186801|3082720|3030910|109326;2|976|200643|171549|1853231|574697;2|1239|186801|186802|715221|715222;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|189330;2|544448|31969|186328|33925|46238;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|33958|2767887;2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803|1649471;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1929305;2|1239|186801|186802|216572|1263|438033;2|1239|909932|909929|1843491|970;2|203691|203692|136|2791015|399320;749906;2|201174|84998|84999|1643824;2|1239|91061;2|1798710|1906119;2|544448|1912503|2975519;2|1239|186801;2|201174|84998|84999;2|201174|84998|1643822|1643826;2|1239|526524|526525|128827;2|1239|186801|186802|216572;2|74201|414999|415001|415002;2|1224|28211|204441;2|1239|909932|909929;2|1239|186801|186802|68298;2|976|200643|171549|2005525;2|1239|526524|526525|128827|331630;2|976|200643|171549;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/7/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 7,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Offspring glucocorticoid (OffspringGC) in 4.7 years old (mean age),Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD),"Assamese macaques aged 2.3 years (equivalent to infant age class), who were affected by increased Offspring Glucocorticoid level (OffspringGC) during the Rich season (periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 5,25 March 2024,Ikehdarlington,"Ikehdarlington,Joan Chuks","Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed during the rich season.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|201174|1760|85004|31953|419014;2|29547|3031852|213849|72294|194;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|216851;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1239|91061|186826|33958|2767887;2|200940|3031449|213115|194924|1981028;2|1239|186801|186802|216572|459786;2|1224|1236|135625|712|1960084;2|1239|186801|3085636|186803|1506577;2|256845|1313211|278082|255528|172900;2|544448|1912503|2975519;2|1224|1236|1706369|1706371;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|1224|1236|72274|135621;2|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:911/7/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 7,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Offspring glucocorticoid (OffspringGC) in 4.7 years old (mean age),Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD),"Assamese macaques aged 2.3 years (equivalent to infant age class), who were affected by increased Offspring Glucocorticoid level (OffspringGC) during the Rich season (periods of abundant food availability)",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 5,25 March 2024,Ikehdarlington,"Ikehdarlington,Joan Chuks","Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed during the rich season.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Parachlamydiales|f__Candidatus Rhabdochlamydiaceae|g__Candidatus Rhabdochlamydia|s__Candidatus Rhabdochlamydia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Entomoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Eukaryota|p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,s__gut metagenome,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1239|186801|3085636|186803|653683;2|204428|204429|1963360|689704|292833|2320511;2|1239|186801|186802|1980681;2|200940|3031449|213115|194924|872;2|544448|31969|186328|33925|46238;2|1239|186801|186802|186806|1730|290054;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|877406;2|1239|186801|3085636|186803|248744;2|1239|186801|186802|216572|119852;2759|2763|2806|31370|31371|2729669;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|1300|1301;2|1224|1236|135624|83763|83770;749906;2|1239|186801|186802|216572|35829;2|1239|91061;2|1798710|1906119;2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|201174|84998|1643822|1643826;2|1239|526524|526525|128827;2|976|200643|171549|2005473;2|1239|186801|186802|216572;2|976|200643|171549|2005523;2|1224|28211|204441;2|1239|909932|909929|1843491;2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|297314;2|976|200643|171549,Complete,Svetlana up
bsdb:911/8/1,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 8,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Offspring glucocorticoid (OffspringGC) in 4.7 years old (mean age),Offspring glucocorticoid (OffspringGC) in 7.1 years old (mean age +1SD),"Assamese macaques aged 7.1 years (equivalent to Adult age class), who were affected by increased Offspring Glucocorticoid level (OffspringGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 5,25 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed within the rich season.",increased,"k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Parachlamydiales|f__Candidatus Rhabdochlamydiaceae|g__Candidatus Rhabdochlamydia|s__Candidatus Rhabdochlamydia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Entomoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,s__gut metagenome,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|204428|204429|1963360|689704|292833|2320511;2|1239|186801|186802|1980681;2|200940|3031449|213115|194924|872;2|544448|31969|186328|33925|46238;2|1239|186801|186802|186806|1730|290054;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|877406;2|200940|3031449|213115|194924|1981028;2|1239|186801|3085636|186803|248744;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|119852;2|1224|1236|135624|83763|83770;2|256845|1313211|278082|255528|172900;749906;2|1239|91061;2|976|200643|171549;2|544448|1912503|2975519;2|1239|186801|3082768|990719;2|1239|186801|186802|31979;2|1239|526524|526525|128827;2|976|200643|171549|2005473;2|1239|186801|186802|216572;2|976|200643|171549|2005523;2|1224|1236|72274|135621;2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:911/8/2,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 8,Thailand,Macaca assamensis,Feces,UBERON:0001988,Response to glucocorticoid,GO:0051384,Offspring glucocorticoid (OffspringGC) in 4.7 years old (mean age),Offspring glucocorticoid (OffspringGC) in 7.1 years old (mean age +1SD),"Assamese macaques aged 7.1 years (equivalent to Adult age class), who were affected by increased Offspring Glucocorticoid level (OffspringGC) during the Rich season (periods of abundant food availability).",16,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 5,25 March 2024,Joan Chuks,"Joan Chuks,Ikehdarlington","Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed within the rich season.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Eukaryota|p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|201174|1760|85004|31953|419014;2|1239|186801|3085636|186803|653683;2|29547|3031852|213849|72294|194;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|216851;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1239|91061|186826|33958|2767887;2759|2763|2806|31370|31371|2729669;2|1224|1236|135625|712|1960084;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1506577;2|1239|186801|186802|216572|35829;2|1798710|1906119;2|1224|1236|1706369|1706371;2|201174|84998|1643822|1643826;2|1239|526524|526525|128827;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|1224|28211|204441;2|1239|909932|909929|1843491;2|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:911/9/NA,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 9,Thailand,Macaca assamensis,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infant macaques,Adult macaques,Assamese macaques aged 6–10 years,16,7,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:911/10/NA,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 10,Thailand,Macaca assamensis,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infant macaques,Juvenile macaques,Assamese macaques aged 4–5 years,16,7,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:911/11/NA,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 11,Thailand,Macaca assamensis,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Lean season,Rich season,"The hot and rainy season in the Assamese macaques' habitat, usually occurring between March to October and marked by abundant food availability",30,16,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:911/12/NA,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 12,Thailand,Macaca assamensis,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,MOT,MST,Second grouping of Assamese macaques by research team.,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:911/13/NA,Study 911,"cross-sectional observational, not case-control",37501202,https://doi.org/10.25625/SFHRIT,NA,"Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J , Schülke O",The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels,Microbiome,2023,"16S rRNA gene, Bacteria, Development, Dysbiosis, Health, Long-term, Macaques, Prenatal stress, Primates, Programming",Experiment 13,Thailand,Macaca assamensis,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,MOT,SST,Third grouping of Assamese macaques by the research team,NA,NA,NA,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:912/1/1,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 1,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Reference diet,Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",36,36,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,General Performance,11 March 2024,Bolanle,Bolanle,Effects of diets containing yeast cell-wall based prebiotics on the gut microbiota of Atlantic Salmon in September: Mycoplasma became more prominent as fish progressed towards April and September.,increased,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,2|544448|31969|2085|2092|2093,Complete,Svetlana up
bsdb:912/1/2,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 1,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Reference diet,Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",36,36,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary material 3,11 March 2024,Bolanle,Bolanle,"Relative abundance of all Amplicon sequence variants (ASVs) for each sample; life stage dietary treatmet
LAB decreasing trend suggests a change in the gut microbiome composition of Atlantic Salmon in response to diets",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243,Complete,Svetlana up
bsdb:912/2/1,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 2,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,January Reference diet,January Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 7,18 April 2024,Bolanle,Bolanle,most abundant taxa at genus level of all samples relative abundance of each taxon,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1243;2|1239|91061|186826|1300|1357;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1239|91061|186826|33958|46255;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817|129337;2|1239|186801|186802|31979|1485;2|1224|1236|135623|641|657;2|1224|1236|135619|28256|2745;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|623282,Complete,Svetlana up
bsdb:912/2/2,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 2,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,January Reference diet,January Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 7,18 April 2024,Bolanle,Bolanle,most abundant taxa at genus level of all samples relative abundance of each taxon,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Ureibacillus,2|1239|91061|1385|186818|160795,Complete,Svetlana up
bsdb:912/3/1,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 3,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Fishes fed with test diet in January,Fishes fed with test diet in April,Atlantic Salmon fed with yeast cell wall based-prebiotics diet in January,18,18,NA,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,unchanged,NA,NA,Signature 1,FIgure 7,14 March 2024,Bolanle,Bolanle,"Compared to January fish, April fish showed a slight increase in genera Proteobacteria (15% and 10% in Reference fed and Test-fed fish, respectively) and Mycoplasma (4% and 29.5% in Reference fed and Test- fed fish, respectively)",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,2|1224|1236|135623|641|657,Complete,Svetlana up
bsdb:912/4/1,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 4,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Fishes fed with test diet in January,Fishes fed with test diet in September,Atlantic Salmon fed with yeast cell wall based-prebiotics diet in September,18,18,NA,16S,12,Illumina,MaAsLin2,0.001,TRUE,2,NA,NA,unchanged,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 7,17 March 2024,Bolanle,Bolanle,"As fish subject progressed towards september, Mycoplasma (50% and 47% in Reference diet fish and Test dit fish respectively) became more prominent.",increased,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,2|544448|31969|2085|2092|2093,Complete,Svetlana up
bsdb:912/4/2,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 4,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Fishes fed with test diet in January,Fishes fed with test diet in September,Atlantic Salmon fed with yeast cell wall based-prebiotics diet in September,18,18,NA,16S,12,Illumina,MaAsLin2,0.001,TRUE,2,NA,NA,unchanged,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 7,17 March 2024,Bolanle,Bolanle,"there was reduction in Lactic acid bacteria(LAB), for example Lactobacillus (12%), Leuconostoc (0.03%) and Lactococcus(0.02%) in Reference diet fish, and Lactobacillus (12%), Leuconostoc (0.05%) and Lactococcus (0.02%) in Test diet fish, respectively.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|91061|186826|33958|1243;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357,Complete,Svetlana up
bsdb:912/5/1,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 5,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,April Reference diet,April Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 7,18 April 2024,Bolanle,Bolanle,most abundant taxa at genus level of all samples relative abundance of each taxon,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Aliivibrio",2|32066|203490|203491|203492|848;2|1224|1236|135619|28256|2745;2|544448|31969|2085|2092|2093;2|1224|1236|135622|267890|22;2|1239|91061|186826|33958|46255;2|1239|186801|186802|216572|2485925;2|1224|1236|135623|641|511678,Complete,Svetlana up
bsdb:912/5/2,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 5,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,April Reference diet,April Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 7,18 April 2024,Bolanle,Bolanle,most abundant taxa at genus level of all samples relative abundance of each taxon,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Ureibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1243;2|1239|91061|186826|1300|1357;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186818|160795;2|1224|1236|135623|641|657;2|32066|203490|203491|203492|623282;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:912/6/1,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 6,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,september Reference diet,september Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 7,18 April 2024,Bolanle,Bolanle,most abundant taxa at genus level of all samples relative abundance of each taxon,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Ureibacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter",2|1239|91061|1385|186818|160795;2|1224|1236|135623|641|657;2|1239|91061|186826|33958|1578;2|1224|1236|135622|267890|22;2|32066|203490|203491|203492|623282,Complete,Svetlana up
bsdb:912/6/2,Study 912,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å , Kortner TM",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 6,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,september Reference diet,september Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,None,16S,12,Illumina,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 7,18 April 2024,Bolanle,Bolanle,most abundant taxa at genus level of all samples relative abundance of each taxon,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",2|1224|1236|135619|28256|2745;2|544448|31969|2085|2092|2093,Complete,Svetlana up
bsdb:913/1/1,Study 913,prospective cohort,NA,https://doi.org/10.1186/s12866-023-03042-1,NA,"Ju Zhang, Xiuhai Lu, Zhiwei Cheng, Dulei Zou",Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children,BMC microbiology,2023,"Orthokeratology lenses, Conjunctiva sac, Microbiome, Microbiome, Brevundimonas, Acinetobacter, Proteus, genomics, 16s rdna gene sequencing",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Myopia,HP:0000545,N group -  Non-wearer group,L group -  Ok Lens group,Myopic patients who had been wearing OK lenses for 12–13 months,22,28,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 4,8 March 2024,Ebere,"Ebere,Peace Sandy","Linear Discriminant Analysis (LDA) Effect Size (LEfSe) multilevel discriminant analysis of the species differences (LDA > 3, P < 0.05, Mann–Whitney U-tests). A: Cladogram. The circle radiating from inside to outside represents the classification level from the kingdom to the genus (or species). Species with no significant differences are uniformly colored in yellow, the red nodes represent the microbial group that plays an important role in the OK group, and the green nodes represent the non-wearer group. B: Histogram of LDA value distribution shows the biomarkers with statistical difference. The LDA value represents the influence of bacterial species, and the longer the length, the higher the degree of influence. L: the OK lens group, N: the non-wearer group",increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces|s__Planctomyces sp. SH-PL62,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Chloroflexota|c__Chloroflexia",2|1224|28211;2|1224|28211|204458|76892;2|1224|28211|204458;2|1224|28211|204458|76892|41275;2|201174;2|1239|91061;2|1224|28211|204457;2|1224|28211|204457|41297;2|201174|1760|85007|1653;2|201174|1760|85007;2|1224|1236|2887326|468;2|1224|1236|2887326|468|469;2|1239|91061|1385;2|1239|91061|1385|90964;2|1224|1236|91347|1903414|583;2|1224|1236|91347;2|201174|1760|85006;2|1239|91061|1385|90964|1279;2|1224|1236|91347|1903414|583;2|1117;2|1224|1236|135614|32033;2|1239|91061|186826|1300;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|201174|1760|85007|1653|1716;2|57723;2|203682|203683|112|126|118|1636152;2|1239|91061|186826|81852;2|201174|1760|85006|1268;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|976|1853228|1853229;2|201174|1760|85009;2|1224|1236|91347|543|547;2|976|117743|200644;2|976|1853228|1853229|563835;2|1239|186801|3085636|186803|572511;2|1239|91061|1385|186817;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1912216;2|200795|32061,Complete,Peace Sandy
bsdb:913/1/2,Study 913,prospective cohort,NA,https://doi.org/10.1186/s12866-023-03042-1,NA,"Ju Zhang, Xiuhai Lu, Zhiwei Cheng, Dulei Zou",Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children,BMC microbiology,2023,"Orthokeratology lenses, Conjunctiva sac, Microbiome, Microbiome, Brevundimonas, Acinetobacter, Proteus, genomics, 16s rdna gene sequencing",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Myopia,HP:0000545,N group -  Non-wearer group,L group -  Ok Lens group,Myopic patients who had been wearing OK lenses for 12–13 months,22,28,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 4,8 March 2024,Ebere,"Ebere,Peace Sandy","Linear Discriminant Analysis (LDA) Effect Size (LEfSe) multilevel discriminant analysis of the species differences (LDA > 3, P < 0.05, Mann–Whitney U-tests). A: Cladogram. The circle radiating from inside to outside represents the classification level from the kingdom to the genus (or species). Species with no significant differences are uniformly colored in yellow, the red nodes represent the microbial group that plays an important role in the OK group, and the green nodes represent the non-wearer group. B: Histogram of LDA value distribution shows the biomarkers with statistical difference. The LDA value represents the influence of bacterial species, and the longer the length, the higher the degree of influence. L: the OK lens group, N: the non-wearer group",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1239|91061|1385|186817|1386;2;2|74201|203494|48461|1647988|239934|1872421;2|976|200643|171549|2005473;2|976|200643|171549|2005473,Complete,Peace Sandy
bsdb:914/1/1,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 1,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),14,13,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3A,30 March 2024,Temi,"Temi,Scholastica",Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) group versus First-degree relatives (FDRs),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|1263;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|543311;2157|2283796|183967|1235850|1577788|1080709;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804|1505657;2|29547|3031852|213849|72293|209;2|1239|91061|186826|186828|117563;2|1239|91061|1385|539738|1378;2|1239|186801|186802|186806|1730;2|1239|526524|526525|2810280|135858;2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|207244;2|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:914/1/2,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 1,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),14,13,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3A,30 March 2024,Temi,"Temi,Scholastica",Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) group versus First-degree relatives (FDRs),decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",2|1239|526524|526525|2810281|191303;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|1263;2|1224|1236|2887326|468|475;2157|2283796|183967|1235850|1577788|1080709;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|572511;2|976|200643|171549|2005519|397864,Complete,NA
bsdb:914/2/1,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 2,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),13,16,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3B,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in duodenal microbiota of celiac disease versus disease control (DC) group,increased,"k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2157|2283796|183967|1235850|1577788|1080709;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1578;2|29547|3031852|213849|72293|209;2|1239|186801|186802|186806|1730;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|572511;2|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:914/2/2,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 2,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),13,16,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3B,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in duodenal microbiota of celiac disease versus disease control (DC) group,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|526524|526525|2810281|191303;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|1263;2|1239|1737404|1737405|1570339|543311;2157|2283796|183967|1235850|1577788|1080709;2|1239|186801|3082720|186804|1505657;2|1239|91061|186826|186828|117563;2|1239|91061|1385|539738|1378;2|1239|186801|186802|186806|1730;2|1239|526524|526525|2810280|135858;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|207244;2|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:914/3/1,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 3,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),Celiac disease (CeD),Patients with celiac disease (CeD),14,16,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC)  versus celiac disease (CeD) patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|976|200643|171549|171552|838;2157|2283796|183967|1235850|1577788|1080709;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1578;2|29547|3031852|213849|72293|209;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:914/3/2,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 3,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),Celiac disease (CeD),Patients with celiac disease (CeD),14,16,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3C,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) versus celiac disease (CeD) patients,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",2|1239|526524|526525|2810281|191303;2|1239|186801|186802|216572|1263;2|1224|1236|2887326|468|475;2157|2283796|183967|1235850|1577788|1080709;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804|1505657;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|572511;2|976|200643|171549|2005519|397864,Complete,Svetlana up
bsdb:914/4/1,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,Fecal samples of first-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) group versus First-degree relatives (FDRs),increased,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,2157|2283796|183967|1235850|1577788|1080709,Complete,Svetlana up
bsdb:914/4/2,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,Fecal samples of first-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) group versus First-degree relatives (FDRs),decreased,"k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2157|2283796|183967|1235850|1577788|1080709;2|1239|91061|186826|33958|1578;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|189330;2|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:914/5/1,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5B,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in fecal microbiota of celiac disease versus disease control (DC) group,increased,"k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2157|2283796|183967|1235850|1577788|1080709;2|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:914/5/2,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5B,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in fecal microbiota of celiac disease versus disease control (DC) group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|91061|186826|33958|1253;2157|2283796|183967|1235850|1577788|1080709;2|1239|186801|3082720|186804|1505657;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:914/6/1,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),15,21,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5C,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) versus celiac disease (CeD) patients,increased,"k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2157|2283796|183967|1235850|1577788|1080709;2|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:914/6/2,Study 914,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS , Makharia GK",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),15,21,None,16S,4,Illumina,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5C,29 May 2024,Scholastica,Scholastica,Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) versus celiac disease (CeD) patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|976|200643|171549|171552|838;2157|2283796|183967|1235850|1577788|1080709;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|189330;2|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:915/1/1,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Breast carcinoma,EFO:0000305,Premenopausal female controls (Pre-C),premenopausal breast cancer patients (Pre-BC),Premenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,50,100,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,FIG 2 (B),8 April 2024,Rahila,"Rahila,Scholastica",Significantly differential gut microbiota in premenopausal breast cancer (Pre-BC) patients compared to premenopausal female controls (Pre-C),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|976|200643|171549|815|816;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|2974265|363265;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263|40519;2|1224|28216|80840|995019|40544;2|976|200643|171549|815;2|976|200643|171549;2|976|200643;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|1224|28211;2|1224|28216|80840|506;2|1224|28216|80840;2|1224|28216;2|1224|1236|135625|712;2|1224|1236|135625,Complete,Svetlana up
bsdb:915/1/2,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Breast carcinoma,EFO:0000305,Premenopausal female controls (Pre-C),premenopausal breast cancer patients (Pre-BC),Premenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,50,100,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,FIG 2 (B),8 April 2024,Rahila,"Rahila,Scholastica",Significantly differential gut microbiota in premenopausal breast cancer (Pre-BC) patients compared to premenopausal female controls (Pre-C),decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes massiliensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|626932;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|216816;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|526524|526525|128827|1573535|1735;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1224|28216|80840|75682|846;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|823;2759|33090|35493|3398|72025|3803|3814|508215;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301;2|976|200643|171549|171550|239759|265312;2|201174|1760|85006|1268;2|201174|1760|2037;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|976|200643|171549|171551;2|976|200643|171549|171550;2|976|200643|171549|2005519;2|1239|91061|1385|539738;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|91061;2|1239|186801|186802|216572;2|1239|909932|1843489|31977;2|1239|186801|186802;2|1239|186801;2|1224|28216|80840|75682;2|74201|203494|48461;2|74201|203494;2|74201|203494|48461|203557,Complete,Svetlana up
bsdb:915/2/1,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Breast carcinoma,EFO:0000305,Postmenopausal female controls (Post-C),Postmenopausal breast cancer patients (Post-BC),Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,17,100,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,FIG 2 (C),8 April 2024,Rahila,"Rahila,Scholastica",Significantly differential gut microbiota in postmenopausal breast cancer (Post-BC) patients compared to postmenopausal female controls (Post-C),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1239|909932|909929|1843491|52225;2|1239|909932|909929|1843491|52225|52226;2|1224|28216|80840|995019|40544;2|201174|1760|2037|2049;2|976|200643|171549;2|976|200643;2|1239|186801|3082720|186804;2|1224|28216|80840|506;2|1224|28216|80840;2|1224|28216;2|1224|1236|135625|712;2|1224|1236|135625,Complete,Svetlana up
bsdb:915/2/2,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Breast carcinoma,EFO:0000305,Postmenopausal female controls (Post-C),Postmenopausal breast cancer patients (Post-BC),Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,17,100,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,FIG 2 (C),8 April 2024,Rahila,"Rahila,Scholastica",Significantly differential gut microbiota in postmenopausal breast cancer (Post-BC) patients compared to postmenopausal female controls (Post-C),decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes massiliensis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|265312;2|200940|3031449|213115|194924|35832;2|201174|84998|84999|84107|102106|74426;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|128827|1573535|1735;2|1224|28216|80840|75682|846;2|1224|28216|80840|75682|846|847;2|976|200643|171549|2005525|375288|823;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|387090;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|976|200643|171549|171550;2|1239|91061|1385|539738;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|186801|3085636|186803;2|1239|186801|186802;2|1239|186801;2|1224|28216|80840|75682;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|28221;2|74201|203494|48461|203557;2|74201|203494|48461;2|74201|203494;2|976|200643|171549|171550|239759|626932;2|201174|84998|1643822|1643826|84111|84112,Complete,Svetlana up
bsdb:915/3/1,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal female controls (Pre-C),Postmenopausal female controls (Post-C),Postmenopausal female controls (Post-C) participants,50,17,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,FIG 2 (A),10 June 2024,Scholastica,Scholastica,Significantly differential gut microbiota in premenopausal female controls (Pre-C) compared to postmenopausal female controls (Post-C),increased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",2|508458|649775|649776;2|508458|649775;2|1239|526524|526525|128827|2749846|31971,Complete,Svetlana up
bsdb:915/3/2,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal female controls (Pre-C),Postmenopausal female controls (Post-C),Postmenopausal female controls (Post-C) participants,50,17,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,FIG 2 (A),10 June 2024,Scholastica,Scholastica,Significantly differential gut microbiota in premenopausal female controls (Pre-C) compared to postmenopausal female controls (Post-C),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174;2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|216851|853;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816,Complete,Svetlana up
bsdb:915/4/1,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal breast cancer patients (Pre-BC),Postmenopausal breast cancer patients (Post-BC),Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,100,100,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,FIG 3 (C),10 June 2024,Scholastica,Scholastica,Significantly differential gut microbiota in premenopausal (Pre-BC) compared to postmenopausal breast cancer (Post-BC) patients,increased,"k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Candidatus Electryoneota|c__Candidatus Tariuqbacteria|o__Candidatus Tariuqbacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2759|33090|35493;2|1239|526524|526525|2810281;2|3031806|3075765|3075766;2|1224|1236;2|200940|3031449|213115|194924|872;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|216572|1263|40519;2|1239|909932|1843489|31977|29465|39778,Complete,Svetlana up
bsdb:915/4/2,Study 915,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ , Chiang CP",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal breast cancer patients (Pre-BC),Postmenopausal breast cancer patients (Post-BC),Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,100,100,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,FIG 3 (C),10 June 2024,Scholastica,Scholastica,Significantly differential gut microbiota in premenopausal (Pre-BC) compared to postmenopausal breast cancer (Post-BC) patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|119852;2|200940|3031449|213115|194924|35832;2|201174|84998|1643822|1643826|447020;2|1239|186801|3085636|186803|841|301302;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816,Complete,Svetlana up
bsdb:916/1/1,Study 916,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim MJ, Lee S, Kwon MY , Kim M",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 1,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Vaginitis,MONDO:0002234,Healthy women (control),Recurrent vaginitis (RV),Women of reproductive age diagnosed with Recurrent vaginitis (RV).,100,40,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,decreased,decreased,NA,decreased,Signature 1,Figure 1,9 April 2024,Rahila,"Rahila,Scholastica",Statistically significant taxa (y-axis) between 40 cases with recurrent vaginitis (RV) and 100 healthy individuals (x-axis).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum",2|1224|1236|91347|543|561|562;2|201174|84998|84999|1643824|2767327|82135;2|201174|1760|85004|31953|2701|2702;2|1239|91061|1385|539738|3076174|502393;2|32066|203490|203491|1129771|168808|187101;2|544448|2790996|2790998|2129|2130,Complete,Svetlana up
bsdb:916/1/2,Study 916,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim MJ, Lee S, Kwon MY , Kim M",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 1,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Vaginitis,MONDO:0002234,Healthy women (control),Recurrent vaginitis (RV),Women of reproductive age diagnosed with Recurrent vaginitis (RV).,100,40,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,decreased,decreased,NA,decreased,Signature 2,Figure 1,20 June 2024,Scholastica,Scholastica,Statistically significant taxa (y-axis) between 40 cases with recurrent vaginitis (RV) and 100 healthy individuals (x-axis).,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1578|109790;2|1239|91061|186826|33958|2742598|1598,Complete,Svetlana up
bsdb:916/2/1,Study 916,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim MJ, Lee S, Kwon MY , Kim M",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 2,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Vaginal microbiome measurement,EFO:0011013,Community state type (CST) I,Community state type (CST) III and IV,Women of reproductive age diagnosed with Recurrent vaginitis (RV) categorized as community state type (CST) III and IV,5,29,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,20 June 2024,Scholastica,Scholastica,"Differential abundance of the bacterial taxa in three CST (I, III, and IV) groups of vaginal samples of patients with recurrent vaginitis (RV)",decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,Svetlana up
bsdb:916/3/1,Study 916,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim MJ, Lee S, Kwon MY , Kim M",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 3,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Vaginal microbiome measurement,EFO:0011013,Community state type (CST) I and IV,Community state type (CST) III,Women of reproductive age diagnosed with Recurrent vaginitis (RV) categorized as community state type (CST) III,26,8,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,20 June 2024,Scholastica,Scholastica,"Differential abundance of the bacterial taxa in three CST (I, III, and IV) groups of vaginal samples of patients with recurrent vaginitis (RV)",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",2|1239|91061|186826|33958|1578|147802;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061;2|1239|91061|186826|33958|1578;2|1239;2|1239|91061|186826|33958|2742598|1598,Complete,Svetlana up
bsdb:916/4/1,Study 916,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim MJ, Lee S, Kwon MY , Kim M",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 4,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Vaginal microbiome measurement,EFO:0011013,Community state type (CST) I and III,Community state type (CST) IV,Women of reproductive age diagnosed with Recurrent vaginitis (RV) categorized as community state type (CST) III and IV,13,21,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,20 June 2024,Scholastica,Scholastica,"Differential abundance of the bacterial taxa in three CST (I, III, and IV) groups of vaginal samples of patients with recurrent vaginitis (RV)",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacillota|c__Tissierellia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174;2|976|200643|171549;2|976|200643;2|976;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|201174|84998|84999|1643824|2767327|82135;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|2701|2702;2|1239|1737404|1737405|1570339;2|1239|1737404|1737405;2|1239|1737404;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:917/1/1,Study 917,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE , Lozupone C",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Healthy controls (HC),Antiretroviral therapy (ART) Naïve at baseline,PLWH (people living with HIV) who were not on ART at the first timepoint but who subsequently commenced first-line ART with efavirenz/lamivudine/tenofovir disoproxil fumarate (EFV/3TC/TDF) and the prophylactic antibiotic cotrimoxazole (ART Naïve) - Baseline,42,67,Use of antibiotics (apart from co-trimoxazole) within 2 months,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4A,11 March 2024,Nwajei Edgar,"Nwajei Edgar,Ayibatari,Keamy","Differential abundance of genera in ART-naïve compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:917/2/2,Study 917,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE , Lozupone C",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 2,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy controls (HC),Antiretroviral therapy (ART) naïve at baseline and after 24 weeks of first-line ART,PLWH (people living with HIV) who were not on antiretroviral therapy (ART) at the first timepoint but who subsequently commenced first-line ART with efavirenz/lamivudine/tenofovir disoproxil fumarate (EFV/3TC/TDF) and the prophylactic antibiotic cotrimoxazole (ART Naïve) - two time points.,42,52,Use of antibiotics (apart from co-trimoxazole) within 2 months,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4B,13 March 2024,Nwajei Edgar,"Nwajei Edgar,Ayibatari,Keamy",ART-naïve compared to HC with Model using two time points.,decreased,"k__Eukaryota|c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2759|2683628|42740|2547934|12967;2|1239|186801|3085636|186803|830;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:917/3/1,Study 917,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE , Lozupone C",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline,PLWH (people living with HIV) who were on  ART regimen and cotrimoxazole at baseline,42,33,Use of antibiotics (apart from co-trimoxazole) within 2 months,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4A,13 April 2024,Keamy,Keamy,"Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|909932|909929|1843491|158846;2|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:917/3/2,Study 917,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE , Lozupone C",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline,PLWH (people living with HIV) who were on  ART regimen and cotrimoxazole at baseline,42,33,Use of antibiotics (apart from co-trimoxazole) within 2 months,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4A,13 April 2024,Keamy,Keamy,"Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.",decreased,"k__Eukaryota|c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2759|2683628|42740|2547934|12967;2|1239|186801|3085636|186803|830;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:917/4/1,Study 917,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE , Lozupone C",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 4,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline and after 24 weeks,PLWH (people living with HIV) who were on ART regimen and cotrimoxazole at both time points,42,NA,Use of antibiotics (apart from co-trimoxazole) within 2 months,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 1,4B,13 April 2024,Keamy,Keamy,"Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using both time points.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|1239|909932|909929|1843491|158846;2|1239|186801|3085636|186803|1506553;2|200940|3031449|213115|194924|35832,Complete,Svetlana up
bsdb:917/4/2,Study 917,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE , Lozupone C",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 4,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline and after 24 weeks,PLWH (people living with HIV) who were on ART regimen and cotrimoxazole at both time points,42,NA,Use of antibiotics (apart from co-trimoxazole) within 2 months,16S,4,Illumina,ANCOM,0.05,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 2,4B,13 April 2024,Keamy,Keamy,"Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using both time points.",decreased,"k__Eukaryota|c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2759|2683628|42740|2547934|12967;2|1239|186801|3085636|186803|830;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:918/1/1,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Constipation,Parkinson's disease","HP:0002019,MONDO:0005180",Healthy Control group,Parkinson's disease patients (PD) before Fecal microbiota transplant (FMT),Parkinson's disease patients with constipation before FMT,13,11,None,16S,NA,NA,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 2C and 2D,8 March 2024,Ikehdarlington,"Ikehdarlington,ChiomaBlessing",Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to the Health Control group (HC),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976,Complete,ChiomaBlessing
bsdb:918/1/2,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Constipation,Parkinson's disease","HP:0002019,MONDO:0005180",Healthy Control group,Parkinson's disease patients (PD) before Fecal microbiota transplant (FMT),Parkinson's disease patients with constipation before FMT,13,11,None,16S,NA,NA,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig. 2C and 2D,10 March 2024,Ikehdarlington,"Ikehdarlington,ChiomaBlessing",Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to the Health Control group (HC),decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota",2|1224|28216;2|1224|28216|80840|119060;2|1239|186801;2|1224|1236|91347|543;2|1239|186801|3082720|186804;2|1239,Complete,ChiomaBlessing
bsdb:918/2/2,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 12 weeks after FMT,11,11,None,16S,NA,NA,LEfSe,0.05,NA,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig. 2C and 2D,10 March 2024,Ikehdarlington,"Ikehdarlington,ChiomaBlessing",Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 12 weeks after FMT,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinomycetota",2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263|41978;2|1239|186801|3085636|186803|2569097|39488;2|201174,Complete,ChiomaBlessing
bsdb:918/3/1,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 12 weeks after FMT,11,11,None,16S,NA,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3B and 3D,16 March 2024,ChiomaBlessing,ChiomaBlessing,Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 12 weeks after FMT,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|976|200643|171549|815|816;2|1224|1236|91347|543|1940338,Complete,ChiomaBlessing
bsdb:918/3/2,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 12 weeks after FMT,11,11,None,16S,NA,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3C and 3E,16 March 2024,ChiomaBlessing,ChiomaBlessing,Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 12 weeks after FMT,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:918/4/1,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 8 weeks after FMT,11,11,None,16S,NA,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3B and 3D,16 March 2024,ChiomaBlessing,ChiomaBlessing,Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 8 weeks after FMT,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|976|200643|171549|815|816;2|1224|1236|91347|543|1940338,Complete,ChiomaBlessing
bsdb:918/4/2,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 8 weeks after FMT,11,11,None,16S,NA,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3E,16 March 2024,ChiomaBlessing,ChiomaBlessing,Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 8 weeks after FMT,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,2|1239|186801|3085636|186803|572511,Complete,ChiomaBlessing
bsdb:918/5/1,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 4 weeks after FMT,11,11,None,16S,NA,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3D,16 March 2024,ChiomaBlessing,ChiomaBlessing,Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 4 weeks after FMT,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,2|1224|1236|91347|543|1940338,Complete,ChiomaBlessing
bsdb:918/5/2,Study 918,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai XY, Yao XH, Xu LJ, Zhou YQ, Zhang LP, Liu Y, Pei SF , Zhou CL",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 4 weeks after FMT,11,11,None,16S,NA,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3C,16 March 2024,ChiomaBlessing,ChiomaBlessing,Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 4 weeks after FMT,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:920/1/1,Study 920,randomized controlled trial,38291301,10.1038/s41591-023-02761-2,https://pubmed.ncbi.nlm.nih.gov/38291301/,"Link VM, Subramanian P, Cheung F, Han KL, Stacy A, Chi L, Sellers BA, Koroleva G, Courville AB, Mistry S, Burns A, Apps R, Hall KD , Belkaid Y",Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans,Nature medicine,2024,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants on vegan diet,Participants on ketogenic diet,"To determine the impact of dietary intervention on human immunity and microbiota, this group of participants were placed on a ketogenic diet, and would later be switched to a vegan diet.",10,10,NA,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig. 4e,10 March 2024,Johnpaul,"Johnpaul,Aleru Divine,Scholastica","Differentially abundant species between ketogenic and vegan diets for all significant taxa, showing the impact of a ketogenic diet on participants compared to a vegan diet.",increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neobittarella|s__Neobittarella massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] sulci",2|200940|3031449|213115|194924|35832|35833;2|976|200643|171549|1853231|574697|1472416;2|976|200643|171549|1853231|574697|544645;2|1239|526524|526525|128827|1472649|1034346;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|2719313|358743;2|1239|186801|186802|186806|1730|39490;2|1239|91061|186826|1300|1357|1358;2|1239|186801|186802|216572|2126544|2041842;2|976|200643|171549|1853231|283168|28118;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|815|909656|671267;2|976|200643|171549|815|909656|821;2|1239|186801|186802|543314|143393,Complete,Svetlana up
bsdb:920/1/2,Study 920,randomized controlled trial,38291301,10.1038/s41591-023-02761-2,https://pubmed.ncbi.nlm.nih.gov/38291301/,"Link VM, Subramanian P, Cheung F, Han KL, Stacy A, Chi L, Sellers BA, Koroleva G, Courville AB, Mistry S, Burns A, Apps R, Hall KD , Belkaid Y",Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans,Nature medicine,2024,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants on vegan diet,Participants on ketogenic diet,"To determine the impact of dietary intervention on human immunity and microbiota, this group of participants were placed on a ketogenic diet, and would later be switched to a vegan diet.",10,10,NA,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig. 4e,10 March 2024,Johnpaul,"Johnpaul,Aleru Divine,Scholastica","Differentially abundant species between ketogenic and vegan diets for all significant taxa, showing the impact of a ketogenic diet on participants compared to a vegan diet.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis|s__Anaerofustis stercorihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|s__Bacillota bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|3085642|2048137|1628085;2|1239|186801|186802|186806|264995|214853;2|1239|186801|3085636|186803|207244|649756;2|1239|1879010;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|1686;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511|1737424;2|1239|186801|186802|3085642|580596|2049021;2|1239|186801|186802|186806|1730|142586;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|3085636|186803|1898203;2|1239|186801|3085636|186803|841|301302;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263|41978;2|1239|186801|186802|216572|292632|2053618;2|1239|186801|3085636|186803|43996|43997;2|1239|186801|3085636|186803|572511|1955243,Complete,Svetlana up
bsdb:921/1/1,Study 921,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S, Li C, Wu X , Zhang T",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depressive disorder in the high bacteroidaceae enterotype (ET-B). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,45,84,None,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2C,9 March 2024,Idiat,"Idiat,Welile,Folakunmi",Primary gut microbiota in Healthy and Depression groups in high bacteroidaceae  enterotype (ET-B) using linear discriminant analysis (LDA) scores.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia|s__Pseudescherichia vulneris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Petroclostridium|s__Petroclostridium xylanilyticum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum",2|1224|1236|91347|543|2055880|566;2|1239|186801|186802|216572|2304687|1792311;2|1239|526524|526525|128827|1522,Complete,Folakunmi
bsdb:921/1/2,Study 921,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S, Li C, Wu X , Zhang T",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depressive disorder in the high bacteroidaceae enterotype (ET-B). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,45,84,None,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2C,9 March 2024,Idiat,"Idiat,Folakunmi,Aananditaa",Primary gut microbiota in Healthy and Depression groups in high bacteroidaceae enterotype (ET-B) using linear discriminant analysis (LDA) scores.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium hattorii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia maritimum",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|3085642|2048137|1628085;2|1239|186801|3085636|186803|43996|2799636;2|1224|1236|91347|543|561|208962;2|1239|186801|186802|186806|1730|290054;2|1239|526524|526525|2810280|2678885|1982626;2|1239|186801|186802|216572|216851|2935520;2|1239|186801|186802|204475|745368;2|1224|28216|80840|995019|577310|487175;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263|40519;2|1239|186801|3085636|186803|1506577|36835;2|1239|186801|3085636|186803|572511|2763028;2|1239|186801|3082720|186804|1501226|2020948,Complete,Folakunmi
bsdb:921/2/1,Study 921,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S, Li C, Wu X , Zhang T",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depression in the high lachnospiraceae enterotype (ET-L). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,47,127,None,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,figure 3D,19 March 2024,Folakunmi,Folakunmi,Primary gut microbiota in Healthy and DP groups at the species level in high lachnospiraceae enterotype (ET-L) using linear discriminant analysis (LDA) scores.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia provencensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea phocaeensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus senegalensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",2|1239|186801|3085636|186803|572511|1936059;2|1239|186801|3085636|186803|572511|89014;2|1239|91061|186826|1300|1301|1308;2|1239|186801|3085636|186803|2316020|33038;2|201174|1760|85004|31953|1678|216816;2|1239|186801|3085636|186803|572511|536633;2|201174|84998|84999|84107|102106|74426;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|3085636|186803|2719313|208479;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|189330|2040291;2|1239|186801|3085636|186803|2719313|1531;2|1239|526524|526525|128827|1522;2|1239|186801|3085636|186803|2316020|1720300;2|1239|186801|186802|3082771|1924093|1673717;2|1239|186801|3085636|3118652|2039240|2358141;2|1239|91061|186826|1300|1301|1318;2|1239|186801|186802|2211178|2211183;2|1239|186801|186802|216572|946234|292800,Complete,Folakunmi
bsdb:921/2/2,Study 921,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S, Li C, Wu X , Zhang T",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depression in the high lachnospiraceae enterotype (ET-L). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,47,127,None,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,figure 3D,19 March 2024,Folakunmi,"Folakunmi,Aananditaa",Primary gut microbiota in Healthy and DP groups at the species level in high lachnospiraceae enterotype (ET-L) using linear discriminant analysis (LDA) scores.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes faecalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides kribbi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia phocaeensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saudiense,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella porci,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium hattorii,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Gehongia|s__Gehongia tenuis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster hominis (ex Hitch et al. 2024),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Petroclostridium|s__Petroclostridium xylanilyticum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor gallinarum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Simiaoa|s__Simiaoa hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Vescimonas|s__Vescimonas coprocola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia maritimum",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|3085642|2048137|1628085;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|207244|2738446;2|976|200643|171549|815|816|1912894;2|976|200643|171549|815|816|820;2|201174|1760|85004|31953|1678|1686;2|1239|186801|3085636|186803|572511|2025493;2|1239|186801|3085636|186803|572511|1917888;2|1239|186801|186802|31979|1485|1414720;2|1239|909932|1843489|31977|39948|2161821;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|1432051|2652274;2|1224|1236|91347|543|561|208962;2|1239|186801|186802|186806|1730|290054;2|1239|526524|526525|2810280|2678885|1982626;2|1239|186801|186802|216572|216851|2935520;2|1239|186801|3082768|990719|2944147|2763655;2|1239|186801|186802|204475|745368;2|1224|1236|135625|712|724|729;2|1239|186801|186802|1392389|1673721;2|1239|186801|3085636|186803|2719313|1917870;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|28050|706562;2|1239|186801|186802|216572|1930587|1852369;2|1239|186801|3085636|186803|2316020|592978;2|1224|28216|80840|995019|577310|487175;2|1239|186801|186802|216572|2304687|1792311;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|815|909656|204516;2|976|200643|171549|815|909656|821;2|1239|186801|186802|216572|1017280|2779352;2|1239|186801|3085636|186803|841|301301;2|1239|186801|3085636|186803|841|360807;2|1239|186801|186802|216572|1263|40518;2|976|200643|171549|171552|2974251|2518605;2|1239|186801|3085636|186803|2944193|2763665;2|1239|91061|186826|1300|1301|2490633;2|1239|91061|186826|1300|1301|1304;2|1239|186801|186802|216572|2892396|2714355;2|1239|186801|3085636|186803|572511|2763028;2|1239|186801|3082720|186804|1501226|2020948,Complete,Folakunmi
bsdb:921/3/NA,Study 921,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S, Li C, Wu X , Zhang T",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depressive disorder in the high prevotellaceae enterotype (ET-P). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,15,15,None,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:922/1/1,Study 922,case-control,31561385,https://doi.org/10.3233%2FJPD-191693,NA,"Vidal-Martinez G, Chin B, Camarillo C, Herrera GV, Yang B, Sarosiek I , Perez RG","A Pilot Microbiota Study in Parkinson's Disease Patients versus Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in Parkinsonian and Multiple System Atrophy Mouse Models",Journal of Parkinson's disease,2020,"FTY720, FTY720-Mitoxy, Microbiota, Parkinson’s disease, multiple system atrophy, transgenic mouse models",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson’s disease,Patients diagnosed with Parkinson’s disease (confirmed by a neurologist) between 35 and 95 years of age.,13,9,Participants who used antibiotics within 2 weeks prior to the initiation of the study.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1 (Column A),8 March 2024,Flo,"Flo,Scholastica",Relative abundance of gut microbial taxa in pilot studies of human PD.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|203557,Complete,Chloe
bsdb:922/2/1,Study 922,case-control,31561385,https://doi.org/10.3233%2FJPD-191693,NA,"Vidal-Martinez G, Chin B, Camarillo C, Herrera GV, Yang B, Sarosiek I , Perez RG","A Pilot Microbiota Study in Parkinson's Disease Patients versus Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in Parkinsonian and Multiple System Atrophy Mouse Models",Journal of Parkinson's disease,2020,"FTY720, FTY720-Mitoxy, Microbiota, Parkinson’s disease, multiple system atrophy, transgenic mouse models",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Wild Type mice,Parkinsonian mice,10-month old transgenic (Tg) parkinsonian mice that expresses A53T mutant human alpha-synuclein (a-Syn) in neurons,2,5,None,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1 (column B),8 March 2024,Flo,"Flo,Scholastica",Relative abundance of relevant taxa in Wild Type compared to Parkinsonian mice,increased,k__Bacteria|p__Bacillota,2|1239,Complete,Chloe
bsdb:923/1/1,Study 923,laboratory experiment,37529095,10.55730/1300-0152.2617,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388120/,"Fan T, Li X, Zhang X, Zhang J, Sun L, Chen J , Fu C",Influence of aerobic exercise training on mice gut microbiota in Parkinson's disease,Turkish journal of biology = Turk biyoloji dergisi,2022,"16S rRNA gene sequencing, Parkinson’s disease, aerobic exercise training, gut microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to exercise,EFO:0007768,Sham group and parkison's disease (PD) group,Aerobic exercise training group (AET),"Mice group that received grasping, rotating, walking and balance training exercises once a day, 6 days a week, 30 min each time, a total of 4 weeks.",10,5,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,9 March 2024,EGO,"EGO,Welile,Folakunmi","Discriminative taxon in sham, PD, and AET groups by linear discriminant analysis (LDA) integrated with effect size (LEfSe)",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Rhodobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|1385|186817|400634;2|1224|28216|80840|2975441|93681;2|1239|91061|1385|186818;2|1239|186801|186802|216572|216851;2|1224|28211|204455|31989|1060;2|976|200643|171549|171552|838|159272,Complete,Folakunmi
bsdb:923/2/1,Study 923,laboratory experiment,37529095,10.55730/1300-0152.2617,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388120/,"Fan T, Li X, Zhang X, Zhang J, Sun L, Chen J , Fu C",Influence of aerobic exercise training on mice gut microbiota in Parkinson's disease,Turkish journal of biology = Turk biyoloji dergisi,2022,"16S rRNA gene sequencing, Parkinson’s disease, aerobic exercise training, gut microbiota",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to exercise,EFO:0007768,Sham group and Aerobic exercise training group (AET) group,parkison's disease (PD) group,"Mice group that were administered intraperitoneally with 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP) at 30 mg/kg for 7 days to construct PD mouse models.",10,5,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,1 April 2024,Folakunmi,Folakunmi,"Discriminative taxon in sham, PD, and AET groups by linear discriminant analysis (LDA) integrated with effect size (LEfSe)",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Thermomonosporaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus",2|1239|526524|526525|128827|1937008;2|201174|1760|85012|2012;2|1239|526524|526525|128827|1937007;2|28221;2|201174|84998|1643822|1643826|580024,Complete,Folakunmi
bsdb:923/3/1,Study 923,laboratory experiment,37529095,10.55730/1300-0152.2617,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388120/,"Fan T, Li X, Zhang X, Zhang J, Sun L, Chen J , Fu C",Influence of aerobic exercise training on mice gut microbiota in Parkinson's disease,Turkish journal of biology = Turk biyoloji dergisi,2022,"16S rRNA gene sequencing, Parkinson’s disease, aerobic exercise training, gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to exercise,EFO:0007768,Aerobic exercise training group (AET) and parkison's disease (PD) group,Sham group,group of mice that were injected intraperitoneally with equivalent volumes of normal saline for 7 days and did not receive any training,10,5,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,1 April 2024,Folakunmi,Folakunmi,"Discriminative taxon in sham, PD, and AET groups by linear discriminant analysis (LDA) integrated with effect size (LEfSe)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia",2|976|200643|171549;2|976|200643;2|1239|186801|3085636|186803;2|1239|91061|186826|186827;2|1239|186801|3085636|186803|297314;2|1224|28211|356|2831106|46913,Complete,Folakunmi
bsdb:924/1/1,Study 924,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D, Cerroni R, Unida V, Farcomeni A, Pierantozzi M, Mercuri NB, Biocca S, Stefani A , Desideri A",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (PD),"Patients with severe and active Parkinson disease.
Recruited patients had a diagnosis of idiopathic PD according to the UK Parkinson's Disease Society Brain Bank criteria with a disease duration (measured as the time following the first diagnosis) longer than 6 months",72,80,4 weeks,16S,34,Illumina,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary Table S7A,8 March 2024,Mojisayo Awolesi,"Mojisayo Awolesi,Welile,Fiddyhamma,Scholastica",Significantly abundant bacterial families and genera in Parkinson's disease versus healthy controls (HC) detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543|544;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826|1300|1357;2|1224|1236|91347|543|590;2|1224|1236|91347|543|620;2|1224|1236|91347|543,Complete,Svetlana up
bsdb:924/1/2,Study 924,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D, Cerroni R, Unida V, Farcomeni A, Pierantozzi M, Mercuri NB, Biocca S, Stefani A , Desideri A",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (PD),"Patients with severe and active Parkinson disease.
Recruited patients had a diagnosis of idiopathic PD according to the UK Parkinson's Disease Society Brain Bank criteria with a disease duration (measured as the time following the first diagnosis) longer than 6 months",72,80,4 weeks,16S,34,Illumina,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Supplementary Table S7A,8 March 2024,Mojisayo Awolesi,"Mojisayo Awolesi,Welile,Fiddyhamma,Scholastica",Significantly abundant bacterial families and genera in Parkinson's disease versus healthy controls (HC) detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:924/2/1,Study 924,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D, Cerroni R, Unida V, Farcomeni A, Pierantozzi M, Mercuri NB, Biocca S, Stefani A , Desideri A",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (excluding iCOMT users),Patients with Parkinson's disease (PD) excluding eight patients taking catechol-O-methyl transferase (COMT) inhibitors,72,72,4 weeks,16S,34,Illumina,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S7B,12 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica",Significantly abundant bacterial families and genera in Parkinson's disease (excluding iCOMT users) versus healthy controls detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543,Complete,Svetlana up
bsdb:924/2/2,Study 924,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D, Cerroni R, Unida V, Farcomeni A, Pierantozzi M, Mercuri NB, Biocca S, Stefani A , Desideri A",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (excluding iCOMT users),Patients with Parkinson's disease (PD) excluding eight patients taking catechol-O-methyl transferase (COMT) inhibitors,72,72,4 weeks,16S,34,Illumina,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S7B,12 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica",Significantly abundant bacterial families and genera in Parkinson's disease (excluding iCOMT users) versus healthy controls detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:925/1/1,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 1,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Jejunal samples from rats treated for 14 sequential days with dopamine (D),6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,9 March 2024,Adeitan,"Adeitan,Scholastica",Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans",2|1239|91061|186826|81852|1350;2|1224|1236|91347|1903409|53335|549,Complete,Svetlana up
bsdb:925/1/2,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 1,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Jejunal samples from rats treated for 14 sequential days with dopamine (D),6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,9 March 2024,Adeitan,"Adeitan,Welile,Scholastica",Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter cholecystus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium",2|1239|186801|3085636|186803|572511;2|1239|526524|526525|128827;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293|209|45498;2|1239|526524|526525|128827|1937007;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|877420;2|976|200643|171549|2005473;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552;2|976|200643|171549|194843;2|201174|84998|84999|349920,Complete,Svetlana up
bsdb:925/2/1,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 2,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Jejunal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Table S1,7 April 2024,Scholastica,Scholastica,"Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Ectobacillus|s__Ectobacillus funiculus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Intrasporangium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Neobacillus|s__Neobacillus drentensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia aryabhattai,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Rummeliibacillus,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|s__uncultured Alphaproteobacteria bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Frankiales|s__uncultured Frankiales bacterium",2|1224|28211|356|41294|374|29448;2|1239|91061|1385|186817|2837502|137993;2|201174|1760|85006|85021|53357;2|1239|91061|1385|186817|400634;2|201174|1760|85006|85023|33882;2|201174|1760|85006|1268;2|201174|1760|85007|1762|1763;2|1239|91061|1385|186817|2675232|220684;2|1224|1236|91347|1903409|53335|549;2|1239|91061|1385|186817|2800373|412384;2|1224|28216|80840|75682|1522432;2|1239|91061|1385|186818|648802;2|201174|1497346|588673|320599|207599;2|201174|1760|85011|2062|1883;2|1239|91061|1385|186823|432330;2|1224|28211|91750;2|201174|1760|85013|2735681,Complete,Svetlana up
bsdb:925/2/2,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 2,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Jejunal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,Supplementary Table S1,8 April 2024,Scholastica,Scholastica,"Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter cholecystus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas paucimobilis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sp. LA61,s__gut metagenome,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__uncultured Desulfovibrionaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|s__uncultured Rhizobiaceae bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|1239|526524|526525|128827|1472649;2|1239|526524|526525|128827;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293|209|45498;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|877420;2|1239|91061|186826;2|976|200643|171549|2005473;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552;2|1239|186801|3082720|186804|1501226;2|1224|28211|204457|41297|13687|13689;2|1239|526524|526525|2810281|191303|1197429;749906;2|976|200643|171549|194843;2|200940|3031449|213115|194924|194926;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003;2|1224|28211|356|82115|271151,Complete,Svetlana up
bsdb:925/3/1,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 3,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Ropinirole treatment group (R),"Jejunal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)",6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Table S1,8 April 2024,Scholastica,Scholastica,"Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|85831;2|201174|84998|1643822|1643826|580024;2|1239|526524|526525|128827;2|29547|3031852|213849|72293|209;2|976|200643|171549|2005473;2|976|200643|171549|815|909656|821;2|976|200643|171549|194843;2|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:925/4/1,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 4,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Ileal samples from rats treated for 14 sequential days with dopamine (D),6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,8 April 2024,Scholastica,Scholastica,Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG_194_44_15,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__uncultured prokaryote",2|1239|526524|526525|128827|174708;2|1239|1897037;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|877420;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;198431,Complete,Svetlana up
bsdb:925/4/2,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 4,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Ileal samples from rats treated for 14 sequential days with dopamine (D),6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,8 April 2024,Scholastica,Scholastica,Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 615,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|s__uncultured Desulfovibrionales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|3085636|186803|31980;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|200940|3031449|213115|194924|872;2|1239|526524|526525|128827|1937008|1862672;2|201174|84998|1643822|1643826|580024;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1156038;2|1239|186801|3085636|186803|397290;2|1239|186801|3085636|186803|1235793;2|1239|186801|3085636|186803|877420;2|976|200643|171549|2005473;2|976|200643|171549|2005473|1918540;2|1239|186801|186802|216572|459786;2|1224|28216|80840|995019|577310;2|976|200643|171549|815|909656|671267;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841;2|976|200643|171549|194843;2|200940|3031449|213115|345727;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:925/5/1,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 5,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Ileal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,9 April 2024,Scholastica,Scholastica,"Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG_194_44_15,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,s__gut metagenome,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__uncultured Desulfovibrionaceae bacterium",2|1239|526524|526525|128827|174708;2|201174|1760|85004|31953|1678;2|1239|1897037;2|1239|526524|526525|128827|1937007;2|1239|186801|3085636|186803;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|3068309;2|1239|186801|3085636|186803|1506577;749906;2|200940|3031449|213115|194924|194926,Complete,Svetlana up
bsdb:925/5/2,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 5,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Ileal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,9 April 2024,Scholastica,Scholastica,"Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium sp. canine oral taxon 238,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 615,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|s__uncultured Desulfovibrionales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|s__uncultured Peptococcaceae bacterium",2|1239|186801|3085636|186803|31980;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|1224|1236|135615|868|2717|1151525;2|200940|3031449|213115|194924|872;2|1239|526524|526525|128827|1937008|1862672;2|201174|84998|1643822|1643826|580024;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1156038;2|1239|186801|3085636|186803|397290;2|1239|186801|3085636|186803|1235793;2|1239|186801|3085636|186803|877420;2|976|200643|171549|2005473;2|1239|186801|186802|216572|459786;2|1224|28216|80840|995019|577310;2|976|200643|171549|815|909656|671267;2|976|200643|171549|171550|28138;2|976|200643|171549|171550;2|976|200643|171549|194843;2|200940|3031449|213115|345727;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|186807|329911,Complete,Svetlana up
bsdb:925/6/1,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 6,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Ropinirole treatment group (R),"Ileal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)",6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,8 April 2024,Scholastica,Scholastica,"Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|s__uncultured Erysipelotrichia bacterium",2|1239|526524|526525|128827|174708;2|1239|526524|526525|128827|1937007;2|1239|91061|186826|33958|1578;2|1239|526524|666559,Complete,Svetlana up
bsdb:925/6/2,Study 925,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel SP, Bullock A, van Dijk G , El Aidy S",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 6,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Ropinirole treatment group (R),"Ileal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)",6,10,None,16S,34,Illumina,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,8 April 2024,Scholastica,Scholastica,"Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|186803|877420;2|976|200643|171549|2005473;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:926/1/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls (HC),Crohn’s disease (CD) patients,Patients with Crohn's disease,50,69,None.,WMS,NA,MGISEQ-2000,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. file: Table S5,8 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Aurantimicrobium|s__Aurantimicrobium minutum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. WP8,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella clarridgeiae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella tribocorum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Blattodea|f__Blattellidae|g__Blattella|s__Blattella germanica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia argi,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter porcelli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Johnevansia|s__Candidatus Johnevansia muelleri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Liberibacter|s__Candidatus Liberibacter americanus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Candidatus Midichloriaceae|g__Candidatus Midichloria|s__Candidatus Midichloria mitochondrii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|g__Candidatus Thioglobus|s__Candidatus Thioglobus autotrophicus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus mundtii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca|s__Jeotgalibaca dankookensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter sp. CP1,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. PYR15,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma|s__Mycoplasma wenyonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus acidilactici,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus marmotae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pluranimalium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus respiraculi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus|s__Synechococcus sp. KORDI-52,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus|s__Companilactobacillus zhachilii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium|s__Exiguobacterium sp. ZWU0009,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter werkmanii",2|201174|1760|2037|2049|1654|544580;2|201174|1760|2037|2049|1654|1852377;2|201174|1760|2037|2049|1654|712122;2|201174|1760|85006|85023|1705353|708131;2|1239|91061|1385|186817|1386|756828;2|1224|28211|356|772|773|56426;2|1224|28211|356|772|773|85701;2|201174|1760|85004|31953|1678|1685;2759|33208|6656|50557|85823|3046527|6972|6973;2|1239|186801|3085636|186803|572511|1912897;2|29547|3031852|213849|72294|194|1660073;2|1224|1236|135619|28256|1495768|1495769;2|1224|28211|356|82115|34019|309868;2|1224|28211|766|1328881|411566|234827;2|1224|1236|655184|1705394;2|1239|91061|186826|186828|2747|2751;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|186802|31979|1485|1492;2|1239|186801|186802|31979|1485|1502;2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|81852|1350|53345;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|81852|1350|160453;2|1239|91061|186826|81852|1350|53346;2|1239|526524|526525|128827|2049044;2|1224|1236|91347|543|561|208962;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|561|564;2|1224|1236|91347|543|561|1499973;2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|186828|1470540|708126;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|570|571;2|1239|91061|186826|33958|1578|33959;2|201174|84998|84999|1643824|2767353|1382;2|1224|1236|72274|2887365|2742|1671721;2|201174|1760|85007|1762|1763|2051552;2|544448|31969|2085|2092|2093|65123;2|1239|91061|186826|33958|1253|1254;2|1224|1236|91347|1903414|583|584;2|1224|1236|91347|543|590|28901;2|1239|91061|1385|90964|1279|1292;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|45634;2|1239|91061|186826|1300|1301|1334;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1338;2|1239|91061|186826|1300|1301|1825069;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|197614;2|1239|91061|186826|1300|1301|82348;2|1239|91061|186826|1300|1301|2021971;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1759399;2|1239|91061|186826|1300|1301|712633;2|1117|3028117|1890424|1890426|1129|585425;2|1239|186801|3085636|186803|1506553|1834196;2|1239|91061|186826|33958|2767879|2304606;2|1239|91061|1385|33986|1224749;2|1224|1236|91347|543|544|67827,Complete,ChiomaBlessing
bsdb:926/1/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls (HC),Crohn’s disease (CD) patients,Patients with Crohn's disease,50,69,None.,WMS,NA,MGISEQ-2000,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. file: Table S5,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to healthy controls (HC),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:926/2/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Ulcerative colitis (UC) patients,Patients with ulcerative colitis,50,198,None.,WMS,NA,MGISEQ-2000,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. file: Table S8,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus respiraculi,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia nimipressuralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus acidilactici",2|201174|1760|85006|1268|32207|43675;2|201174|1760|2037|2049|1654|1852377;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|45634;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|712633;2|1239|91061|186826|1300|1301|2021971;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1759399;2|1224|1236|91347|543|1330545|69220;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|33958|1253|1254,Complete,ChiomaBlessing
bsdb:926/2/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Ulcerative colitis (UC) patients,Patients with ulcerative colitis,50,198,None.,WMS,NA,MGISEQ-2000,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. file: Table S8,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. G11,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|s__Victivallales bacterium CCUG 44730,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp. ORS 278,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|976|200643|171549|171550|239759|328814;2|200940|3031449|213115|194924|872|631220;2|256845|1313211|278082|2094242;2|976|200643|171549|1853231|283168|28118;2|1224|28211|356|41294|374|114615;2|74201|203494|48461|1647988|239934|239935,Complete,ChiomaBlessing
bsdb:926/3/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis (UC) patients,Crohn's disease (CD) patients,Patients with Crohn's disease,198,69,None.,WMS,NA,MGISEQ-2000,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. file: Table S2,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to Ulcerative colitis (UC),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter werkmanii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium strain FGI 57",2|1224|1236|91347|543|544|67827;2|1224|1236|91347|543|561|208962;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|561|564;2|1224|1236|91347|543|561|1499973;2|1224|1236|91347|543|590|28901;2|1224|1236|91347|543|620|622;2|1224|1236|91347|543|620|623;2|1224|1236|91347|543|693444,Complete,ChiomaBlessing
bsdb:926/3/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis (UC) patients,Crohn's disease (CD) patients,Patients with Crohn's disease,198,69,None.,WMS,NA,MGISEQ-2000,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. file: Table S2,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to Ulcerative colitis (UC),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Alicycliphilus|s__Alicycliphilus denitrificans,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Archangiaceae|g__Stigmatella|s__Stigmatella aurantiaca",2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|28050|39485;2|1239|91061|186826|33958|2767887|1623;2|1224|28216|80840|80864|201096|179636;2|2818505|32015|29|39|40|41,Complete,ChiomaBlessing
bsdb:926/4/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Health controls (HC),Crohn's disease patients- Mild group,Patients with Crohn's disease in the mild group according to disease activity,50,49,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 2J,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- mild group compared to Healthy controls (HC),decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio aespoeensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",2|200940|3031449|213115|194924|2035811|182210;2|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:926/5/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Health controls (HC),Crohn's disease patients- Moderate group,Patients with Crohn's disease in the moderate group according to disease activity,50,19,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 2J,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- moderate group compared to Healthy controls (HC),decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio aespoeensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",2|200940|3031449|213115|194924|2035811|182210;2|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:926/5/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Health controls (HC),Crohn's disease patients- Moderate group,Patients with Crohn's disease in the moderate group according to disease activity,50,19,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 2J,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- moderate group compared to Healthy controls (HC),increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter|s__Polynucleobacter wuianus,2|1224|28216|80840|119060|44013|1743168,Complete,ChiomaBlessing
bsdb:926/6/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Health controls (HC),"Ulcerative colitis disease patients- Mild, moderate and severe groups","Patients with Ulcerative colitis disease in the mild, moderate and severe groups according to disease activity",50,NA,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3J,1 April 2024,ChiomaBlessing,ChiomaBlessing,"Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:926/6/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Health controls (HC),"Ulcerative colitis disease patients- Mild, moderate and severe groups","Patients with Ulcerative colitis disease in the mild, moderate and severe groups according to disease activity",50,NA,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3J,1 April 2024,ChiomaBlessing,ChiomaBlessing,"Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Candidatus Pantoea carbekii,2|1224|1236|91347|1903409|53335|1235990,Complete,ChiomaBlessing
bsdb:926/7/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3J,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group (Mann-Whitney and T-test),decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:926/7/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3J,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group (Mann-Whitney and T-test),increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Candidatus Pantoea carbekii,2|1224|1236|91347|1903409|53335|1235990,Complete,ChiomaBlessing
bsdb:926/8/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 8,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis disease patients- Moderate group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,25,11,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3J,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- moderate group,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,2|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:926/8/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 8,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis disease patients- Moderate group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,25,11,None.,WMS,NA,MGISEQ-2000,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3J,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- moderate group,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Candidatus Pantoea carbekii,2|1224|1236|91347|1903409|53335|1235990,Complete,ChiomaBlessing
bsdb:926/9/1,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 9,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,None.,WMS,NA,MGISEQ-2000,Linear Regression,0.01,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. Table S9,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group,decreased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfarculia|o__Desulfarculales|f__Desulfarculaceae|g__Desulfarculus|s__Desulfarculus baarsii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Denitrobacterium|s__Denitrobacterium detoxificans",2|200940|3031646|453227|453228|453229|453230;2|201174|84998|1643822|1643826|79603|79604,Complete,ChiomaBlessing
bsdb:926/9/2,Study 926,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS , Kim SY",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 9,South Korea,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,None.,WMS,NA,MGISEQ-2000,Linear Regression,0.01,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. Table S9,1 April 2024,ChiomaBlessing,ChiomaBlessing,Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. SJ-10,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Blattodea|f__Blattellidae|g__Blattella|s__Blattella germanica",2|1239|91061|1385|186817|1386|563169;2759|33208|6656|50557|85823|3046527|6972|6973,Complete,ChiomaBlessing
bsdb:927/1/1,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a,8 March 2024,Fiddyhamma,"Fiddyhamma,Welile,ChiomaBlessing",Differentially abundant genera in Behcet's disease subjects compared to healthy controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. HGB5,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:239,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:770,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila sp. 4_1_30,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. 4_8_47FAA,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. CAG:166,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:202,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:240,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp. CAG:815,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1728,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1745,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium VE202-24,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium cv2,k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|o__Crassvirales|s__uncultured crAssphage",2|976|200643|171549|171550|239759|1470347;2|976|200643|171549|171550|239759|908612;2|1224|28211|204441|2829815|191|1262705;2|976|200643|171549|815|816;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|1262751;2|200940|3031449|213115|194924|35832|693988;2|200940|3031449|213115|194924|35832|35833;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107|102106|742722;2|201174|84998|84999|84107|102106|1262850;2|1239|186801|186802|186806|1730|1262884;2|1239|1263013;2|1239|1262992;2|32066|203490|203491|203492|848|1262901;2|1239|909932|909929|1843491|52225|52226;2|1239|186801|186802|216572|459786|1226322;2|1239|186801|186802|216572|459786|1226323;2|1239|186801|186802|216572|1232459;2|976|200643|171549|171552|577309|454154;2|976|200643|171549|815|909656|387090;2|1239|186801|186802|216572|1627893;10239|2731360|2731618|2731619|1978007|1211417,Complete,ChiomaBlessing
bsdb:927/1/2,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,8 March 2024,Fiddyhamma,"Fiddyhamma,ChiomaBlessing",Differentially abundant genera in Behcet's disease subjects compared to healthy controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acidiphilium|s__Acidiphilium sp. CAG:727,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:268,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1024,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:127,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:349,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:813,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. CAG:782,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanomicrobiaceae|g__Methanoculleus|s__Methanoculleus sp. CAG:1088,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. CAG:314",2|1224|28211|204441|433|522|1262689;2|976|200643|171549|171550|239759|1262693;2|1239|186801|186802|216572|244127|1262700;2|1239|186801|186802|31979|1485|1262770;2|1239|186801|186802|31979|1485|1262774;2|1239|186801|186802|31979|1485|1262797;2|1239|186801|186802|31979|1485|1262843;2|1239|186801|3085636|186803|33042|1262863;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|186806|1730|1262889;2|32066|203490|203491|203492|848|850;2|1239|909932|1843489|31977|906|907;2157|28890|224756|2191|2194|45989|1262903;2157|2283796|183967|1235850|2517203|1291539|1291540;2|508458|649775|649776|3029088|638847|638849;2|1239|186801|186802|216572|292632|1262970,Complete,ChiomaBlessing
bsdb:927/2/1,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,Patients with Behcet's disease (case-control),43,15,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Figure S2, Supplementary Table S8",8 March 2024,Fiddyhamma,"Fiddyhamma,ChiomaBlessing",Differences in altered oral microbial composition in Behcet's disease (BD) patients compared to healthy controls,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|1239|526524|526525|128827|174708;2|201174|1760|85004|31953|419014;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|830;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924|872;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|201174|1760|2037|2049|2050;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|196081;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|976|200643|171549|171552|577309,Complete,ChiomaBlessing
bsdb:927/2/2,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,Patients with Behcet's disease (case-control),43,15,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary Figure S2, Supplementary Table S8",12 March 2024,Fiddyhamma,"Fiddyhamma,Omojokunoluwatomisin,ChiomaBlessing",Differences in altered oral microbial composition in Behcet's disease (BD) patients compared to healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota",2|1224|28216;2|1224|28216|206351|481;2|1224|28216|206351;2|1224,Complete,ChiomaBlessing
bsdb:927/3/1,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control feces treated group,Behcet's disease (BD) feces treated group,B10RIII mice (mice undergoing autoimmune uveitis) colonized with untreated BD patients stool samples (experimental),4,4,None,NA,NA,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplementary Figure S1c, Supplementary Table S9",8 March 2024,Fiddyhamma,"Fiddyhamma,ChiomaBlessing",Abundance of altered genera	in Behcet's disease (BD) patients’ feces treated group compared to healthy control feces treated mice,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|1239|186801|186802|216572|52784;2|200940|3031449|213115|194924|35832;2|976|200643|171549|1853231|574697;2|976|200643|171549|2005519|1348911;2|200930|68337|191393|2945020|248038;2|976|200643|171549|171552|577309,Complete,ChiomaBlessing
bsdb:927/3/2,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control feces treated group,Behcet's disease (BD) feces treated group,B10RIII mice (mice undergoing autoimmune uveitis) colonized with untreated BD patients stool samples (experimental),4,4,None,NA,NA,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Supplementary Figure S1c, Supplementary Table S9",8 March 2024,Fiddyhamma,"Fiddyhamma,ChiomaBlessing",Abundance of altered genera	in Behcet's disease (BD) patients’ feces treated group compared to healthy control feces treated mice,decreased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,2|201174|84998|84999|84107|102106,Complete,ChiomaBlessing
bsdb:927/4/1,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S3,29 March 2024,ChiomaBlessing,ChiomaBlessing,Enriched/ depleted species in Behcet's disease subjects compared to healthy controls,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Atkinsonella|s__Atkinsonella texensis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Epichloe|s__Epichloe aotearoae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Macrophomina|s__Macrophomina phaseolina,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp. Leaf70,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe|s__Diaporthe ampelina,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum higginsianum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Orbiliomycetes|o__Orbiliales|f__Orbiliaceae|g__Drechslerella|s__Drechslerella stenobrocha,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma parareesei,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Cladophialophora|s__Cladophialophora psammophila,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum orbiculare,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas rhizophila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ph3,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Claviceps|s__Claviceps paspali,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium argentoratense,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Exophiala|s__Exophiala mesophila,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Ogataea|s__Ogataea methanolica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Shiraiaceae|g__Shiraia|s__Shiraia sp. slf14,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora|s__Neurospora crassa",2759|4751|4890|147550|5125|34397|40612|51582;2759|4751|4890|147550|5125|34397|5112|170559;2759|4751|4890|147541|451869|45131|35724|35725;2|1224|1236|135614|32033|40323|1736233;2759|4751|4890|147550|5114|767018|36922|1214573;2759|4751|4890|147550|1028384|681950|5455|80884;2759|4751|4890|189478|189479|47021|314126|314127;2759|4751|4890|147550|5125|5129|5543|858221;2759|4751|4890|147545|34395|43219|82105|1182553;2759|4751|4890|147550|1028384|681950|5455|5465;2|1224|1236|135614|32033|40323|216778;2|201174|1760|2037|2049|1654|1118058;2759|4751|4890|3239874|2916678|766764|5475|5480;2759|4751|4890|147550|5125|34397|5110|40601;2|201174|1760|85007|1653|1716|42817;2759|4751|4890|147545|34395|43219|5583|212818;2759|4751|4890|3239874|3243775|1156497|461281|1156966;2|201174|1760|2037|2049|1654|55565;2|1224|1236|135614|32033|40323|40324;2759|4751|4890|147541|92860|224418|224419|665115;2759|4751|4890|147550|5139|5148|5140|5141,Complete,ChiomaBlessing
bsdb:927/4/2,Study 927,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6,"Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N , Yang P",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S3,29 March 2024,ChiomaBlessing,ChiomaBlessing,Enriched/ depleted species in Behcet's disease subjects compared to healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. CAG:196,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Epichloe|s__Epichloe glyceriae",2|1224|1236|2887326|468|469|1262690;2759|4751|4890|147550|5125|34397|5112|79591,Complete,ChiomaBlessing
bsdb:928/1/1,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy controls,Chronic granulomatous disease,Patients with Chronic granulomatous disease and only receiving prophylactic antimicrobials and without a history of inflammatory bowel disease at the time of stool collection,16,17,Recent treatment with nonprophylactic antibiotics (acute antibiotics),16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,"antibiotic,antimicrobial agent,inflammatory bowel disease",NA,decreased,decreased,NA,NA,NA,Signature 1,Fig 2,14 March 2024,Ifyohondu,Ifyohondu,Difference between the intestinal microbiome of patients with Chronic granulomatous disease and healthy controls by LEfSe.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,k__Bacteria|s__uncultured bacterium",2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|1769710;2|1239|526524|526525|2810280|3025755;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803|841|512314;2|77133,Complete,Folakunmi
bsdb:928/1/2,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy controls,Chronic granulomatous disease,Patients with Chronic granulomatous disease and only receiving prophylactic antimicrobials and without a history of inflammatory bowel disease at the time of stool collection,16,17,Recent treatment with nonprophylactic antibiotics (acute antibiotics),16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,"antibiotic,antimicrobial agent,inflammatory bowel disease",NA,decreased,decreased,NA,NA,NA,Signature 2,Fig 2,14 March 2024,Ifyohondu,"Ifyohondu,Folakunmi",Difference between the intestinal microbiome of patients with Chronic granulomatous disease and healthy controls by LEfSe .,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__uncultured Lachnospira sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|3085642|580596|2049021;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|1392389|1297617;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|841|301301;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|128827|331630;2|1239|186801|186802|186806|1730|165185;2|1239|186801|3085636|186803|28050|446043;2|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:928/2/1,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy individuals,Chronic granulomatous disease (CGD) patients,CGD patients without a history of IBD and only receiving prophylactic antimicrobials,17,16,N/A,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Fig. 2G,6 May 2024,ChiomaBlessing,ChiomaBlessing,Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,k__Bacteria|s__uncultured bacterium",2|1239|186801|3085636|186803|841|512314;2|77133,Complete,ChiomaBlessing
bsdb:928/2/2,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy individuals,Chronic granulomatous disease (CGD) patients,CGD patients without a history of IBD and only receiving prophylactic antimicrobials,17,16,N/A,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Fig. 2G,6 May 2024,ChiomaBlessing,ChiomaBlessing,Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis",2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|28050|39485;2|77133;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|1392389|1297617;2|1239|186801|3085636|186803|841|301301,Complete,ChiomaBlessing
bsdb:928/2/3,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy individuals,Chronic granulomatous disease (CGD) patients,CGD patients without a history of IBD and only receiving prophylactic antimicrobials,17,16,N/A,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 3,Fig. 2G,6 May 2024,ChiomaBlessing,ChiomaBlessing,Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,k__Bacteria|s__uncultured bacterium",2|1239|186801|3085636|186803|841|512314;2|77133,Complete,ChiomaBlessing
bsdb:928/4/1,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 4,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD without IBD),NIHCC Cohort (CGD without IBD),Patients with Chronic granulomatous disease (CGD) without a history of Inflammatory bowel disease (IBD) and not receiving any medications other than prophylactic antimicrobials.,23,16,Recent treatment with nonprophylactic antibiotics (acute antibiotics),16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig. 3C,18 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing",Comparison of microbiome signatures between patients with CGD (without a history of IBD) from NIHCC VS PIDTC cohorts using LEfSe,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:928/4/2,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 4,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD without IBD),NIHCC Cohort (CGD without IBD),Patients with Chronic granulomatous disease (CGD) without a history of Inflammatory bowel disease (IBD) and not receiving any medications other than prophylactic antimicrobials.,23,16,Recent treatment with nonprophylactic antibiotics (acute antibiotics),16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig. 3C,18 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing",Comparison of microbiome signatures between patients with CGD (without a history of IBD) from NIHCC VS PIDTC cohorts using LEfSe,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|877420;2|1239|186801|3085656|3085657|2039302;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|1769710;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:928/5/1,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 5,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD Patients),NIHCC Cohort (CGD Patients),Patients with Chronic granulomatous disease (CGD) regardless of IBD status or antimicrobial use,36,79,Recent treatment with non prophylactic antibiotics (acute antibiotics),16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig E4C,19 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing",Comparison of microbiome signatures between patients with CGD (regardless of IBD status) from NIHCC VS PIDTC cohorts using LEfSe,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|3085642|580596;2|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:928/5/2,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 5,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD Patients),NIHCC Cohort (CGD Patients),Patients with Chronic granulomatous disease (CGD) regardless of IBD status or antimicrobial use,36,79,Recent treatment with non prophylactic antibiotics (acute antibiotics),16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig E4C,19 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing",Comparison of microbiome signatures between patients with CGD (regardless of IBD status) from NIHCC VS PIDTC cohorts using LEfSe,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|3085636|186803|1766253;2|1239|186801|186802|1671661;2|1239|186801|3085636|186803|2005359|290055;2|1239|186801|3085636|186803|877420;2|1239|186801|3085656|3085657|2039302;2|1239|186801|3085636|186803|437755;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|1769710;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:928/6/1,Study 928,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM , Falcone EL",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 6,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,CGD patients less than or equal to 12 years,CGD patients above 12 years,CGD patients above 12 years old with no active IBD or history of IBD,26,12,Recent treatment with non prophylactic antibiotics (acute antibiotics),16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig E5D,19 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing",Effect of age on microbiome signatures in CGD patients (with no active IBD or history of IBD) comparing participants less than or equal to 12 years VS above 12 years using LEfSe,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|976|200643|171549|171550|239759;2|200940|3031449|213115|194924|35832;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|877420;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|1769710;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:929/1/1,Study 929,"laboratory experiment,time series / longitudinal observational",35017199,10.1136/gutjnl-2021-326269,NA,"Chen C, Liao J, Xia Y, Liu X, Jones R, Haran J, McCormick B, Sampson TR, Alam A , Ye K",Gut microbiota regulate Alzheimer's disease pathologies and cognitive disorders via PUFA-associated neuroinflammation,Gut,2022,brain/gut interaction,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy control FMT mice,Alzheimer's disease FMT mice,ex germ-free mice inoculated with fecal samples from human Alzheimer's disease donors,3,3,human donors had no antimicrobial exposure within the preceding 4 weeks,16S,4,Illumina,ANOVA,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,9 March 2024,Graycepaul,"Graycepaul,Welile,Folakunmi","Microbiome analysis in humanised ex-germ-free 3xTg mouse stool, revealing the significant abundance in the faeces from human AD fecal inoculated germ-free mice and faeces from healthy human inoculated germ-free mice",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens",2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|371601,Complete,Folakunmi
bsdb:929/1/2,Study 929,"laboratory experiment,time series / longitudinal observational",35017199,10.1136/gutjnl-2021-326269,NA,"Chen C, Liao J, Xia Y, Liu X, Jones R, Haran J, McCormick B, Sampson TR, Alam A , Ye K",Gut microbiota regulate Alzheimer's disease pathologies and cognitive disorders via PUFA-associated neuroinflammation,Gut,2022,brain/gut interaction,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy control FMT mice,Alzheimer's disease FMT mice,ex germ-free mice inoculated with fecal samples from human Alzheimer's disease donors,3,3,human donors had no antimicrobial exposure within the preceding 4 weeks,16S,4,Illumina,ANOVA,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,9 March 2024,Graycepaul,"Graycepaul,Welile,Muqtadirat,Folakunmi","Microbiome analysis in humanised ex-germ-free 3xTg mouse stool, revealing the significant abundance in the faeces from human AD fecal inoculated germ-free mice and faeces from healthy human inoculated germ-free mice",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii",2|1239|186801|3085636|186803|2719313|208479;2|976|200643|171549|2005525|375288|328812,Complete,Folakunmi
bsdb:930/1/1,Study 930,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H, Ji Y, Yin C, Deng M, Tang T, Deng B, Ren W, Deng J, Yin Y , Tan C",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,High litter performance sows at G109,Low litter performance sows at G109,Low litter performance sows group at day 109 of gestation,10,10,None,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 1,Figure 4B,14 April 2024,Scholastica,Scholastica,Differences in fecal microbiota in day 109 of gestation of high litter performance sows compared to day 109 of gestation of low litter performance sows,increased,"k__Bacteria|p__Candidatus Electryoneota|c__Candidatus Tariuqbacteria|o__Candidatus Tariuqbacterales,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|3031806|3075765|3075766;2|1117;2|1239|909932|1843488|909930|33024;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:930/1/2,Study 930,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H, Ji Y, Yin C, Deng M, Tang T, Deng B, Ren W, Deng J, Yin Y , Tan C",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,High litter performance sows at G109,Low litter performance sows at G109,Low litter performance sows group at day 109 of gestation,10,10,None,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 2,Figure 4B,14 April 2024,Scholastica,Scholastica,Differences in fecal microbiota in day 109 of gestation of high litter performance sows compared to day 109 of gestation of low litter performance sows,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:930/2/1,Study 930,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H, Ji Y, Yin C, Deng M, Tang T, Deng B, Ren W, Deng J, Yin Y , Tan C",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,High litter performance sows at L21,Low litter performance sows at L21,Low litter performance sows group at day 21 of lactation (L21),10,10,None,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 1,Figure 4E,15 April 2024,Scholastica,Scholastica,Differences in fecal microbiota in day 21 of lactation of high litter performance sows compared to day 21 of lactation of low litter performance sows,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801;2|1239|186801|186802,Complete,Svetlana up
bsdb:930/2/2,Study 930,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H, Ji Y, Yin C, Deng M, Tang T, Deng B, Ren W, Deng J, Yin Y , Tan C",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,High litter performance sows at L21,Low litter performance sows at L21,Low litter performance sows group at day 21 of lactation (L21),10,10,None,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 2,Figure 4E,15 April 2024,Scholastica,Scholastica,Differences in fecal microbiota in day 21 of lactation of high litter performance sows compared to day 21 of lactation of low litter performance sows,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes",2|1239|186801|3085636|186803|33042;2|544448|31969;2|544448;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|544448|31969,Complete,Svetlana up
bsdb:930/3/1,Study 930,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H, Ji Y, Yin C, Deng M, Tang T, Deng B, Ren W, Deng J, Yin Y , Tan C",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 3,China,Sus scrofa domesticus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Day 109 of gestation (G109) of H group,Day 21 of lactation (L21) of H group,Day 21 of lactation (L21) of high litter performance sows group,10,10,None,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4H,14 April 2024,Scholastica,Scholastica,Differences in fecal microbiota in day 109 of gestation (G109) compared to day 21 of lactation (L21) of high litter performance sows,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",2|1239|91061|186826|33958;2|544448|31969;2|544448;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239|186801|186802|216572|1263;2|1239|186801|3082720|3030910|86331,Complete,Svetlana up
bsdb:930/3/2,Study 930,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H, Ji Y, Yin C, Deng M, Tang T, Deng B, Ren W, Deng J, Yin Y , Tan C",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 3,China,Sus scrofa domesticus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Day 109 of gestation (G109) of H group,Day 21 of lactation (L21) of H group,Day 21 of lactation (L21) of high litter performance sows group,10,10,None,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4H,14 April 2024,Scholastica,Scholastica,Differences in fecal microbiota in day 109 of gestation (G109) compared to day 21 of lactation (L21) of high litter performance sows,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Propionicimonas,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",2|1224|1236|135624;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|1236;2|201174|1760|85009|85015;2|201174|1760|85009|85015|236052;2|1224;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|201174|84998|84999|84107;2|29547|3031852|213849|72293,Complete,Svetlana up
bsdb:930/4/1,Study 930,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H, Ji Y, Yin C, Deng M, Tang T, Deng B, Ren W, Deng J, Yin Y , Tan C",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 4,China,Sus scrofa domesticus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Day 109 of gestation (G109) of L group,Day 21 of lactation (L21) of L group,Day 21 of lactation (L21) of low litter performance sows group,10,10,None,16S,34,Illumina,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4K,14 April 2024,Scholastica,Scholastica,Differences in fecal microbiota in day 109 of gestation (G109) compared to day 21 of lactation (L21) of low litter performance sows,decreased,"k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Propionicimonas,k__Bacteria|p__Pseudomonadota,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1117;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|1239|186801|3085636|186803;2|201174|1760|85009|85015;2|1239|909932|1843488|909930|33024;2|201174|1760|85009|85015|236052;2|1224;2759|33090|35493;2|1239|909932|1843489|31977;2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:931/1/1,Study 931,"cross-sectional observational, not case-control",37460569,https://doi.org/10.1038/s41531-023-00554-5,NA,"Huang P, Zhang P, Du J, Gao C, Liu J, Tan Y , Chen S",Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson's disease,NPJ Parkinson's disease,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Essential tremor,EFO:0003108,Healthy Control,Essential Tremor,"Participants face an action tremor of the upper limbs, possibly with the involvement of other parts of the body, such as the head, vocal cords, and lower limbs. Not only motor symptoms but also some nonmotor features, including gastrointestinal disorders, were experienced by them.",35,37,One month,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S5",19 March 2024,Nityasinghal 14,"Nityasinghal 14,Svetlana up",Exploration of discriminant gut microbiota using LEfSE analysis and the genus level of the relative abundance data was selected for further study.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,2|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:931/1/2,Study 931,"cross-sectional observational, not case-control",37460569,https://doi.org/10.1038/s41531-023-00554-5,NA,"Huang P, Zhang P, Du J, Gao C, Liu J, Tan Y , Chen S",Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson's disease,NPJ Parkinson's disease,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Essential tremor,EFO:0003108,Healthy Control,Essential Tremor,"Participants face an action tremor of the upper limbs, possibly with the involvement of other parts of the body, such as the head, vocal cords, and lower limbs. Not only motor symptoms but also some nonmotor features, including gastrointestinal disorders, were experienced by them.",35,37,One month,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Table S5",19 March 2024,Nityasinghal 14,"Nityasinghal 14,Svetlana up","Exploration of discriminant gut microbiota using LEfSE analysis, and the genus level of the relative abundance data was selected for further study.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella",2|1239|186801|186802|31979|49082;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|216572|216851;2|1239|186801|186802|404402;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|160674,Complete,Svetlana up
bsdb:931/2/2,Study 931,"cross-sectional observational, not case-control",37460569,https://doi.org/10.1038/s41531-023-00554-5,NA,"Huang P, Zhang P, Du J, Gao C, Liu J, Tan Y , Chen S",Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson's disease,NPJ Parkinson's disease,2023,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Essential tremor,EFO:0003108,Parkinson's Disease,Essential Tremor,"Participants face an action tremor of the upper limbs, possibly with the involvement of other parts of the body, such as the head, vocal cords, and lower limbs. Not only motor symptoms but also some nonmotor features, including gastrointestinal disorders, were experienced by them.",37,37,One month,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Table S5",19 March 2024,Nityasinghal 14,"Nityasinghal 14,Svetlana up",Examination of the fecal levels of SCFAs and linkage to changes in gut microbiota and symptom severity.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,2|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:932/1/1,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 1,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD),Elective Cesarean Section (ECS),Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure 2 c.,11 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter braakii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii complex sp. CFNIH9,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. E20,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897",2|201174|1760|2037|2049|1654|544580;2|201174|1760|85004|31953|1678|1689;2|1224|1236|91347|543|544|57706;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1502;2|1224|1236|135614|32033|40323|40324;2|1224|1236|91347|543|544|2077149;2|1224|1236|91347|543|547|1560339;2|201174|1760|2037|2049|1654|712122;2|201174|1760|2037|2049|1654|2081702,Complete,Folakunmi
bsdb:932/1/2,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 1,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD),Elective Cesarean Section (ECS),Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Figure 2 c.,17 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",2|976|200643|171549|171550|239759|328814;2|976|200643|171549;2|976|200643|171549|815|816|290053;2|976|200643|171549|815|816|28113;2|976|200643|171549|815|816|28116;2|976|200643;2|201174|1760|85004|31953|1678|28026;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|2161821;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|823,Complete,Folakunmi
bsdb:932/2/1,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 2,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 0,Elective Cesarean Section (ECS) at Day 0,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 A.,11 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1239|186801;2|1239|186801|186802,Complete,Folakunmi
bsdb:932/2/2,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 2,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 0,Elective Cesarean Section (ECS) at Day 0,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 A.,17 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum populi",2|1224|28211|356|119045|2282523;2|1224|28211|356|119045|2282523|223967,Complete,Folakunmi
bsdb:932/3/1,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 3,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 15,Elective Cesarean Section (ECS) at Day 15,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 B.,11 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium actinocoloniiforme",2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|1678|1689;2|201174|1760|2037|2049|1654|544580;2|201174|1760|2037|2049|1654|2081702;2|201174|1760|85004|31953|1678|638619,Complete,Folakunmi
bsdb:932/3/2,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 3,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 15,Elective Cesarean Section (ECS) at Day 15,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 B.,17 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae",2|1224|1236|91347;2|1224|1236|91347|543;2|1224;2|1224|1236;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|976|200643;2|976|200643|171549;2|1224|1236|91347|543|620;2|201174|1760|85004|31953|1678|28026;2|201174|1760|85004|31953|1678|1686|630129;2|1224|1236|91347|543|620|622;2|976|200643|171549|815|816|28113;2|1224|1236|91347|543|544|545;2|1239|909932|1843489|31977|906;2|1224|1236|91347|543|561|1499973;2|1224|1236|91347|1903410,Complete,Folakunmi
bsdb:932/4/1,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 4,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 30,Elective Cesarean Section (ECS) at Day 30,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 C.,11 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. Crenshaw,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. M5al,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter braakii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia nimipressuralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Candidatus Hamiltonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Candidatus Hamiltonella|s__Candidatus Hamiltonella defensa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales",2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|547|2027919;2|1224|1236|91347|543|547|1977566;2|1224|1236|91347|543|570|1934254;2|1224|1236|91347|543|544|57706;2|1224|1236|91347|543|547|881260;2|1224|1236|91347|543|1330545|69220;2|1224|1236|91347|543|568987;2|1224|1236|91347|543|568987|138072;2|1239|186801|3085636|186803|1164882|617123;2|1239|186801|3085636|186803|1164882;2|1239|91061|1385,Complete,Folakunmi
bsdb:932/4/2,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 4,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 30,Elective Cesarean Section (ECS) at Day 30,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 C.,17 March 2024,Ayibatari,Ayibatari,Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium diphtheriae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|201174|1760|85004|31953|1678|28026;2|976|200643|171549|815|816|28116;2|976|200643|171549|2005525;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|823;2|976|117743|200644;2|976|117743;2|976|117743|200644|49546;2|976|200643|171549|171551;2|201174|1760|85007|1653|1716|1717;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775;2|508458;2|1239|909932|1843489|31977|39948|2161821;2|201174|1760|85004|31953|2701|2702;2|201174|1760|85004|31953|2701,Complete,Folakunmi
bsdb:932/5/1,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 5,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 0) vs. group 0 (days 15 and 30),Tunisian newborns' at day 0 sampling time points.,5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 1,Supplementary Table_3.,17 March 2024,Ayibatari,Ayibatari,Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 0 with Day 15 and Day 30 .,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum",2|1224|28216|80840|80864;2|1224|1236|135614|32033;2|1224|1236|135614;2|1224|1236|135614|32033|40323;2|1224|1236|72274|135621;2|1224|1236|72274|135621|286;2|1224|28211|356|119045|2282523,Complete,Svetlana up
bsdb:932/6/1,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 6,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 15) vs. group 0 (days 0 and 30),Tunisian newborns' at day 15 sampling time points.,5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 1,Supplementary Table_3.,17 March 2024,Ayibatari,Ayibatari,Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 15 with Day 0 and Day 30 .,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus|s__Negativicoccus massiliensis,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus",2|1239|909932|1843488|909930|904;2|201174;2|1239|91061|1385;2|1239|91061;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|1686;2|201174|1760|85004|31953|1678|1686|630129;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653|1716|191610;2|1224|1236|91347|543|547;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1224|1236;2|1224|1236|91347|543|570;2|1224|1236|91347|543|570|548;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|2742598|1613;2|201174|1760|85007;2|1239|909932|1843489|31977|909928;2|1239|909932|1843489|31977|909928|1702287;2|1224;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|28901;2|1224|1236|91347|543|620;2|1224|1236|91347|543|620|622;2|1224|1236|91347|543|620|623;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1290;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|197614,Complete,NA
bsdb:932/6/2,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 6,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 15) vs. group 0 (days 0 and 30),Tunisian newborns' at day 15 sampling time points.,5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 2,Supplementary Table_3.,8 April 2024,Folakunmi,Folakunmi,Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 15 with Day 0 and Day 30 .,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus|s__Negativicoccus massiliensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum",2|201174;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|201174|1760|85004|31953|1678|1685;2|1224|1236|91347|543|570;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|1681;2|1239|91061;2|1239|91061|186826|81850;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|28901;2|1239|91061|1385;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1224|1236|91347|543|570|548;2|1239|909932|1843489|31977|909928|1702287;2|1239|909932|1843489|31977|909928;2|1239|91061|1385|90964|1279|1282;2|1224|1236|91347|543|620;2|1224|1236|91347|543|620|623;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|1385|90964|1279|1290;2|1239|91061|186826|1300|1301|197614;2|201174|1760|85004|31953|1678|1686|630129;2|1224|1236|91347|543|620|622;2|201174|1760|85004|31953|1678|1686;2|1239|909932|1843488|909930|904|187327;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|1760|85007;2|1224|1236|91347|543|547|881260;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|33958|1578|47770;2|201174|1760|85007|1653|1716|191610,Complete,Svetlana up
bsdb:932/7/1,Study 932,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A , Souiai O",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 7,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 30) vs. group 0 (days 0 and 15),Tunisian newborns' at day 30 sampling time points.,5,5,Last trimester of pregnancy.,WMS,NA,NA,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 1,Supplementary Table_3.,17 March 2024,Ayibatari,Ayibatari,Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 30 with Day 0 and Day 15.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. Crenshaw,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. FDAARGOS_192,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rodentium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella planticola,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasivariicola",2|976|200643|171549|815|816|818;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|28026;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|1322;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1502;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|201174|1760|85009|31957|1912216|33010;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|61645;2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|547|2027919;2|1224|1236|91347|543|547|158836;2|1224|1236|91347|543|547|1977566;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|1351;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186806|1730|1736;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570|1134687;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|1463165;2|1224|1236|91347|543|570|244366;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|909932;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|1236|91347|1903410;2|1224|1236|91347|543|160674;2|1224|1236|91347|543|160674|54291;2|1224|1236|91347|1903411|613;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1335;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|102684;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1839799;2|1239|91061|186826|1300|1301|1308;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|248315;2|1239|909932|1843489|31977;2|1239|909932|1843489;2|1224|1236|91347|1903411;2|1239;2|1239|186801|186802;2|1224|1236|91347|543|160674|575;2|1239|91061|186826|33958|2759736|47715;2|1224|1236|91347|543|570|2026240,Complete,Svetlana up
bsdb:933/1/1,Study 933,case-control,37980506,0.1186/s12866-023-03115-1,https://doi.org/10.1186/s12866-023-03115-1,"Huijuan Ning, Jing Yuan, Jinghua Cui, Kunyu Yao, Meijuan Wang, Meng Jin, Wenwen Liu, Xuemei Zhong",Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis,BMC microbiology,2023,"Infantile cholestasis (IC), Gut microbiota, Microbiota-derived metabolites, Ruminococcus, Butyrivibrio,  Veillonella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cholestasis,MONDO:0001751,Healthy Control (CON),Infantile  cholestasis (IC),Infants aged less than 1 year with all diagnostic criteria for cholestasis met upon admission.,20,20,No antibiotics were administered over the preceding 2 weeks.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1 C,10 March 2024,Amara,"Amara,Ayibatari,Peace Sandy",Characteristics of gut microbiota in infantile cholestasis (IC; n = 20) and control (CON; n = 20) groups. C. score plot of differential species showing linear discriminant analysis of differentially abundant genera between the two groups;,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|2005520;2|976|200643|171549|2005520|156973;2|1224|1236;2|1239|186801|3085636|186803|1506553;2|1224;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:933/1/2,Study 933,case-control,37980506,0.1186/s12866-023-03115-1,https://doi.org/10.1186/s12866-023-03115-1,"Huijuan Ning, Jing Yuan, Jinghua Cui, Kunyu Yao, Meijuan Wang, Meng Jin, Wenwen Liu, Xuemei Zhong",Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis,BMC microbiology,2023,"Infantile cholestasis (IC), Gut microbiota, Microbiota-derived metabolites, Ruminococcus, Butyrivibrio,  Veillonella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cholestasis,MONDO:0001751,Healthy Control (CON),Infantile  cholestasis (IC),Infants aged less than 1 year with all diagnostic criteria for cholestasis met upon admission.,20,20,No antibiotics were administered over the preceding 2 weeks.,16S,34,Illumina,LEfSe,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1 C,10 March 2024,Amara,"Amara,Welile,Peace Sandy",Characteristics of gut microbiota in infantile cholestasis (IC; n = 20) and control (CON; n = 20) groups. C. score plot of differential species showing linear discriminant analysis of differentially abundant genera between the two groups;,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Amorphaceae|g__Amorphus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhodobiaceae",2|1239|186801;2|1239|186801|186802|216572;2|1239|186801|3082720|186804|1501226;2|1239|526524|526525|128827;2|1239|526524|526525;2|1224|28211|204458|76892|75;2|1239|526524|526525|2810280|3025755;2|1239|186801|3082768|990719;2|1239|186801|3082768;2|1224|28211|356|2685818|580880;2|1224|28211|356|119043,Complete,Peace Sandy
bsdb:934/1/1,Study 934,case-control,25476529,https://doi.org/10.1002/mds.26069,NA,"Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola-Rautio J, Pohja M, Kinnunen E, Murros K , Auvinen P",Gut microbiota are related to Parkinson's disease and clinical phenotype,Movement disorders : official journal of the Movement Disorder Society,2015,"biomarker, gastrointestinal dysfunction, gut-brain-axis, microbiome, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls,Parkinson's disease,Patients diagnosed with Parkinson's disease,72,72,Within the last month,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,eTable 4,9 March 2024,Junie,"Junie,Svetlana up",Difference between the gut microbiome of patients with Parkinson's disease and healthy controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|91061|186826|33958;2|1224|28211|356|41294;2|1239|186801|186802|216572;2|74201|203494|48461|203557,Complete,Svetlana up
bsdb:934/1/2,Study 934,case-control,25476529,https://doi.org/10.1002/mds.26069,NA,"Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola-Rautio J, Pohja M, Kinnunen E, Murros K , Auvinen P",Gut microbiota are related to Parkinson's disease and clinical phenotype,Movement disorders : official journal of the Movement Disorder Society,2015,"biomarker, gastrointestinal dysfunction, gut-brain-axis, microbiome, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls,Parkinson's disease,Patients diagnosed with Parkinson's disease,72,72,Within the last month,16S,123,Roche454,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,eTable 4,9 March 2024,Junie,Junie,Difference in the abundance of the gut microbiome in patients with Parkinson's disease.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,Svetlana up
bsdb:935/1/1,Study 935,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, Mardinoglu A , Shoaie S",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Patients with Parkinson's Disease,Patient with Early-stage L-DOPA-Naive Parkinson's Disease,11,26,N/A,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,9 March 2024,Raihanat,"Raihanat,Peace Sandy",Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and controls.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Archaea|p__Euryarchaeota,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|1239;2|976|200643|171549|815|816;2|1239|186801|3082768|990719|2054177;2157|28890;2157|28890|183925|2158|2159;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1905344;2|74201|203494;2|1239|186801|186802|1392389;2|1239|186801|3082768|990719|990721;2|1239|186801|3082768|990719,Complete,Peace Sandy
bsdb:935/1/2,Study 935,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, Mardinoglu A , Shoaie S",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Patients with Parkinson's Disease,Patient with Early-stage L-DOPA-Naive Parkinson's Disease,11,26,N/A,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1,12 March 2024,Raihanat,Raihanat,Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and controls.,decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",2|976;2|1239|186801|186802|216572|216851;2|32066|203490|203491|203492;2|1224|1236|135625|712|724;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|976|200643|171549|2005473;2|1239|186801|3085636|186803|841;2|201174|84998|1643822|1643826|84108;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|29465;2|32066|203490;2|1239|526524|526525|128827;2|1224|1236|135625|712;2|1224|28216|80840|995019,Complete,Peace Sandy
bsdb:935/2/1,Study 935,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, Mardinoglu A , Shoaie S",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Diseased Controls,Patients with Parkinson's Disease,Patients with Early-stage L-DOPA-Naive Parkinson's Disease,14,26,N/A,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,16 March 2024,Raihanat,"Raihanat,Peace Sandy",Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and Diseased Controls(DC),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1224|28211|204441|2829815|191;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085656|3085657|2039302;2|1239|186801|3082720|186804;2|1224|28211|204441|41295;2759|4751|5204|155619|139380|1124673;2|1239|186801|3082720|186804|1501226;2|1239|526524|526525|2810280|3025755|1547;2|74201|203494;2|256845|1313211|278082|255528;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|216572|1508657|1757166;2|1239|186801|3085636|186803|2023266,Complete,Peace Sandy
bsdb:935/2/2,Study 935,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, Mardinoglu A , Shoaie S",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Diseased Controls,Patients with Parkinson's Disease,Patients with Early-stage L-DOPA-Naive Parkinson's Disease,14,26,N/A,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1,16 March 2024,Raihanat,"Raihanat,Peace Sandy",Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and Diseased Controls (DC),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fournierella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1239|909932|1843489|31977|156454|156456;2|201174|84998|84999|1643824;2|201174|84998|84999|1643824|1380;2|976;2|203691|203692|1643686|143786|29521;2|203691|203692|1643686|143786;2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106;2|976|200643|171549|2005519|1348911;2|201174|84998|84999|84107;2|1239|526524|526525|128827;2|1239|186801|186802|216572|1940255;2|1224|1236|135625|712|724;2|1239|526524|526525|128827|1573535;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|201174|84998|84999|1643824|133925;2|976|200643|171549|171552|577309;2|1224|1236|135625|712;2|976|200643|171549|171552|838;2|203691|203692|136|137|146;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|1236|135624|83763|674963;2|1224|1236|135624|83763;2|1239|186801|3085636|186803|1506577;2|976|200643|171549|2005473,Complete,Peace Sandy
bsdb:936/1/1,Study 936,case-control,38548910,10.1038/s41598-024-58118-3,NA,"Prasanchit P, Pongchaikul P, Lertsittichai P, Tantitham C , Manonai J",Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms,Scientific reports,2024,NA,Experiment 1,Thailand,Homo sapiens,Vaginal fluid,UBERON:0036243,Vulvovaginitis,EFO:1001240,Non-vulvovaginal symptoms (control),Vulvovaginal symptoms,Breast cancer survivors treated with aromatase inhibitors with vulvovaginal symptoms,20,20,Within 7 days,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,FIG 3 (A),9 April 2024,Rahila,"Rahila,Scholastica",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between breast cancer survivors treated with aromatase inhibitors with versus without vulvovaginal symptoms.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium riegelii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila|s__Fastidiosipila sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.",2|201174|1760|85004|31953|419014;2|201174|1760|85004|31953|419014|419015;2|201174|1760|85007|1653|1716|156976;2|1239|186801|186802|216572|236752;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|2701|2702;2|1239|91061|1385|539738|3076174|502393;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771|168808|40543;2|1239|186801|186802|216572|236752|1938886;2|1239|1737404|1737405|1570339|162289|1971214,Complete,Svetlana up
bsdb:936/1/2,Study 936,case-control,38548910,10.1038/s41598-024-58118-3,NA,"Prasanchit P, Pongchaikul P, Lertsittichai P, Tantitham C , Manonai J",Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms,Scientific reports,2024,NA,Experiment 1,Thailand,Homo sapiens,Vaginal fluid,UBERON:0036243,Vulvovaginitis,EFO:1001240,Non-vulvovaginal symptoms (control),Vulvovaginal symptoms,Breast cancer survivors treated with aromatase inhibitors with vulvovaginal symptoms,20,20,Within 7 days,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,FIG 3 (A),9 April 2024,Rahila,"Rahila,Scholastica",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between breast cancer survivors treated with aromatase inhibitors with versus without vulvovaginal symptoms.,decreased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,2|1239|1737404|1737405|1570339|543311|33033,Complete,Svetlana up
bsdb:937/1/1,Study 937,case-control,34631595,10.3389/fcimb.2021.654202,NA,"Hao X, Li P, Wu S , Tan J",Association of the Cervical Microbiota With Pregnancy Outcome in a Subfertile Population Undergoing <i>In Vitro</i> Fertilization: A Case-Control Study,Frontiers in cellular and infection microbiology,2021,"16S r RNA, IVF (in vitro fertilization), cervical microbiota, infertility, pregnancy",Experiment 1,China,Homo sapiens,Cervical mucus,UBERON:0000316,Pregnancy,EFO:0002950,Non-pregnant (FN),Clinical pregnancy (FP),Female IVF patients undergoing fresh embryo transfer (ET) who achieved clinical pregnancy,26,25,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,FIG 4 (A),9 April 2024,Rahila,"Rahila,Scholastica",Differential abundance and association analysis among the cervical microbiota of the fresh pregnancy group (FP) compared to the non-pregnancy group (FN),decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1224|28211|204441|433|434;2|1224|28211|204441|433;2|1239|909932|1843488|909930;2|1239|91061;2|1239;2|1239|186801|186802|216572|216851;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1239|186801|186802|204475;2|1224|1236|135625|712|724;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|909932|1843488|909930|33024;2|74201|203494|48461|203557|48463;2|1239|186801|3085636|186803|841;2|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:937/1/2,Study 937,case-control,34631595,10.3389/fcimb.2021.654202,NA,"Hao X, Li P, Wu S , Tan J",Association of the Cervical Microbiota With Pregnancy Outcome in a Subfertile Population Undergoing <i>In Vitro</i> Fertilization: A Case-Control Study,Frontiers in cellular and infection microbiology,2021,"16S r RNA, IVF (in vitro fertilization), cervical microbiota, infertility, pregnancy",Experiment 1,China,Homo sapiens,Cervical mucus,UBERON:0000316,Pregnancy,EFO:0002950,Non-pregnant (FN),Clinical pregnancy (FP),Female IVF patients undergoing fresh embryo transfer (ET) who achieved clinical pregnancy,26,25,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,FIG 4 (A),9 April 2024,Rahila,"Rahila,Scholastica",Differential abundance and association analysis among the cervical microbiota of the fresh pregnancy group (FP) compared to the non-pregnancy group (FN),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Candidatus Parcubacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Bacteroidota",2|1239|186801|3085636|186803|1427378;2|57723;2|201174;2|1239|91061|186826|186827;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171552|1283313;2|544448|31969|186332|186333|2086;2|544448|31969|186332;2|1239|186801|186802|216572|244127;2|29547|3031852|213849|2808963|28196;2|201174|84998|84999|1643824|1380;2|976|200643|171549;2|976|200643;2|200940|3031449|213115|194924|35832;2|1224|28216|80840|119060;2|976|200643|171549|1853231|574697;2|29547|3031852|213849;2|221216;2|201174|84998|84999|84107;2|201174|84998|84999;2|28221;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|909932|1843489|31977|39948;2|29547|3031852;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|201174|1760|85004|31953|2701;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|201174|1760|85009|85015;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1224|28216|80840|995019|577310;2|1224|28216|80840|119060|44013;2|976|200643|171549|171551;2|201174|1760|85007|85025|1827;2|1224|28216|206389|75787;2|1224|28216|206389;2|1224|28211|766;2|1239|186801|186802|216572|1263;2|1239|526524|526525|2810281|191303;2|74201|203494|48461|203557;2|74201|203494|48461;2|74201|203494;2|74201;2|1224|28211|356|212791;2|1224|28211|766|775;2|544448|31969|186332|186333;2|976,Complete,Svetlana up
bsdb:938/1/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 1,China,Ovis aries,Rumen,UBERON:0007365,Gut microbiome measurement,EFO:0007874,Rumen of Dorper sheep (D_R),Rumen of Tan Sheep (T_R),"Rumen of Tan sheep bred in Ningxia, China",4,4,No antibiotics during the experiment period,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3A,11 April 2024,Scholastica,Scholastica,LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from metagenomic data at the species level.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter xylosoxidans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri",2|1224|28216|80840|506|222|85698;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|216572|1637257|884684;2|1239|186801|186802|216572|459786|2109687;2|1224|1236|135614|32033|40323|40324;2|1224|1236|72274|135621|2901164|316,Complete,Svetlana up
bsdb:938/1/2,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 1,China,Ovis aries,Rumen,UBERON:0007365,Gut microbiome measurement,EFO:0007874,Rumen of Dorper sheep (D_R),Rumen of Tan Sheep (T_R),"Rumen of Tan sheep bred in Ningxia, China",4,4,No antibiotics during the experiment period,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3A,11 April 2024,Scholastica,Scholastica,LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from metagenomic data at the species level.,decreased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter millerae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera sp. BMS",2157|28890|183925|2158|2159|2172|230361;2157|28890|183925|2158|2159|2316|1789762,Complete,Svetlana up
bsdb:938/2/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 2,China,Ovis aries,Duodenum,UBERON:0002114,Gut microbiome measurement,EFO:0007874,Duodenum of Dorper sheep (D_Du),Duodenum of Tan Sheep (T_Du),"Duodenum of Tan sheep bred in Ningxia, China",3,3,No antibiotics during the experiment period,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4A,11 April 2024,Scholastica,Scholastica,LEfSe analysis of differences in duodenal microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium tumefaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter alpinus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella|s__Friedmanniella luteola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter|s__Modestobacter marinus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium dioxanotrophicus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium|s__Ornithinimicrobium avium",2|1224|28211|356|82115|357|358;2|201174|1760|85006|1268|1663|656366;2|201174|1760|85009|85015|53387|546871;2|201174|1760|1643682|85030|88138|477641;2|201174|1760|85007|1762|1763|482462;2|201174|1760|85006|2805590|125287|2283195,Complete,Svetlana up
bsdb:938/2/2,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 2,China,Ovis aries,Duodenum,UBERON:0002114,Gut microbiome measurement,EFO:0007874,Duodenum of Dorper sheep (D_Du),Duodenum of Tan Sheep (T_Du),"Duodenum of Tan sheep bred in Ningxia, China",3,3,No antibiotics during the experiment period,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4A,11 April 2024,Scholastica,Scholastica,LEfSe analysis of differences in duodenal microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Advenella|s__Advenella mimigardefordensis,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Nostoc|s__Nostoc sphaeroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Solibacillus|s__Solibacillus silvestris",2|1224|28216|80840|506|290425|302406;2|1117|3028117|1161|1162|1177|446679;2|1239|91061|1385|186818|648800|76853,Complete,Svetlana up
bsdb:938/3/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 3,China,Ovis aries,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,Colon of Dorper sheep (D_Co),Colon of Tan Sheep (T_Co),"Colon of Tan sheep bred in Ningxia, China",4,4,No antibiotics during the experiment period,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5A,11 April 2024,Scholastica,Scholastica,LEfSe analysis of differences in colonic microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio thermocellus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium CF,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides coprosuis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gallinarum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium efficiens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium humireducens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium marinum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia lutea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter mallensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Mucinivorans|s__Mucinivorans hirudinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus sp. FSL H7-0737,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus rhodochrous,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Solitalea|s__Solitalea canadensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans",2|1239|186801|186802|216572|35829|1515;2|1239|91061|1385|186817|1386|1423;2|976|200643|171549|1400053;2|976|200643|171549|815|816|151276;2|976|117743|200644|2762318|59732|1324352;2|201174|1760|85007|1653|1716|152794;2|201174|1760|85007|1653|1716|1223514;2|201174|1760|85007|1653|1716|349751;2|201174|1760|85007|85029|37914|546160;2|1239|186801|3085636|186803|1663717|1679721;2|976|117747|200666|84566|423349|652787;2|976|200643|171549|171550|1611681|1433126;2|1239|91061|1385|186822|44249|1536775;2|976|200643|171549|2005525|375288|823;2|201174|1760|85007|85025|1827|1829;2|1239|909932|909929|1843491|970|971;2|976|117747|200666|84566|929509|995;2|1239|91061|186826|1300|1301|1309,Complete,Svetlana up
bsdb:938/4/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 4,China,Ovis aries,Rumen,UBERON:0007365,Gut microbiome measurement,EFO:0007874,Rumen of Dorper sheep (D_R),Rumen of Tan Sheep (T_R),"Rumen of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S6,11 April 2024,Scholastica,Scholastica,LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium CG2,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium",2|1239|186801|3085636|186803|1394809;2|1239|186801|186802|216572|100175;2|1239|186801|186802|216572|1200657;2|976|200643|171549|171552|370804,Complete,Svetlana up
bsdb:938/5/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 5,China,Ovis aries,Duodenum,UBERON:0002114,Gut microbiome measurement,EFO:0007874,Duodenum of Dorper sheep (D_Du),Duodenum of Tan Sheep (T_Du),"Duodenum of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S7,11 April 2024,Scholastica,Scholastica,LEfSe analysis of duodenal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Candidatus Melainabacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1798710|1906119;2|1798710;2|1239|186801|186802|186807;2|1239|186801|186802|216572|1200657;2|201174|84998|84999|84107|1473205;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:938/6/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 6,China,Ovis aries,Jejunum,UBERON:0002115,Gut microbiome measurement,EFO:0007874,Jejunum of Dorper sheep (D_J),Jejunum of Tan Sheep (T_J),"Jejunum of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S8,11 April 2024,Scholastica,Scholastica,LEfSe analysis of jejunal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,2|976|200643|171549|171552|370804,Complete,Svetlana up
bsdb:938/6/2,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 6,China,Ovis aries,Jejunum,UBERON:0002115,Gut microbiome measurement,EFO:0007874,Jejunum of Dorper sheep (D_J),Jejunum of Tan Sheep (T_J),"Jejunum of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S8,11 April 2024,Scholastica,Scholastica,LEfSe analysis of jejunal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli",2|1239|91061|1385;2|1239|91061,Complete,Svetlana up
bsdb:938/7/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 7,China,Ovis aries,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,Colon of Dorper sheep (D_Co),Colon of Tan Sheep (T_Co),"Colon of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S9,11 April 2024,Scholastica,Scholastica,LEfSe analysis of colonic microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Candidatus Melainabacteria,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1798710|1906119;2|1798710;2|1117;2|256845|1313211|278082|255528|172900;2|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:938/7/2,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 7,China,Ovis aries,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,Colon of Dorper sheep (D_Co),Colon of Tan Sheep (T_Co),"Colon of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S9,11 April 2024,Scholastica,Scholastica,LEfSe analysis of colonic microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,"k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2;2|976|200643|171549|171550;2|976|200643|171549|194843;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:938/8/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 8,China,Ovis aries,Caecum,UBERON:0001153,Gut microbiome measurement,EFO:0007874,Cecum of Dorper sheep (D_C),Cecum of Tan Sheep (T_C),"Cecum of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S10,11 April 2024,Scholastica,Scholastica,LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1224;2|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:938/8/2,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 8,China,Ovis aries,Caecum,UBERON:0001153,Gut microbiome measurement,EFO:0007874,Cecum of Dorper sheep (D_C),Cecum of Tan Sheep (T_C),"Cecum of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S10,11 April 2024,Scholastica,Scholastica,LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Svetlana up
bsdb:939/1/1,Study 939,case-control,28891262,10.1111/ene.13398,https://pubmed.ncbi.nlm.nih.gov/28891262/,"Mertsalmi TH, Aho VTE, Pereira PAB, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",More than constipation - bowel symptoms in Parkinson's disease and their connection to gut microbiota,European journal of neurology,2017,"Parkinson's disease, constipation, irritable bowel syndrome, microbiota, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Irritable Bowel Syndrome negative (IBS-),Irritable Bowel Syndrome positive (IBS+),Parkinson’s Disease patients with Irritable Bowel Syndrome (IBS)-like symptoms.,56,18,Within the last month.,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,18 April 2024,Abiola-Salako,Abiola-Salako,Bacteria with significant differences in relative abundance between PD Patients with or without IBS-like symptoms,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,NA
bsdb:940/1/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 1,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19 group,This group consists of 71 patients with Covid-19.,132,71,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 4g,19 April 2024,Victoria,Victoria,"This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina|s__Angustimassarina camporesii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus subflavus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria|s__Chrysosphaeria jannelii,k__Eukaryota|k__Fungi|c__Entorrhizomycetes|o__Entorrhizales|f__Entorrhizaceae|g__Entorrhiza,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces|s__Fantasmomyces hyalinus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Fuscosporellales|f__Fuscosporellaceae|g__Parafuscosporella,k__Eukaryota|k__Fungi|p__Ascomycota|g__Vanakripa|s__Vanakripa mucosa,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella|s__Parasympodiella longispora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium|s__Simplicillium sympodiophorum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber|s__Tuber alcaracense,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|s__[Cryptococcus] ater,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces",2759|4751|4890|147550|1827388;2759|4751|4890|147550|1827388|2571388;2759|4751|4890|147541|92860|1859218|1762950;2759|4751|4890|147541|92860|1859218|1762950|2599739;2759|4751|4890|147545|5042|1131492|5052|2175223;2759|4751|4890|147550|5151|5152|2875642;2759|4751|4890|147550|5151|5152|2875642|2745882;2759|4751|62907|62910|62911|63255;2759|4751|4890|147550|1932873|1925498;2759|4751|4890|147549|5185|5186|405928;2759|4751|4890|147549|5185|5186|405928|2489165;2759|4751|4890|147550|1963390|1963370|1963373;2759|4751|4890|2081268|1963375;2759|4751|4890|147550|252166|307582|673167;2759|4751|4890|147550|252166|307582|673167|756022;2759|4751|4890|4891|4892|4893|4930;2759|4751|4890|4891|4892|4893|4930|4932;2759|4751|4890|147550|5125|474943|292631;2759|4751|4890|147550|5125|474943|292631|935215;2759|4751|4890|147549|5185|40289|36048;2759|4751|4890|147549|5185|40289|36048|2698902;2759|4751|5204|155616|90886|5408|104670;2759|4751|4890|147550|1932873,Complete,Svetlana up
bsdb:940/1/2,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 1,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19 group,This group consists of 71 patients with Covid-19.,132,71,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 4g,19 April 2024,Victoria,Victoria,"This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium|s__Milospium graphideorum,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula|s__Russula xerophila,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus amstelodami,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium kenpeggii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Ophiostoma,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis|s__Arthrographis grakistii,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis",2759|4751|4890|147550|261460|103886|1323519|2040582;2759|4751|4890|1666919|1664392;2759|4751|1913637|214506|214509|308925|308926;2759|4751|4890|147550|261460|103886|1323519;2759|4751|4890|147550|5114|767018|36922;2759|4751|5204|155616|1851469|1759442|1851468|181171;2759|4751|5204|155619|452342|5401|5402|278596;2759|4751|4890|147545|5042|28568|5094;2759|4751|4890|1666919;2759|4751|4890|147545|5042|1131492|5052|5054;2759|4751|1913637|214506|214509|308925|308926|308927;2759|4751|4890|147541|2726946|452563|5498|2016221;2759|4751|4890|147550|5151|5152|5159;2759|4751|4890|147550|5151|5152|45340;2759|4751|4890|147541|2714147|241722|241727|2682943;2759|4751|5204|155619|452342|5401|5402;2759|4751|5204|155616|5234|1884633|5206;2759|4751|4890|147548|5120|34371|34372;2759|4751|4890|147550|5151|5152|2933754|483707;2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|4890|147541|2714147|241722|241727;2759|4751|4890|3239874|2916678|766764|5475|5480,Complete,Svetlana up
bsdb:940/2/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 2,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19 group,Post-Covid-19 group,This group consists of patients who have recovered from Covid-19.,71,22,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 4g,19 April 2024,Victoria,Victoria,"This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor|s__Actinomucor elegans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus versicolor,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Botryosphaeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Dipodascus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Galactomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Galactomyces|s__Galactomyces pseudocandidus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum candidum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor circinelloides,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor pseudolusitanicus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces scorteus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces megalosporus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces pyricola",2759|4751|1913637|2212703|4827|34489|64644;2759|4751|1913637|2212703|4827|34489|64644|64647;2759|4751|4890|147545|5042|1131492|5052|41959;2759|4751|4890|147545|5042|1131492|5052|46472;2759|4751|4890|147541|451869|45131|45132;2759|4751|4890|3239874|2916678|766764|5475;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|3239873|3243772|34353|27314;2759|4751|4890|3239873|3243772|34353|27316;2759|4751|4890|3239873|3243772|34353|27316|1206149;2759|4751|4890|3239873|3243772|34353|43987|1173061;2759|4751|5204|1538075|162474|742845|55193;2759|4751|1913637|2212703|4827|34489|4830;2759|4751|1913637|2212703|4827|34489|4830|36080;2759|4751|1913637|2212703|4827|34489|4830|2021227;2759|4751|5204|162481|231213|1799696|5533;2759|4751|5204|162481|231213|1799696|5533|5537;2759|4751|4890|147545|5042|28568|5094|1400007;2759|4751|5204|155616|90883|1851551|42658;2759|4751|5204|155616|90883|1851551|42658|42659;2759|4751|5204|155616|90883|1851551|42658|42661,Complete,Svetlana up
bsdb:940/2/2,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 2,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19 group,Post-Covid-19 group,This group consists of patients who have recovered from Covid-19.,71,22,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 4g,19 April 2024,Victoria,Victoria,"This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium|s__Simplicillium sympodiophorum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella|s__Parasympodiella longispora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina|s__Angustimassarina camporesii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus subflavus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria|s__Chrysosphaeria jannelii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|s__[Cryptococcus] ater,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces|s__Fantasmomyces hyalinus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus,k__Eukaryota|k__Fungi|p__Ascomycota|g__Vanakripa|s__Vanakripa mucosa,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber|s__Tuber alcaracense,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Fuscosporellales|f__Fuscosporellaceae|g__Parafuscosporella,k__Eukaryota|k__Fungi|c__Entorrhizomycetes|o__Entorrhizales|f__Entorrhizaceae|g__Entorrhiza,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina",2759|4751|4890|147550|5125|474943|292631|935215;2759|4751|4890|147550|252166|307582|673167|756022;2759|4751|4890|147550|5151|5152|2875642;2759|4751|4890|147541|92860|1859218|1762950|2599739;2759|4751|4890|147545|5042|1131492|5052|2175223;2759|4751|4890|147550|5151|5152|2875642|2745882;2759|4751|4890|147549|5185|5186|405928;2759|4751|5204|155616|90886|5408|104670;2759|4751|4890|147550|1827388;2759|4751|4890|147550|1932873|1925498;2759|4751|4890|4891|4892|4893|4930|4932;2759|4751|4890|147550|252166|307582|673167;2759|4751|4890|147550|1932873;2759|4751|4890|147550|5125|474943|292631;2759|4751|4890|147550|1827388|2571388;2759|4751|4890|4891|4892|4893|4930;2759|4751|4890|147549|5185|5186|405928|2489165;2759|4751|4890|2081268|1963375;2759|4751|4890|147549|5185|40289|36048;2759|4751|4890|147549|5185|40289|36048|2698902;2759|4751|4890|147550|1963390|1963370|1963373;2759|4751|62907|62910|62911|63255;2759|4751|4890|147541|92860|1859218|1762950,Complete,Svetlana up
bsdb:940/3/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 3,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Post-Covid-19 group,This group consists of 22 patients who have recovered from Covid-19.,132,22,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 4g,24 April 2024,Victoria,Victoria,"This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor|s__Actinomucor elegans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus versicolor,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Botryosphaeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Dipodascus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Galactomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Galactomyces|s__Galactomyces pseudocandidus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum candidum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor circinelloides,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor pseudolusitanicus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces scorteus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces megalosporus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces pyricola",2759|4751|1913637|2212703|4827|34489|64644;2759|4751|1913637|2212703|4827|34489|64644|64647;2759|4751|4890|147545|5042|1131492|5052|41959;2759|4751|4890|147545|5042|1131492|5052|46472;2759|4751|4890|147541|451869|45131|45132;2759|4751|4890|3239874|2916678|766764|5475;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|3239873|3243772|34353|27314;2759|4751|4890|3239873|3243772|34353|27316;2759|4751|4890|3239873|3243772|34353|27316|1206149;2759|4751|4890|3239873|3243772|34353|43987|1173061;2759|4751|5204|1538075|162474|742845|55193;2759|4751|1913637|2212703|4827|34489|4830;2759|4751|1913637|2212703|4827|34489|4830|36080;2759|4751|1913637|2212703|4827|34489|4830|2021227;2759|4751|5204|162481|231213|1799696|5533;2759|4751|5204|162481|231213|1799696|5533|5537;2759|4751|4890|147545|5042|28568|5094|1400007;2759|4751|5204|155616|90883|1851551|42658;2759|4751|5204|155616|90883|1851551|42658|42659;2759|4751|5204|155616|90883|1851551|42658|42661,Complete,NA
bsdb:940/4/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 4,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-N group,This group consists of 56 Covid-19 patients without comorbidities.,132,56,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Supplemental Figure S4,3 June 2024,Victoria,Victoria,"The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans",2759|4751|4890|147550|1827388;2759|4751|4890|3239874|2916678|766764|5475;2759|4751|4890|147549|5185|5186|405928;2759|4751|4890|147550|5151|5152|45340;2759|4751|4890|147550|5151|5152|2933754|483707;2759|4751|4890|147550|1827388|2571388;2759|4751|4890|147549|5185|5186|405928|2489165;2759|4751|4890|3239874|2916678|766764|5475|5476,Complete,NA
bsdb:940/4/2,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 4,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-N group,This group consists of 56 Covid-19 patients without comorbidities.,132,56,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Supplemental Figure S4,3 June 2024,Victoria,Victoria,"The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels",decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium kenpeggii",2759|4751|4890|147550|261460|103886|1323519;2759|4751|4890|147548|5120|34371|34372;2759|4751|5204|155616|5234|1884633|5206;2759|4751|4890|147541|2726946|452563|5498;2759|4751|5204|1538075|162474|742845|55193;2759|4751|1913637|214506|214509|308925|308926;2759|4751|4890|147550|261460|103886|1323519|2040582;2759|4751|5204|155616|1851469|1759442|1851468|181171;2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|1913637|214506|214509|308925|308926|308927;2759|4751|4890|147541|2726946|452563|5498|2016221,Complete,NA
bsdb:940/5/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 5,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-C group,This group consists of 15 Covid-19 patients with comorbidities.,132,15,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplemental Figure S4,3 June 2024,Victoria,Victoria,"The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus",2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|3239874|2916678|766764|5475;2759|4751|4890|147550|5151|5152|45340;2759|4751|4890|147549|5185|5186|405928;2759|4751|4890|147549|5185|5186|405928|2489165,Complete,NA
bsdb:940/5/2,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 5,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-C group,This group consists of 15 Covid-19 patients with comorbidities.,132,15,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Supplemental Figure S4,3 June 2024,Victoria,Victoria,"The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa",2759|4751|4890|147550|261460|103886|1323519;2759|4751|5204|155616|5234|1884633|5206;2759|4751|1913637|214506|214509|308925|308926;2759|4751|4890|147550|261460|103886|1323519|2040582;2759|4751|1913637|214506|214509|308925|308926|308927;2759|4751|5204|155616|1851469|1759442|1851468|181171,Complete,NA
bsdb:940/6/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,NA,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 6,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19-N group,Covid-19-C group,This group consists of 15 Covid-19 patients with comorbidities.,56,15,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S4,3 June 2024,Victoria,Victoria,"The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",increased,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,2759|4751|4890|147548|5120|34371|34372,Complete,NA
bsdb:941/1/1,Study 941,case-control,38225541,https://doi.org/10.1186/s12866-023-03173-5,NA,"Li Liu, Shangren Wang, Xiaoqiang Liu, Yang Pan",Characteristics of gut microbiota in patients with asthenozoospermia: a Chinese pilot study,BMC microbiology,2024,"16s rrna, Asthenozoospermia, Semen quality, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Abnormal sperm morphology,HP:0012864,Healthy Control,Asthenozoospermia,Patients with reduced sperm mortility,60,48,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 5B,10 March 2024,Eve10111,"Eve10111,Folakunmi",The differentially expressed gut microbiota identified by LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|909932|1843488|909930;2|1239|909932|1843488;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313;2|1224|28211|204441|2829815|191;2|976|200643|171549|815|816|817;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|1224|28216|80840;2|1224|1236|91347|543|544|546;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|200940|3031449;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|526524|526525|128827;2|1224|1236|91347|543|1940338;2|1224|1236;2|1239|526524|526525|128827|61170;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2767887|1624;2|976|200643|171549|2005473;2|1224|28216|80840|995019|577310;2|1224|1236|135625|712;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930|33024|33025;2|1224;2|1239|91061|186826|1300|1301|28037;2|1224|28216|80840|995019;2|200940;2|1239|526524|526525|128827,Complete,Folakunmi
bsdb:941/1/2,Study 941,case-control,38225541,https://doi.org/10.1186/s12866-023-03173-5,NA,"Li Liu, Shangren Wang, Xiaoqiang Liu, Yang Pan",Characteristics of gut microbiota in patients with asthenozoospermia: a Chinese pilot study,BMC microbiology,2024,"16s rrna, Asthenozoospermia, Semen quality, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Abnormal sperm morphology,HP:0012864,Healthy Control,Asthenozoospermia,Patients with reduced sperm mortility,60,48,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 5B,10 March 2024,Eve10111,"Eve10111,Folakunmi",The differentially expressed gut microbiota identified by LEfSe analysis,decreased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacteria|p__Actinomycetota|c__Thermoleophilia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|57723;2|1224|28211;2|1239;2|1239|526524|526525|128827;2|1224|28211|356;2|201174|1760|85009|85015;2|976|200643|171549|815|909656|387090;2|976|200643|171549|171552|838|59823;2|201174|1760|85009;2|201174|1497346;2|74201;2|976|200643|171549|171552,Complete,Folakunmi
bsdb:942/1/1,Study 942,case-control,36209079,doi: 10.1186/s12967-022-03669-0.,https://pubmed.ncbi.nlm.nih.gov/36209079/,"Zhao L, Wang C, Peng S, Zhu X, Zhang Z, Zhao Y, Zhang J, Zhao G, Zhang T, Heng X , Zhang L",Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke,Journal of translational medicine,2022,"Gut microbiota, Integrative analysis, Ischemic stroke, Metabolomics, Microbiome",Experiment 1,China,Homo sapiens,"Feces,Urine,Blood plasma","UBERON:0001988,UBERON:0001088,UBERON:0001969",Stroke,EFO:0000712,Healthy individuals,Cerebral ischemic stroke patients,Patients diagnosed with ischemic stroke by skull computed tomography examination who have not experienced any pre-existing metabolic or gut diseases.,30,60,1 month,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure. 6,15 March 2024,Adeoyo Olajumoke,Adeoyo Olajumoke,Significantly different abundant taxa with LDA score (log10) > 2.0 and P < 0.05,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter sp. CAG:267,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:239,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides oleiciplenus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1024,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:226,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:715,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita|s__Coraliomargarita sp. CAG:312,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:105,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:488,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Verrucomicrobiota|c__Opitutia,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|1224|28211|204441|433|434|1262684;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|1288121;2|976|200643|171549|171550|239759|328814;2|1224|28211|204441|2829815|191|1262705;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|626931;2|1239|186801|186802|31979|1485|1262770;2|1239|186801|186802|31979|1485|1262781;2|1239|186801|186802|31979|1485|1262834;2|74201|414999|415001|3056371|442430|1262865;2|200940|3031449|213115|194924|872|901;2|1239|186801|3085636|186803|189330|1262872;2|1239|186801|186802|186806|1730|1736;2|976|200643|171549|171552|2974265|363265;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|459786|1262911;2|1239|186801|186802|216572|459786|1519439;2|976|200643|171549|171552|838|419005;2|1239|186801|186802|216572|1263|1262959;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|2485925;2|1224|28211;2|1224|28211|204441|433|434;2|201174|84998|84999|84107;2|976|200643|171549|1853231|283168;2|201174|84998|84999|84107|102106;2|200940|3031449|213115|194924|872;2|74201|414999;2|74201|414999|415001|415002;2|74201|414999|415001;2|74201|414999|415001|3056371|442430;2|1224|1236|135625|712;2|1224|1236|135625,Complete,Peace Sandy
bsdb:942/1/2,Study 942,case-control,36209079,doi: 10.1186/s12967-022-03669-0.,https://pubmed.ncbi.nlm.nih.gov/36209079/,"Zhao L, Wang C, Peng S, Zhu X, Zhang Z, Zhao Y, Zhang J, Zhao G, Zhang T, Heng X , Zhang L",Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke,Journal of translational medicine,2022,"Gut microbiota, Integrative analysis, Ischemic stroke, Metabolomics, Microbiome",Experiment 1,China,Homo sapiens,"Feces,Urine,Blood plasma","UBERON:0001988,UBERON:0001088,UBERON:0001969",Stroke,EFO:0000712,Healthy individuals,Cerebral ischemic stroke patients,Patients diagnosed with ischemic stroke by skull computed tomography examination who have not experienced any pre-existing metabolic or gut diseases.,30,60,1 month,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure. 6,15 March 2024,Adeoyo Olajumoke,Adeoyo Olajumoke,Significantly different abundant taxa with LDA score (log10) > 2.0 and P < 0.05,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter sp. CAG:977,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:260,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:841,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae",2|1224|28211|204441|433|434|1262685;2|1224|28211|204441|2829815|191;2|1224|28211|204441|2829815|191|1262706;2|976|200643|171549|815|816|1796613;2|976|200643|171549|2005519|397864|487174;2|1239|186801|186802|186806|1730|1262894;2|1224|28211|204441|41295,Complete,Peace Sandy
bsdb:943/1/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Major depressive disorder (MDD),"First-episode, drug-naïve patients with major depressive disorder (MDD) ages of 18–55.",85,85,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,FIG 1 (C),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with major depressive disorder (MDD) compared to healthy controls (HC),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Chloroflexota|c__Anaerolineae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Actinomycetota|c__Thermoleophilia",2|201174|84998|1643822|1643826|447020;2|200795|292625;2|201174|1760|85008|28056;2|2818505|32015|29;2|1224|28211|204441|41295;2|1224|28211|204441;2|201174|1497346,Complete,Svetlana up
bsdb:943/1/2,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Major depressive disorder (MDD),"First-episode, drug-naïve patients with major depressive disorder (MDD) ages of 18–55.",85,85,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,FIG 1 (C),2 August 2024,Scholastica,Scholastica,A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with major depressive disorder (MDD) compared to healthy controls (HC),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|186801|3085636|186803|841;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|1236|135625|712|724;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:943/2/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Healthy controls (HC) and inflammatory depression group,Non-inflammatory depression,Patients with major depressive disorder (MDD) who had non-inflammatory depression,127,43,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2.72,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|186801|186802|216572;2|1224|1236|135625|712;2|1224|1236|135625,Complete,Svetlana up
bsdb:943/3/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Healthy controls (HC) and non-inflammatory depression group,Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,128,42,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2.72,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Aquincola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Candidatus Tectimicrobiota|c__Candidatus Entotheonellia|o__Candidatus Entotheonellales|f__Candidatus Entotheonellaceae|g__Candidatus Entotheonella|s__Candidatus Entotheonella sp.,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria|g__Candidatus Xiphinematobacter,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacteria|p__Chlamydiota,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Kaistibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Noviherbaspirillum|s__Noviherbaspirillum malthae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Steroidobacterales|f__Steroidobacteraceae|g__Steroidobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Maricaulales|f__Maricaulaceae|g__Woodsholea",2|1224|28216|80840|2975441|391952;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|1224|28211|204458|76892|41275;2|1802339|3277336|3277337|3277338|93171|2066855;2|74201|134549|134550;2|204428|204429|51291|809|810;2|204428;2|200795|32061;2|1224|28211|204457|335929;2|201174|1497346|1154584|1154585|1154586;2|1224|1236|135614|32033|505691;2|1239|91061|186826|1300|1357;2|201174|1760|85008|28056;2|201174|1760|1643684|85031;2|1224|28216|80840|75682|1344552|1260987;2759|4751|5204|155619|452342|103393;2|1224|28211|204441|2829815|204447;2|1224|1236|3060226|2689614|469322;2|201174|1760|85012|2004;2|1224|28211|2800059|2800061|240236,Complete,Svetlana up
bsdb:943/4/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Non-inflammatory depression,Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,43,42,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2.45,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory versus non-inflammatory depression,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1357;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|201174|1760|85006|85017;2|201174|1497346|588673|320599|207599;2|1224|28211|356|335928,Complete,Svetlana up
bsdb:943/4/2,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Non-inflammatory depression,Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,43,42,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2.45,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (A2),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory versus non-inflammatory depression,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|1239;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|186801|186802|216572;2|1224|1236|135625|712;2|1224|1236|135625,Complete,Svetlana up
bsdb:943/5/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,20,20,3 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (C),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory depression compared to healthy controls (HC) at species level using shotgun metagenomic sequencing,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces bouchesdurhonensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:138,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",2|201174|1760|2037|2049|1654|1852361;2|201174|1760|2037|2049|1654|55565;2|201174|1760|2037|2049|1654|936548;2|1239|186801|186802|31979|1485|1262775;2|1239|186801|3082720|3030910|86331|114527;2|201174|1760|2037|2049|2529408|1660;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1313,Complete,Svetlana up
bsdb:943/5/2,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,20,20,3 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (C),2 August 2024,Scholastica,Scholastica,A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory depression compared to healthy controls (HC) at species level using shotgun metagenomic sequencing,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__Sarcina ventriculi,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 60_17,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Thermotaleaceae|g__Geosporobacter|s__Geosporobacter subterraneus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:417,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF28-13AC,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF22-5LB,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF17-7,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF36-5BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:343,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:37_48_57,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF10-46,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF14-40,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. OF03-13,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF32-4BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-13LB,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF27-11BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:413,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. OM07-7,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF17-9LB,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. OM04-11BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF34-35BH,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:18,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:192,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fournierella|s__Fournierella massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AM43-5AT,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp. AM42-5AC,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74_58_120,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241_62_21,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:37",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|204475|745368;2|1239|186801|186802|31979|1266|1267;2|1239|186801|186802|216572|292632|1897022;2|1239|186801|3082720|3118657|390805|390806;2|1239|186801|186802|31979|1485|1262804;2|1239|186801|186802|216572|216851|2292234;2|1239|186801|3085636|186803|572511|2292964;2|1239|186801|186802|186806|1730|2293105;2|976|200643|171549|171550|239759|2585118;2|1239|186801|186802|31979|1485|1502;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|186802|31979|1485|1492;2|1239|186801|3085636|186803|572511|2292960;2|1239|186801|186802|186806|1730|2293108;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|186802|31979|1485|1262796;2|1239|186801|3085636|186803|572511|1896976;2|1239|186801|186802|216572|216851|2302955;2|1239|186801|3085636|186803|572511|2292958;2|1239|186801|3085636|186803|572511|2292980;2|1239|186801|3085636|186803|572511|2292967;2|1239|186801|3085636|186803|572511|2292962;2|1239|186801|186802|216572|216851|2302956;2|1239|186801|186802|31979|1485|1262803;2|1239|186801|186802|216572|1263|2293234;2|1239|186801|3085636|186803|572511|2292959;2|1239|186801|186802|216572|216851|2292357;2|1239|186801|186802|186806|1730|2293107;2|1239|186801|186802|216572|459786|1897011;2|1239|186801|3085636|186803|841|1262941;2|1239|186801|186802|186806|1730|1262883;2|976|200643|171549|171550|239759|1470347;2|1239|186801|186802|216572|459786|1262911;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|216572|459786|1945593;2|1239|186801|186802|216572|1940255|1650663;2|1239|186801|186802|216572|216851|2302957;2|1239|186801|186802|3085642|580596|2292297;2|1239|186801|186802|216572|216851|1897005;2|1239|186801|186802|216572|459786|1897012;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|3085636|186803|572511|1262757,Complete,Svetlana up
bsdb:943/6/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy control (HC),Inflammatory and non-inflammatory depression,Patients with major depressive disorder (MDD) grouped into inflammatory and non-inflammatory depression groups,85,85,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2.72,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|841;2|1239|186801|186802|31979;2|1239|186801|3082720|186804;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:943/7/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,"Low-inflammatory, healthy control and blank groups",High-inflammatory group,Mice classified into the high-inflammatory group,24,20,None,16S,34,Illumina,LEfSe,0.05,NA,4.31,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D3),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|526524|526525|128827|174708;2|1239|526524;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524|526525|2810281;2|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:943/8/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,"High-inflammatory, healthy control and blank groups",Low-inflammatory group,Mice classified into the low-inflammatory group,36,8,None,16S,34,Illumina,LEfSe,0.05,NA,4.31,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D3),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus",2|1239|186801;2|1239|186801|186802;2|1224|28211|204455|31989|265,Complete,Svetlana up
bsdb:943/9/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Healthy control (HC) group,"High-inflammatory, low-inflammatory and blank groups","Mice classified into the high-inflammatory, low-inflammatory and blank groups",7,37,None,16S,34,Illumina,LEfSe,0.05,NA,4.31,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D3),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups,decreased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1224;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|1236;2|1224|1236|91347|543;2|1224|1236|91347|543|620;2|1224|1236|91347,Complete,Svetlana up
bsdb:943/10/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,"High-inflammatory, low-inflammatory and healthy control groups",Blank group,Mice administered normal saline and classified into the blank group,35,9,None,16S,34,Illumina,LEfSe,0.05,NA,4.31,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D3),18 April 2024,Rahila,"Rahila,Scholastica",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|976|200643|171549|2005473;2|1239|186801|3085636|186803;2|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:943/11/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Clostridium butyricum (CB) and normal saline (NS) groups,High-inflammatory group,Mice classified into the high-inflammatory group,13,7,None,16S,34,Illumina,LEfSe,0.05,NA,4.22,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 6 (C),5 August 2024,Scholastica,Scholastica,A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups,increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|c__Deltaproteobacteria",2|1239|186801;2|1239|186801|186802;2|1239;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|200940|3031449|213115|194924|872;2|28221,Complete,Svetlana up
bsdb:943/12/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,High-inflammatory and normal saline (NS) groups,Clostridium butyricum (CB),Mice administered probiotics (Clostridium butyricum),13,7,None,16S,34,Illumina,LEfSe,0.05,NA,4.22,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 6 (C),5 August 2024,Scholastica,Scholastica,A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|1224|1236;2|1224;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|543|620;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231,Complete,Svetlana up
bsdb:943/13/1,Study 943,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P, Liu Z, Wang J, Wang J, Gao M, Zhang Y, Yang C, Zhang A, Li G, Li X, Liu S, Liu L, Sun N , Zhang K",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Normal saline (NS),High-inflammatory and Clostridium butyricum (CB) groups,Mice administered normal saline (NS),6,14,None,16S,34,Illumina,LEfSe,0.05,NA,4.22,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 6 (C),5 August 2024,Scholastica,Scholastica,A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|2005473;2|976|200643;2|976;2|976|200643|171549,Complete,Svetlana up
bsdb:944/1/1,Study 944,case-control,27591074,10.1016/j.parkreldis.2016.08.019,NA,"Unger MM, Spiegel J, Dillmann KU, Grundmann D, Philippeit H, Bürmann J, Faßbender K, Schwiertz A , Schäfer KH",Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls,Parkinsonism & related disorders,2016,"Butyrate, Enteric nervous system, Gut microbiota, Parkinson's disease, Short chain fatty acids",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control (control matched- CM),Parkinson's disease group,Patients with Parkinson's disease,34,34,Three months,PCR,NA,RT-qPCR,Kruskall-Wallis,0.01,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 March 2024,EniolaAde,"EniolaAde,Peace Sandy",significant taxa observed in the fecal microbiota of patients with Parkinson's disease compared with healthy control matched group (CM),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|201174|1760|85004|31953|1678|41200;2|1224|1236|91347|543,Complete,Peace Sandy
bsdb:944/1/2,Study 944,case-control,27591074,10.1016/j.parkreldis.2016.08.019,NA,"Unger MM, Spiegel J, Dillmann KU, Grundmann D, Philippeit H, Bürmann J, Faßbender K, Schwiertz A , Schäfer KH",Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls,Parkinsonism & related disorders,2016,"Butyrate, Enteric nervous system, Gut microbiota, Parkinson's disease, Short chain fatty acids",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control (control matched- CM),Parkinson's disease group,Patients with Parkinson's disease,34,34,Three months,PCR,NA,RT-qPCR,Kruskall-Wallis,0.01,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,10 March 2024,EniolaAde,"EniolaAde,Peace Sandy,ChiomaBlessing",significant taxa observed in the fecal microbiota of patients with Parkinson's disease compared with healthy control matched group (CM),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|976|200643;2|1239|186801|186802|216572|216851|853;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1357,Complete,Peace Sandy
bsdb:944/2/1,Study 944,case-control,27591074,10.1016/j.parkreldis.2016.08.019,NA,"Unger MM, Spiegel J, Dillmann KU, Grundmann D, Philippeit H, Bürmann J, Faßbender K, Schwiertz A , Schäfer KH",Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls,Parkinsonism & related disorders,2016,"Butyrate, Enteric nervous system, Gut microbiota, Parkinson's disease, Short chain fatty acids",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control group (control young-CY),Parkinson's disease group,Patients with Parkinson's disease,10,34,Three months,PCR,NA,RT-qPCR,Kruskall-Wallis,0.01,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 March 2024,EniolaAde,"EniolaAde,Peace Sandy",significant taxa observed in the fecal microbiota of patients with Parkinson's disease compared with healthy control young group (CY),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia,2|976|200643,Complete,Peace Sandy
bsdb:945/1/1,Study 945,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R, Neth BJ, Wang S, Craft S , Yadav H",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitive Normal,Mild Cognitive Impairment,Participants diagnosed with early Mild Cognitive Impairment (diagnosed using ADNI-2 criteria) randomly assigned to either a modified Mediterranean-ketogenic diet (MMKD) or an American heart association diet (AHAD) group,6,11,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 1d-n and Result text,10 March 2024,MyleeeA,"MyleeeA,Welile,Scholastica",Differences in the gut microbiome between subjects clinically diagnosed with mild cognitive impairment (MCI) versus cognitively normal (CN) counterparts.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota",2|1239|186801|3085636|186803|33042;2|1224|1236|91347|543;2|1239|909932|1843488|909930|33024;2|1224,Complete,Svetlana up
bsdb:945/1/2,Study 945,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R, Neth BJ, Wang S, Craft S , Yadav H",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitive Normal,Mild Cognitive Impairment,Participants diagnosed with early Mild Cognitive Impairment (diagnosed using ADNI-2 criteria) randomly assigned to either a modified Mediterranean-ketogenic diet (MMKD) or an American heart association diet (AHAD) group,6,11,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Fig. 1d-n and Result text,10 March 2024,MyleeeA,"MyleeeA,Scholastica",Differences in the gut microbiome between subjects clinically diagnosed with mild cognitive impairment (MCI) versus cognitively normal (CN) counterparts.,decreased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,2|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:945/2/1,Study 945,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R, Neth BJ, Wang S, Craft S , Yadav H",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Post American heart association diet (AHAD) in MCI,Post modified Mediterranean-ketogenic diet (MMKD) in MCI,Participants diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,11,11,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 4 and Text,12 March 2024,MyleeeA,"MyleeeA,Scholastica",Significant bacterial taxa at endpoint American heart association diet (Post-AHAD) intervention compared to endpoint modified Mediterranean-ketogenic diet (Post-MMKD) intervention,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:945/3/1,Study 945,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R, Neth BJ, Wang S, Craft S , Yadav H",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Post American heart association diet (AHAD) in CN and MCI,Post modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,All Participants including cognitively normal (CN) and those diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,17,17,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 4,12 March 2024,MyleeeA,"MyleeeA,Scholastica",Significant bacterial taxa at endpoint American heart association diet (Post-AHAD) intervention compared to endpoint modified Mediterranean-ketogenic diet (Post-MMKD) intervention,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:945/4/1,Study 945,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R, Neth BJ, Wang S, Craft S , Yadav H",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Pre modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,Post modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,All Participants including cognitively normal (CN) and those diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,17,17,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Suppl. Fig.4.,17 March 2024,MyleeeA,"MyleeeA,Scholastica",Lefse analysis showing bacterial taxa contributing to the microbiome difference at baseline (pre) compared to endpoint (post) modified Mediterranean-ketogenic diet (MMKD),increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,2|1239|91061|186826|1300|1357,Complete,Svetlana up
bsdb:945/4/2,Study 945,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R, Neth BJ, Wang S, Craft S , Yadav H",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Pre modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,Post modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,All Participants including cognitively normal (CN) and those diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,17,17,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Suppl. Fig.4.,28 May 2024,Scholastica,Scholastica,Lefse analysis showing bacterial taxa contributing to the microbiome difference at baseline (pre) compared to endpoint (post) modified Mediterranean-ketogenic diet (MMKD),decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:946/1/1,Study 946,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A , Mazmanian SK",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,HC: household controls,PD: individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale.
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",56,88,12 weeks,WMS,NA,Illumina,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,10 March 2024,Idiaru angela,Idiaru angela,Summary of differential abundance results contrasting household controls and PD patients.,increased,k__Bacteria|p__Verrucomicrobiota,2|74201,Complete,Folakunmi
bsdb:946/1/2,Study 946,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A , Mazmanian SK",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,HC: household controls,PD: individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale.
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",56,88,12 weeks,WMS,NA,Illumina,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,11 March 2024,Idiaru angela,Idiaru angela,Summary of differential abundance results contrasting household controls and PD patients.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,2|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:946/2/1,Study 946,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A , Mazmanian SK",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PC: healthy population controls without Parkinson's Disease,PD: Individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale. 
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",83,88,12 weeks,WMS,NA,Illumina,MaAsLin2,0.1,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2 & figure S2,11 March 2024,Idiaru angela,"Idiaru angela,Folakunmi",Summary of differential abundance results contrasting healthy population controls and PD patients.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",2|201174;2|1239|186801|3085636|186803|1432051;2|1239|186801|3085636|186803|1432051|1432052;2|1239|186801|186802|216572|1905344;2|1239|186801|186802|216572|1905344|1550024,Complete,Folakunmi
bsdb:946/2/2,Study 946,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A , Mazmanian SK",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PC: healthy population controls without Parkinson's Disease,PD: Individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale. 
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",83,88,12 weeks,WMS,NA,Illumina,MaAsLin2,0.1,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2 & figure S2,11 March 2024,Idiaru angela,"Idiaru angela,Folakunmi",Summary of differential abundance results contrasting healthy population controls and PD patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",2|1239|186801|186802|216572|216851|853;2|1239|1262988;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|830,Complete,Folakunmi
bsdb:947/1/NA,Study 947,laboratory experiment,38479554,https://doi.org/10.1016/j.neulet.2024.137714,NA,"Wang Y, Ullah H, Deng T, Ren X, Zhao Z, Xin Y , Qiu J",Social isolation induces intestinal barrier disorder and imbalances gut microbiota in mice,Neuroscience letters,2024,"Gut microbiota, Intestinal barrier, Social isolation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Social deprivation,EFO:0009696,Normal Control NCd (8-week normal control group),Socially Isolated SId (8-week socially isolated group),Individually housed mice without any sensory communication with other mice for 8 weeks,10,10,None,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:947/2/1,Study 947,laboratory experiment,38479554,https://doi.org/10.1016/j.neulet.2024.137714,NA,"Wang Y, Ullah H, Deng T, Ren X, Zhao Z, Xin Y , Qiu J",Social isolation induces intestinal barrier disorder and imbalances gut microbiota in mice,Neuroscience letters,2024,"Gut microbiota, Intestinal barrier, Social isolation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Social deprivation,EFO:0009696,Normal Control NCc (15-week normal control group),Socially Isolated SIc (15-week socially isolated group),Individually housed mice without any sensory communication with other mice for 15 weeks,10,10,None,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 9B,18 April 2024,Barrakat,"Barrakat,Peace Sandy",Differentially abundant bacterial in Normal control (NCc) and Socially isolated (SIc) mice housed for 15 weeks,increased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|57723;2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|1224|28216|80840|506;2|1239|186801|3085636|186803|207244;2|1239|186801|3082720|3030910;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643;2|1224|28216|80840|80864;2|201174|84998|84999;2|201174|84998;2|200930|68337|191393|191394;2|200930|68337|191393;2|200930|68337;2|1239|91061|186826|1300|1357;2|200930|68337|191393|2945020|248038;2|1224|28211|204457|41297|13687;2|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:947/2/2,Study 947,laboratory experiment,38479554,https://doi.org/10.1016/j.neulet.2024.137714,NA,"Wang Y, Ullah H, Deng T, Ren X, Zhao Z, Xin Y , Qiu J",Social isolation induces intestinal barrier disorder and imbalances gut microbiota in mice,Neuroscience letters,2024,"Gut microbiota, Intestinal barrier, Social isolation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Social deprivation,EFO:0009696,Normal Control NCc (15-week normal control group),Socially Isolated SIc (15-week socially isolated group),Individually housed mice without any sensory communication with other mice for 15 weeks,10,10,None,16S,4,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 9B,18 April 2024,Barrakat,"Barrakat,Peace Sandy",Differentially abundant bacterial taxa in Normal control (NCc) and Socially isolated (SIc) mice housed for 15 weeks,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|1239|91061;2|1239;2|1117;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1224|1236|135619|135620|28253;2|1224|28211|356|119045;2|1224|28211|356|119045|407;2|1224|1236|135619|135620;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231,Complete,Peace Sandy
bsdb:948/1/1,Study 948,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T, Maeda T, Fujisawa Y, Tsuji H, Nomoto K, Ohno K , Hirayama M",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Disease staging,EFO:0000410,Stable Group at year 0,Deteriorated Group at year 0,The Deteriorated Group is the group of patients with significantly higher UPDRS(United Parkinson's Disease Rating Scale) score at year 0,18,18,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1A,16 April 2024,Idiaru angela,Idiaru angela,Abundance of Bifidobacterium at year 0 in the deteriorated and stable groups.,decreased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:948/2/1,Study 948,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T, Maeda T, Fujisawa Y, Tsuji H, Nomoto K, Ohno K , Hirayama M",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Timepoint,EFO:0000724,Parkinson's disease patients at year 0,Parkinson's disease patients at year 2,Patients with Parkinson's disease followed up after year 2,36,28,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & supplementary Table 2,16 April 2024,Idiaru angela,Idiaru angela,Difference of bacterial counts between years 0 and 2 in Parkinson's disease patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria",2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816|817;2|201174|84998|84999|1643824|1380;2|976|200643|171549|171552|838;2|1239|91061|186826|81852|1350;2,Complete,Svetlana up
bsdb:948/3/1,Study 948,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T, Maeda T, Fujisawa Y, Tsuji H, Nomoto K, Ohno K , Hirayama M",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Timepoint,EFO:0000724,Deteriorated Group at year 0,Deteriorated Group at year 2,The Deteriorated Group is the group of patients with significantly higher UPDRS(United Parkinson's Disease Rating Scale) score at year 2,18,11,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & supplementary Table 2,18 April 2024,Idiaru angela,Idiaru angela,Difference of bacterial counts between years 0 and 2 in the Deteriorated group.,decreased,k__Bacteria,2,Complete,Svetlana up
bsdb:948/4/1,Study 948,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T, Maeda T, Fujisawa Y, Tsuji H, Nomoto K, Ohno K , Hirayama M",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Timepoint,EFO:0000724,Stable group at year 0,Stable group at year 2,The Stable Group is the group of patients with significantly lower UPDRS(United Parkinson's Disease Rating Scale) score at year 2,18,17,NA,PCR,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & supplementary Table 2,18 April 2024,Idiaru angela,Idiaru angela,Difference of bacterial counts between years 0 and 2 in the Stable group.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|201174|84998|84999|1643824|1380;2;2|976|200643|171549|815|816|817;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:949/8/1,Study 949,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A, Jarquín-Díaz VH, Ebner F, Löber U, Hayani R, Kundik A, Cardilli A, Heitlinger E, Forslund SK , Hartmann S",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 8,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Gut microbiome measurement,EFO:0007874,Ascaris summ (Males),Ascaris suum (Females),Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,NA,NA,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,"Figure 4D, Table S7",12 April 2024,Barrakat,"Barrakat,Scholastica",Differentially abundant bacterial taxa in male versus female worms (Ascaris suum) present in German Landrace pig gut.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|186802|31979|1485;2|1239|909932|909929|1843491|52225|187979;2|1239|186801|3082720|186804|1505652;2|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:949/8/2,Study 949,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A, Jarquín-Díaz VH, Ebner F, Löber U, Hayani R, Kundik A, Cardilli A, Heitlinger E, Forslund SK , Hartmann S",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 8,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Gut microbiome measurement,EFO:0007874,Ascaris summ (Males),Ascaris suum (Females),Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,NA,NA,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,"Figure 4D, Table S7",12 April 2024,Barrakat,"Barrakat,Scholastica",Differentially abundant bacterial taxa in male versus female worms (Ascaris suum) present in German Landrace pig gut.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus porcorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|39948;2|65842|204430|218872|204431|832;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301|701526;2|1239|186801|186802|216572|292632;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:949/9/1,Study 949,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A, Jarquín-Díaz VH, Ebner F, Löber U, Hayani R, Kundik A, Cardilli A, Heitlinger E, Forslund SK , Hartmann S",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 9,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Gut microbiome measurement,EFO:0007874,Host (Ascaris suum infected Pigs) Microbiome,Parasite (Ascaris suum) Microbiome,Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,10,NA,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Figure 5A, Table S8",12 April 2024,Barrakat,"Barrakat,Scholastica",Differentially abundant bacteria taxa in Host (Pig) versus Parasite (Ascaris suum) Microbiome,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171552|1283313;2|1239|186801|3085636|186803|653683;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:949/9/2,Study 949,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A, Jarquín-Díaz VH, Ebner F, Löber U, Hayani R, Kundik A, Cardilli A, Heitlinger E, Forslund SK , Hartmann S",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 9,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Gut microbiome measurement,EFO:0007874,Host (Ascaris suum infected Pigs) Microbiome,Parasite (Ascaris suum) Microbiome,Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,10,NA,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,"Figure 5A, Table S8",12 April 2024,Barrakat,"Barrakat,Scholastica",Differentially abundant bacteria taxa in Host (Pig) versus Parasite (Ascaris suum) Microbiome,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Asaccharospora,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3082720|186804|1505660;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186807|2740;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|1302778;2|976|200643|171549|171552|370804;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:950/1/1,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 1,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,FIG 3a,12 March 2024,Imaspecial,"Imaspecial,Scholastica",Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using LEfSe,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|976|200643|171549;2|976|200643;2|976;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:950/1/2,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 1,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,FIG 3a,12 March 2024,Imaspecial,"Imaspecial,Scholastica",Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using LEfSe,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales",2|1239|91061;2|1239;2|1239|526524|526525|2810280|135858;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|909932;2|1239|909932|909929;2|1239|526524|526525|128827|123375;2|1239|909932|1843489|31977;2|1239|909932|1843489,Complete,Svetlana up
bsdb:950/2/1,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 2,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 3c,12 March 2024,Imaspecial,"Imaspecial,Scholastica",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|976|200643|171549;2|976|200643;2|976;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:950/2/2,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 2,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 3c,12 March 2024,Imaspecial,"Imaspecial,Scholastica",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis",2|201174;2|201174|84998|84999|1643824;2|1239|91061;2|1239|186801|186802|3085642;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|626935;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|526524|526525;2|201174|84998|84999|1643824|2082587;2|1239|526524|526525|2810280|3025755;2|1239|526524|526525|2810280|3025755|29348,Complete,Svetlana up
bsdb:950/3/1,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 3,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,WMS,NA,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 3e,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|976|200643|171549|171552|838;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:950/3/2,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 3,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,WMS,NA,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 3e,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,decreased,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,2|201174|84998|84999|84107|102106|147207,Complete,Svetlana up
bsdb:950/4/1,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 4,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 2a,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH)  using LEfSe,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|976|200643|171549;2|976|200643;2|976;2|1224|1236|91347;2|1224|1236;2|1224|1236|91347|1903414;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1224|1236|91347|1903414|586;2|1224;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:950/4/2,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 4,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 2a,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using LEfSe,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum",2|1239;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|536633;2|1239|186801;2|1117;2|1239|186801|3085636|186803;2|1239|186801|3085636;2|1239|186801|186802|216572;2|1239|186801|3082720|3120161|1481960;2|1239|186801|3082720|186804;2|1239|186801|3082720;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|1737404|1737405;2|1239|186801|3085636|186803|1506577|36835,Complete,Svetlana up
bsdb:950/5/1,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 5,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Table S3,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using Metastat,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota,k__Archaea|p__Euryarchaeota|c__Halobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|976;2|1224;2157|28890|183963;2|976|200643|171549|171552|838;2|1224|1236|91347|1903414|586;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|906,Complete,Svetlana up
bsdb:950/5/2,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 5,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Table S3,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using Metastat,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis",2|1239;2|200940;2|1117;2|74201;2|203682;2|67819;2|1239|186801|3085636|186803|572511;2|1239|186801|3082720|3120161|1481960;2|1239|186801|3085636|186803|1506577;2|1239|186801|186802|31979|1266;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|1407607;2|1224|1236|2887326|468|469;2|1239|91061|1385|186817|1386;2|1239|91061|1385|90964|1279;2|1239|186801|186802|186806|264995,Complete,Svetlana up
bsdb:950/6/1,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 6,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,Supplementary Table S3,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using Metastat,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Gemmatimonadota,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Myxococcota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Acidobacteriota|c__Thermoanaerobaculia|o__Thermoanaerobaculales|f__Thermoanaerobaculaceae|s__Thermoanaerobaculaceae bacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Acidobacteriota|c__Vicinamibacteria|s__Vicinamibacteria bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Arenimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella",2|976;2|57723;2|200940;2|142182;2|200795|32061;2|2818505;2|976|200643|171549|171552|838;2|976|200643|171549|2005473;2|1224|28216|80840|119060|48736;2|976|200643|171549|171552|370804;2|976|200643|171549|2005473|1918540;2|1239|91061|1385|186817|1386;2|57723|1562571|2562241|2562242|2699758;2|201174|1760|1643682|85030|38501;2|57723|1813735|2793154;2|1224|1236|135614|32033|490567;2|1224|28211|204441|2829815|204447,Complete,Svetlana up
bsdb:950/6/2,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 6,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,Supplementary Table S3,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using Metastat,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Anaerovoracaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",2|1239;2|1239|526524|526525|128827|123375;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|1506577;2|201174|84998|84999|1643824|2082587;2|1239|526524|526525|128827|1774107;2|1239|186801|3082720|3030910|3030912;2|1239|186801|186802|1392389,Complete,Svetlana up
bsdb:950/7/1,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 7,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Table S3,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using Metastat,increased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|57723;2|976;2|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:950/7/2,Study 950,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S , Wang Z",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 7,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Table S3,6 June 2024,Scholastica,Scholastica,Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using Metastat,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella",2|201174;2|203682;2|67819;2|201174|84998|84999|84107|102106;2|1239|526524|526525|2810280|3025755;2|201174|84998|84999|1643824|2082587,Complete,Svetlana up
bsdb:951/1/1,Study 951,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y, Qian F, Cheng X, Wang D, Wang Y, Pan Y, Chen L, Wang W , Tian Y",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Saliva samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,"Participants were excluded if they used antibiotics in the past 6 months, or if they used local antibiotics in the past 7 days",WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1E,12 March 2024,Aishat,"Aishat,Folakunmi",LEfSe analysis of salivary microorganisms in the T2DM (Type 2 Diabetes Mellitus) group and healthy control group,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus|s__Morococcus cerebrosus",2|1224|1236|135625|712|416916|739;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|43996|43997;2|1239|186801;2|1239|186801|186802|543314|2137877;2|1239|186801|186802|1898207;2|32066|203490|203491|203492|848|851;2|1239|186801|3085636|186803;2|1224|28216|206351|481|212742;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|28129;2|201174|1760|85006|1268|32207|43675;2|203691|203692|136|137;2|203691|203692|136;2|203691|203692;2|203691|203692|136|2845253|157;2|203691|203692|136|2845253|157|69710;2|1224|28216|206351|481|212742|1056807,Complete,Folakunmi
bsdb:951/1/2,Study 951,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y, Qian F, Cheng X, Wang D, Wang Y, Pan Y, Chen L, Wang W , Tian Y",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Saliva samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,"Participants were excluded if they used antibiotics in the past 6 months, or if they used local antibiotics in the past 7 days",WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1E,12 March 2024,Aishat,"Aishat,Folakunmi",LEfSe analysis of salivary microorganisms in the T2DM (Type 2 Diabetes Mellitus) group and healthy control group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aurantiaca",2|976|200643|171549|171552|1283313;2|1224|28216|80840|119060;2|1224|28216|80840;2|95818;2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060|47670|47671;2|976|200643|171549|171552|838|596085,Complete,Folakunmi
bsdb:951/2/1,Study 951,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y, Qian F, Cheng X, Wang D, Wang Y, Pan Y, Chen L, Wang W , Tian Y",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Supragingival dental plaque samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,"Participants were excluded if they used antibiotics in the past 6 months, or if they used local antibiotics in the past 7 days",WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1F,20 March 2024,Folakunmi,Folakunmi,LEfSe analysis of supragingival plaque samples between patients with type II diabetes and healthy controls,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. CM59,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 329",2|976|200643;2|976|117743|200644|49546|1016;2|976|117743|200644|49546|1016|45242;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743|200644|49546|237;2|1224|28216|206351|481|482|484;2|976|200643|171549|171552|838|28132;2|976|117743|200644|49546|1016|936370;2|976|117743|200644|49546|1016|706435,Complete,Folakunmi
bsdb:951/2/2,Study 951,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y, Qian F, Cheng X, Wang D, Wang Y, Pan Y, Chen L, Wang W , Tian Y",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Supragingival dental plaque samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,"Participants were excluded if they used antibiotics in the past 6 months, or if they used local antibiotics in the past 7 days",WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1F,20 March 2024,Folakunmi,Folakunmi,LEfSe analysis of supragingival plaque samples between patients with type II diabetes and healthy controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 170,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. oral taxon 014,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|544581;2|201174|1760|2037|2049|1654|461393;2|201174|1760|2037|2049|1654|1655;2|201174|1760|2037|2049|1654|712117;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|1224|28216|80840|506;2|201174|1760|85009|31957|2801844|1750;2|1224|28216|80840|119060;2|1224|28216|80840;2|1224|1236|135615|868;2|1224|1236|135615|868|2717;2|1224|1236|135615|868|2717|2718;2|201174|1760|85007|1653|1716|61592;2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060|47670|47671;2|201174|1760|85006|1268;2|1224|1236|2887326|468;2|1224|28216|206351|481|482|641148;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|172042;2|1239|91061|186826|1300|1301|1305;2|1224|1236|135615,Complete,Folakunmi
bsdb:952/1/1,Study 952,"cross-sectional observational, not case-control",35463646,10.3389/fcimb.2022.837019,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022099/,"Fu SC, Lee CH, Hsieh YC, Wu PH, Lin SH , Wang H","A Pilot Study Exploring the Association of Entacapone, Gut Microbiota, and the Subsequent Side Effects in Patients With Parkinson's Disease",Frontiers in cellular and infection microbiology,2022,"Parkinson’s disease, constipation, drowsiness, entacapone, levodopa, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Parkinson's disease (PD) patients treated with levodopa only (PD_L),Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE),"Parkinson's disease (PD) patients treated with both levodopa and Entacapone, a peripherally acting catechol-O-methyltransferase (COMT) inhibitor that is used in addition to levodopa to control symptoms.",13,11,None,16S,45,Ion Torrent,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3, text",9 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica",Genera significantly different in abundance in Parkinson's disease patients treated with levodopa only (PD_L) versus Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE).,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|201174|1760|85004|31953|1678;2|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:952/1/2,Study 952,"cross-sectional observational, not case-control",35463646,10.3389/fcimb.2022.837019,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022099/,"Fu SC, Lee CH, Hsieh YC, Wu PH, Lin SH , Wang H","A Pilot Study Exploring the Association of Entacapone, Gut Microbiota, and the Subsequent Side Effects in Patients With Parkinson's Disease",Frontiers in cellular and infection microbiology,2022,"Parkinson’s disease, constipation, drowsiness, entacapone, levodopa, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Parkinson's disease (PD) patients treated with levodopa only (PD_L),Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE),"Parkinson's disease (PD) patients treated with both levodopa and Entacapone, a peripherally acting catechol-O-methyltransferase (COMT) inhibitor that is used in addition to levodopa to control symptoms.",13,11,None,16S,45,Ion Torrent,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3, text",9 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica",Genera significantly different in abundance in Parkinson's disease patients treated with levodopa only (PD_L) versus Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|186804|1505657;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|1769710,Complete,Svetlana up
bsdb:953/1/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Esophagus samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2B,12 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,NA
bsdb:953/1/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Esophagus samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 2B,14 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|724,Complete,NA
bsdb:953/2/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Cardia biopsy samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2B,12 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,NA
bsdb:953/2/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Cardia biopsy samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 2B,14 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,2|1239|91061|186826|33958|46255,Complete,NA
bsdb:953/3/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Non-cardia biopsy samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2B,12 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,NA
bsdb:953/3/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Non-cardia biopsy samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 2B,14 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|29547|3031852|213849|72293|209,Complete,NA
bsdb:953/4/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Gastric juice sample,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2B,12 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,NA
bsdb:953/4/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Gastric juice sample,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 2B,14 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,NA
bsdb:953/5/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Fecal samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2B,12 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,NA
bsdb:953/5/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Upper digestive tract disease,MONDO:0044991,Fecal samples,Saliva samples,Saliva samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 2B,14 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511,Complete,NA
bsdb:953/6/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 6,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Cardia biopsy samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,12 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|724,Complete,NA
bsdb:953/6/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 6,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Cardia biopsy samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,14 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,2|1239|91061|186826|33958|46255,Complete,NA
bsdb:953/7/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 7,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Non-cardia biopsy samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2B,14 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|724,Complete,NA
bsdb:953/7/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 7,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Non-cardia biopsy samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|29547|3031852|213849|72293|209,Complete,NA
bsdb:953/8/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 8,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Gastric juice samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|724,Complete,NA
bsdb:953/8/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 8,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Gastric juice samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,NA
bsdb:953/9/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 9,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Fecal samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|724,Complete,NA
bsdb:953/9/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 9,China,Homo sapiens,Esophagus,UBERON:0001043,Upper digestive tract disease,MONDO:0044991,Fecal samples,Esophageal swab samples,Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511,Complete,NA
bsdb:953/10/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 10,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Upper digestive tract disease,MONDO:0044991,Non-cardia biopsy samples,Cardia biopsy samples,Cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,2|1239|91061|186826|33958|46255,Complete,NA
bsdb:953/10/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 10,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Upper digestive tract disease,MONDO:0044991,Non-cardia biopsy samples,Cardia biopsy samples,Cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|29547|3031852|213849|72293|209,Complete,NA
bsdb:953/11/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 11,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Upper digestive tract disease,MONDO:0044991,Gastric juice samples,Cardia biopsy samples,Cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,2|1239|91061|186826|33958|46255,Complete,NA
bsdb:953/11/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 11,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Upper digestive tract disease,MONDO:0044991,Gastric juice samples,Cardia biopsy samples,Cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,NA
bsdb:953/12/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 12,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Upper digestive tract disease,MONDO:0044991,Fecal samples,Cardia biopsy samples,Cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,2|1239|91061|186826|33958|46255,Complete,NA
bsdb:953/12/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 12,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Upper digestive tract disease,MONDO:0044991,Fecal samples,Cardia biopsy samples,Cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511,Complete,NA
bsdb:953/13/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 13,China,Homo sapiens,Body of stomach,UBERON:0001161,Upper digestive tract disease,MONDO:0044991,Gastric juice samples,Non-cardia biopsy samples,Non-cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|29547|3031852|213849|72293|209,Complete,NA
bsdb:953/13/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 13,China,Homo sapiens,Body of stomach,UBERON:0001161,Upper digestive tract disease,MONDO:0044991,Gastric juice samples,Non-cardia biopsy samples,Non-cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,NA
bsdb:953/14/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 14,China,Homo sapiens,Body of stomach,UBERON:0001161,Upper digestive tract disease,MONDO:0044991,Fecal samples,Non-cardia biopsy samples,Non-cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|29547|3031852|213849|72293|209,Complete,NA
bsdb:953/14/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 14,China,Homo sapiens,Body of stomach,UBERON:0001161,Upper digestive tract disease,MONDO:0044991,Fecal samples,Non-cardia biopsy samples,Non-cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511,Complete,NA
bsdb:953/15/1,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 15,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,Fecal samples,Gastric juice samples,Gastric juice samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,NA
bsdb:953/15/2,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 15,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,Fecal samples,Gastric juice samples,Gastric juice samples from 40 participants undergoing upper gastrointestinal endoscopy.,40,40,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,15 March 2024,Aleru Divine,Aleru Divine,LEfSe results for characteristic genera in different GI sites.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|572511,Complete,NA
bsdb:953/16/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 16,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Upper digestive tract disease,MONDO:0044991,H. pylori negative group,H. pylori positive group,Participants who tested positive for H. pylori infection (cardia samples),20,20,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/17/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 17,China,Homo sapiens,Body of stomach,UBERON:0001161,Upper digestive tract disease,MONDO:0044991,H. pylori negative group,H. pylori positive group,Participants who tested positive for H. pylori infection (non-cardia samples),20,20,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/18/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 18,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,H (higher pH) group,HP (higher pH and H. pylori positive) group,Participants with higher pH and H. pylori positive.,12,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/19/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 19,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,HN (higher pH and H. pylori negative) group,HP (higher pH and H. pylori positive) group,Participants with higher pH and H. pylori positive.,NA,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/20/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 20,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,P (H. pylori positive) group,HP (higher pH and H. pylori positive) group,Participants with higher pH and H. pylori positive.,20,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/21/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 21,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LP (Lower pH and H. pylori positive) group,HP (higher pH and H. pylori positive) group,Participants with higher pH and H. pylori positive.,NA,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/22/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 22,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,L (Lower pH ) group,HP (higher pH and H. pylori positive) group,Participants with higher pH and H. pylori positive.,28,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/23/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 23,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,N (H. pylori negative) group,HP (higher pH and H. pylori positive) group,Participants with higher pH and H. pylori positive.,20,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/24/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 24,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LN (Lower pH and H. pylori negative) group,HP (higher pH and H. pylori positive) group,Participants with higher pH and H. pylori positive.,NA,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/25/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 25,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,HN (higher pH and H. pylori negative) group,H (higher pH ) group,Participants with higher pH (pH of gastric juice of >2).,NA,12,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/26/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 26,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,P (H. pylori positive) group,H (higher pH ) group,Participants with higher pH (pH of gastric juice of >2).,20,12,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/27/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 27,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LP (Lower pH and H. pylori positive) group,H (higher pH ) group,Participants with higher pH (pH of gastric juice of >2).,NA,12,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/28/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 28,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,L (Lower pH ) group,H (higher pH ) group,Participants with higher pH (pH of gastric juice of >2).,28,12,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/29/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 29,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,N (H. pylori negative) group,H (higher pH ) group,Participants with higher pH (pH of gastric juice of >2).,20,12,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/30/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 30,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LN (Lower pH and H. pylori negative) group,H (higher pH ) group,Participants with higher pH (pH of gastric juice of >2).,NA,12,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/31/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 31,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,P (H. pylori positive) group,HN (Higher pH and H. pylori negative ) group,Participants with Higher pH and are H. pylori negative.,20,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/32/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 32,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LP (Lower pH and H. pylori positive) group,HN (Higher pH and H. pylori negative ) group,Participants with Higher pH and are H. pylori negative.,NA,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/33/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 33,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,L (Lower pH) group,HN (Higher pH and H. pylori negative ) group,Participants with Higher pH and are H. pylori negative.,28,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/34/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 34,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,N (H. pylori negative) group,HN (Higher pH and H. pylori negative ) group,Participants with Higher pH and are H. pylori negative.,20,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/35/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 35,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LN (Lower pH and H. pylori negative) group,HN (Higher pH and H. pylori negative ) group,Participants with Higher pH and are H. pylori negative.,NA,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/36/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 36,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LP (Lower pH and H. pylori positive) group,P (H. pylori positive) group,Participants that tested positive for the H. pylori infection.,NA,20,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/37/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 37,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,L (Lower pH) group,P (H. pylori positive) group,Participants that tested positive for the H. pylori infection.,28,20,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/38/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 38,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,N (H. pylori negative) group,P (H. pylori positive) group,Participants that tested positive for the H. pylori infection.,20,20,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/39/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 39,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LN (Lower pH and H. pylori negative) group,P (H. pylori positive) group,Participants that tested positive for the H. pylori infection.,NA,20,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/40/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 40,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,L (Lower pH) group,LP (Lower pH and H. pylori positive) group,Participants with lower pH and tested positive for the H. pylori infection.,28,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/41/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 41,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,N (H. pylori negative) group,LP (Lower pH and H. pylori positive) group,Participants with lower pH and tested positive for the H. pylori infection.,20,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/42/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 42,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LN (Lower pH and H. pylori negative) group,LP (Lower pH and H. pylori positive) group,Participants with lower pH and tested positive for the H. pylori infection.,NA,NA,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/43/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 43,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,N (H. pylori negative) group,L (Lower pH) group,Participants with lower pH (pH of gastric juice of <2).,20,28,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/44/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 44,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LN (Lower pH and H. pylori negative) group,L (Lower pH) group,Participants with lower pH (pH of gastric juice of <2).,NA,28,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:953/45/NA,Study 953,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C , Wei W","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 45,China,Homo sapiens,Gastric juice,UBERON:0001971,Upper digestive tract disease,MONDO:0044991,LN (Lower pH and H. pylori negative) group,N (H. pylori negative) group,Participants that tested negative for the H. pylori infection.,NA,20,One month before sample collection.,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:954/1/1,Study 954,laboratory experiment,37819112,10.1128/msphere.00431-23,NA,"Cui C, Song H, Han Y, Yu H, Li H, Yang Y , Zhang B",Gut microbiota-associated taurine metabolism dysregulation in a mouse model of Parkinson's disease,mSphere,2023,"Lactobacillus, Parkinson's disease, metabolism, microbiota, taurine",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control mice,MPTP-treated mice,"Mice were injected with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), to induce Parkinson's disease.",10,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3I,12 March 2024,Victoria,Victoria,"Cladogram of linear discriminant analysis scores for differentially abundant bacteria (phylum, class, order, and family). Only taxa meeting a linear discriminant analysis significant threshold of >2.0 are shown.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|2037;2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|84998|84999|84107;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|1760|85007|85025;2|976|200643|171549|1853231|283168;2|201174|1760|85007|85025|1827;2|976|200643|171549|171550|28138;2|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:954/1/2,Study 954,laboratory experiment,37819112,10.1128/msphere.00431-23,NA,"Cui C, Song H, Han Y, Yu H, Li H, Yang Y , Zhang B",Gut microbiota-associated taurine metabolism dysregulation in a mouse model of Parkinson's disease,mSphere,2023,"Lactobacillus, Parkinson's disease, metabolism, microbiota, taurine",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control mice,MPTP-treated mice,"Mice were injected with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), to induce Parkinson's disease.",10,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3I,12 March 2024,Victoria,Victoria,"Cladogram of linear discriminant analysis scores for differentially abundant bacteria (phylum, class, order, and family). Only taxa meeting a linear discriminant analysis significant threshold of >2.0 are shown.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|201174|84998|1643822|1643826|447020;2|976|200643|171549|815;2|976|200643|171549;2|976|200643;2|976;2|976|200643|171549|1853231|574697;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|976|200643|171549|2005473;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:955/1/1,Study 955,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J, Wang Y, Chen D, Xu X, Li W, Li K, He J, Su W , Luo Q",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease (PD) Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),22,19,None,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5c,12 March 2024,Scholastica,Scholastica,Taxa significantly abundant in the duodenal mucosal microbiota composition in control versus Parkinson's disease (PD) patients,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia",2|1224|28216|80840|119060;2|1224|28216|80840;2|1224|1236;2|1239|91061|186826|1300|1357;2|1224|28216|80840|75682|149698;2|1224|28216|80840|75682;2|1224;2|1224|28216|80840|119060|48736,Complete,Svetlana up
bsdb:955/1/2,Study 955,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J, Wang Y, Chen D, Xu X, Li W, Li K, He J, Su W , Luo Q",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease (PD) Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),22,19,None,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5c,12 March 2024,Scholastica,Scholastica,Taxa significantly abundant in the duodenal mucosal microbiota composition in control versus Parkinson's disease (PD) patients,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",2|976|117743|200644|49546;2|1224|28211|204441,Complete,Svetlana up
bsdb:955/2/1,Study 955,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J, Wang Y, Chen D, Xu X, Li W, Li K, He J, Su W , Luo Q",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 2,China,Homo sapiens,Mucosa of sigmoid colon,UBERON:0004993,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),21,19,None,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5d,12 March 2024,Scholastica,Scholastica,Taxa significantly abundant in the sigmoid mucosal microbiota composition in control versus Parkinson's disease (PD) patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|201174|1760|85004|31953|1678|216816;2|976|200643|171549|171552,Complete,Svetlana up
bsdb:955/2/2,Study 955,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J, Wang Y, Chen D, Xu X, Li W, Li K, He J, Su W , Luo Q",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 2,China,Homo sapiens,Mucosa of sigmoid colon,UBERON:0004993,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),21,19,None,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5d,12 March 2024,Scholastica,Scholastica,Taxa significantly abundant in the sigmoid mucosal microbiota composition in control versus Parkinson's disease (PD) patients,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,2|1239|91061|1385|186824,Complete,Svetlana up
bsdb:955/3/NA,Study 955,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J, Wang Y, Chen D, Xu X, Li W, Li K, He J, Su W , Luo Q",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 3,China,Homo sapiens,Mucosa of sigmoid colon,UBERON:0004993,Parkinson's disease,MONDO:0005180,Duodenal mucosa,Sigmoid mucosa,Samples from the sigmoid mucosa of Parkinson's disease (PD) patients,19,19,None,16S,4,Illumina,Kruskall-Wallis,0.05,FALSE,4,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:956/1/1,Study 956,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen YH, Yu H, Xue F, Bai J, Guo L , Peng ZW",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia patients with prominent negative symptoms (SCH-N),Patients with schizophrenia with prominent negative symptoms (SCH-N) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60 according to the Statistical Clinical Interview for DSM-5 by two psychiatrists.,36,30,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Differential species abundance in gut microbiome between healthy controls versus schizophrenia patients with prominent negative symptoms (SCH-N) based on (LEfSe) analysis.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales",2|1224|28216|80840|506|222;2|1239|526524|526525|2810280|100883;2|201174|1760|85007|1653;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|526524|526525|128827|1573534;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|1224|1236;2|1239|186801|3085636|186803|1506553;2|976|200643|171549|2005473;2|1224|1236|135625|712|1960084;2|1239|186801|186802|31979|1266;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|976|200643|171549|2005473;2|1224;2|201174|1760|85007,Complete,Svetlana up
bsdb:956/1/2,Study 956,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen YH, Yu H, Xue F, Bai J, Guo L , Peng ZW",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia patients with prominent negative symptoms (SCH-N),Patients with schizophrenia with prominent negative symptoms (SCH-N) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60 according to the Statistical Clinical Interview for DSM-5 by two psychiatrists.,36,30,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Differential species abundance in gut microbiome between healthy controls versus schizophrenia patients with prominent negative symptoms (SCH-N) based on (LEfSe) analysis.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota",2|1239|186801|3085636|186803|1766253;2|1224|28216|80840|506|507;2|1239|186801|186802|3085642;2|1239|186801|186802|3085642|580596;2|1239|186801;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|216572|216851;2|976|117743|200644|49546;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|877420;2|1239|186801|3085636;2|1239|909932|909929|1843491|52225;2|1239|186801|3085656|3085657;2|1239|186801|3085656;2|1239|186801|3085656|3085657|2039302;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|216572;2|1239|186801|186802;2|1239,Complete,Svetlana up
bsdb:956/2/1,Study 956,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen YH, Yu H, Xue F, Bai J, Guo L , Peng ZW",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients with prominent negative symptoms (SCH-N),Schizophrenia patients with prominent positive symptoms (SCH-P),"Patients with schizophrenia with prominent positive symptoms (SCH-P) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60; at least three out of seven items of PANSS positive subscale score ≥4, or at least two items score ≥5, and a total PANSS positive subscale score ≥20, and at least 3 points more than the total PANSS negative subscale score.",30,32,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Differential species abundance in gut microbiome between schizophrenia patients with prominent negative (SCH-N) versus positive (SCH-P) symptoms based on (LEfSe) analysis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",2|976|200643|171549;2|1224|28211|204458|76892|41275;2|1224|1236|72274;2|1239|186801|186802|31979|1266,Complete,Svetlana up
bsdb:956/2/2,Study 956,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen YH, Yu H, Xue F, Bai J, Guo L , Peng ZW",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients with prominent negative symptoms (SCH-N),Schizophrenia patients with prominent positive symptoms (SCH-P),"Patients with schizophrenia with prominent positive symptoms (SCH-P) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60; at least three out of seven items of PANSS positive subscale score ≥4, or at least two items score ≥5, and a total PANSS positive subscale score ≥20, and at least 3 points more than the total PANSS negative subscale score.",30,32,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Differential species abundance in gut microbiome between schizophrenia patients with prominent negative (SCH-N) versus positive (SCH-P) symptoms based on (LEfSe) analysis.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",2|1224|28211;2|1239|1737404|1582879;2|1224|28211|356|82115;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|356,Complete,Svetlana up
bsdb:957/1/1,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 1,South Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,69,74,participants using antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 1f,30 March 2024,Idiaru angela,Idiaru angela,"comparison of the oral microbiome between PD and HCs using genus level
LEfSe analysis.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|201174|1760|85004|31953|419014;2|976|117743|200644|49546|1016;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|3030910|86331;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186806|113286;2|201174|1760|85004|31953|196081;2|201174|84998|1643822|1643826|84108,Complete,Svetlana up
bsdb:957/1/2,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 1,South Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,69,74,participants using antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,figure 1f,30 March 2024,Idiaru angela,Idiaru angela,comparison of the oral microbiome between PD and HCs using genus level LEfSe analysis.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1239|91061|186826|186827|46123;2|1224|28216|80840|119060|47670;2|1239|186801|186802|216572|459786;2|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:957/2/1,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,South Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Patients with Parkinson's disease whose H&Y stage was 3 or greater,NA,NA,participants using antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 3d,30 March 2024,Idiaru angela,Idiaru angela,Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",2|1239|909932|1843489|31977|906;2|201174|1760|85004|31953|1678;2|976|117743|200644|49546|1016;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|1578;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186806|113286;2|201174|1760|85004|31953|196081,Complete,Svetlana up
bsdb:957/2/2,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,South Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Patients with Parkinson's disease whose H&Y stage was 3 or greater,NA,NA,participants using antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary figure 3d,30 March 2024,Idiaru angela,Idiaru angela,Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,2|1224|28216|80840|119060|47670,Complete,Svetlana up
bsdb:957/3/1,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Parkinson's disease patients whose H&Y scale stage was 3 or greater.,NA,NA,participants using antibiotics.,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 3b,30 March 2024,Idiaru angela,Idiaru angela,Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",2|201174|1760|85004|31953|1678;2|1239|186801|3085636|3018741|698776;2|1239|186801|3085636|186803|33042;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|201174|84998|84999|1643824|133925;2|1224|1236|91347|1903414|583,Complete,Svetlana up
bsdb:957/3/2,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Parkinson's disease patients whose H&Y scale stage was 3 or greater.,NA,NA,participants using antibiotics.,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary figure 3b,30 March 2024,Idiaru angela,Idiaru angela,Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|3118652|2039240;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|28050,Complete,Svetlana up
bsdb:957/4/1,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,participants using antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,"figure 1e & text in paragraph 4, page 4",30 March 2024,Idiaru angela,Idiaru angela,Comparison of the gut microbiome between PD and HCs using genus level LEfSe analysis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|976|200643|171549|171550|239759;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803|1649459;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|44748,Complete,Svetlana up
bsdb:957/4/2,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,participants using antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,figure 1e,30 March 2024,Idiaru angela,Idiaru angela,Comparison of gut microbiome between PD and HCs using genus level LEfSe analysis.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|33042;2|1239|91061|186826|81852|1350;2|1224|1236|135625|712|724;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:957/5/1,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,participants using antibiotics,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,"Figure 3c & paragraph 2, page 5",30 March 2024,Idiaru angela,Idiaru angela,Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",2|976|200643|171549|171550|239759|328813;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|818;2|976|200643|171549|2005519|397864|487174;2|200940|3031449|213115|194924|35832|35833;2|976|200643|171549|1853231|574697|544645;2|1239|186801|3085636|186803|3342669|45851;2|1239|186801|186802|216572|2591381|2093857;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|375288|46503;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|815|909656|357276,Complete,Svetlana up
bsdb:957/5/2,Study 957,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW , Chung SJ",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,participants using antibiotics,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3c,30 March 2024,Idiaru angela,Idiaru angela,Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|204475|745368;2|1239|186801|3085636|186803|841|301302;2|1239|186801|186802|216572|1263|40519;2|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:958/1/1,Study 958,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant event-free group (EF),cases without any symptoms and with negative pathology were considered event-free patients after transplantation.,20,15,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,figure 3 A,13 March 2024,Glorious,"Glorious,Fiddyhamma,Folakunmi",Lefse analysis to identify the microbial species that exhibited the most significant differences between NT and EF,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|1239|91061;2|1239|91061|1385|186817|1386;2|1239|186801|186802|31979;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|186801|186802;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810280|3025755,Complete,Folakunmi
bsdb:958/1/2,Study 958,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant event-free group (EF),cases without any symptoms and with negative pathology were considered event-free patients after transplantation.,20,15,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,figure 3 A,18 March 2024,Glorious,"Glorious,Fiddyhamma,Folakunmi",Lefse analysis to identify the microbial species that exhibited the most significant differences between NT and EF,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|186801|3085636|186803|1766253;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976;2|1239|186801|3085636|186803|2383;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|976|200643|171549|171552|2974265|363265;2|1239|909932;2|1239|186801|186802|216572;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Folakunmi
bsdb:958/2/1,Study 958,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant chronic rejection group (CR),The lung transplant rejection participants were patients who survived more than 6 months after transplant and were all cases of chronic rejection.,20,17,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 3B,13 March 2024,Glorious,"Glorious,Fiddyhamma","From the LEfSe analysis, CR group exhibited a higher abundance of Lacticaseibacillus, Enterococcus, Streptococcus and other significant taxas",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|91061;2|1239|91061|1385|186817|1386;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|2759736;2|1239|91061|186826;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1224|1236|91347|543;2|1239|91061|186826|33958,Complete,Folakunmi
bsdb:958/2/2,Study 958,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant chronic rejection group (CR),The lung transplant rejection participants were patients who survived more than 6 months after transplant and were all cases of chronic rejection.,20,17,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 3B,18 March 2024,Glorious,"Glorious,Fiddyhamma","Within the lung transplant cohort, a significant decrease in Bacteroides, Epulopiscium, Faecalibacterium, Prevotella and other significant taxas was observed.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976;2|1239|186801|3085636|186803|2383;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|1239|186801|3085636|186803;2|1239|186801|3085636;2|976|200643|171549|171552|2974265|363265;2|1239|909932;2|1239|186801|186802|216572;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Folakunmi
bsdb:958/3/1,Study 958,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,Lung transplant event-free group (EF),Lung transplant chronic rejection group (CR),The lung transplant rejection participants were patients who survived more than 6 months after transplant and were all cases of chronic rejection.,15,17,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3c,10 April 2024,Fiddyhamma,"Fiddyhamma,Folakunmi","In analyzing the EF and CR cohorts (Fig. 3C), only Ruminococcus gnavus group was
found dominant in the EF group.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,2|1239|186801|3085636|186803|2316020|33038,Complete,Folakunmi
bsdb:959/1/1,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Essential thrombocythemia (ET),"Patients with essential thrombocythemia (ET), a cancer characterized by thrombocyte overproduction",42,54,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Fig 6a,12 March 2024,Deacme,Deacme,Differential abundance analysis identified using LEfSe between healthy controls and patients with Essential Thrombocythemia,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174;2|201174|84998|84999;2|201174|84998;2|1239|526524|526525|128827;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:959/1/2,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Essential thrombocythemia (ET),"Patients with essential thrombocythemia (ET), a cancer characterized by thrombocyte overproduction",42,54,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 2,Fig 6a,12 March 2024,Deacme,"Deacme,Scholastica",Differential abundance analysis identified using LEfSe between healthy controls and patients with Essential Thrombocythemia,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota",2|1239|186801|3085636|186803|1766253;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|186801|3085636;2|1239|186801|186802|216572;2|1239,Complete,Svetlana up
bsdb:959/2/1,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,42,36,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Fig 6b,14 March 2024,Deacme,Deacme,Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients positive for the JAK2V617F mutation,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174;2|201174|84998|84999;2|201174|84998;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:959/2/2,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,42,36,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 2,Fig 6b,14 March 2024,Deacme,"Deacme,Scholastica",Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients positive for the JAK2V617F mutation,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3085636|186803|1766253;2|1239|186801;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|186801|3085636;2|1239|186801|186802|216572;2|1239;2|1239|186801|186802,Complete,Svetlana up
bsdb:959/3/1,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-negative,Essential thrombocythemia patients negative for the Janus-kinase 2 (JAK2V617F) mutation,42,16,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Fig 6c,14 March 2024,Deacme,Deacme,Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients negative for the JAK2V617F mutation,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|201174|84998|84999;2|201174|84998;2|1239|186801|186802|216572;2|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:959/3/2,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-negative,Essential thrombocythemia patients negative for the Janus-kinase 2 (JAK2V617F) mutation,42,16,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 2,Fig 6c,14 March 2024,Deacme,"Deacme,Scholastica",Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients negative for the JAK2V617F mutation,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803|1766253;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803;2|1239|186801|3085636;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:959/4/1,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Janus-kinase 2 (JAK2V617F)-negative,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,16,36,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Fig 6d,14 March 2024,Deacme,Deacme,Differential abundance analysis identified using LEfSe between Essential thrombocythemia patients negative for the JAK2V617F mutation and patients positive for the JAK2V617F mutation,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",2|1239|91061;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|526524|526525,Complete,Svetlana up
bsdb:959/4/2,Study 959,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ , Nielsen XC",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Janus-kinase 2 (JAK2V617F)-negative,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,16,36,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 2,Fig 6d,16 March 2024,Deacme,Deacme,Differential abundance analysis identified using LEfSe between Essential thrombocythemia patients negative for the JAK2V617F mutation and patients positive for the JAK2V617F mutation,decreased,NA,NA,Complete,Svetlana up
bsdb:960/1/1,Study 960,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H, Zhang H, Hou B, Xu B, Ji L , Wu Y",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-L,"Curcumin low-dose (CUR-L) group received a combination of both treatments in
which curcumin (40 mg/kg)",12,12,NA,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Fig 5 and Text,13 March 2024,MyleeeA,MyleeeA,Differential distribution of Specie in the gut Microbiota between MPTP and CUR-L.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. S457,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Cyanobacteriota,k__Bacteria,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. L-YJ,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",2|201174|84998|1643822|1643826|447020;2|201174|84998|1643822|1643826|447020|446660;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|1501391;2|976|200643|171549|171550|239759|1647659;2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|1283313|76122;2|544448|31969|186332|186333|2086;2|544448|31969|186332|186333;2|544448|31969|186332;2|1239|186801|3085636|3118652|2039240;2|1239|186801|3085636|3118652|2039240|2039241;2|976|200643|171549;2|976|200643;2|1798710|1906119;2|1117;2;2|201174|84998|1643822|1643826;2|201174|84998|1643822;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|1506553|2028282;2|1239|91061|186826|33958|1578|215530;2|976|200643|171549|2005473|2518497;2|976|200643|171549|2005473|2518497|2094151;2|976|200643|171549|171552;2|976|200643|171549|171550;2|1239|186801|186802|543314|35517;2|544448|31969|186332|186333|2086;2|1798710|1906119;;2|1239|186801|186802|31979|1485|59620,Complete,Svetlana up
bsdb:960/1/2,Study 960,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H, Zhang H, Hou B, Xu B, Ji L , Wu Y",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-L,"Curcumin low-dose (CUR-L) group received a combination of both treatments in
which curcumin (40 mg/kg)",12,12,NA,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Fig 5 and Text,14 March 2024,MyleeeA,MyleeeA,"Differential distribution of Specie in the gut Microbiota between MPTP and CUR-L
.",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus hilgardii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Bacteria,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|74201|203494|48461|1647988;2|201174|84998|84999|1643824;2;2|95818|2093818|2093825|2171986;2|95818|2093818|2093825;2|95818|2093818;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|1392389;2|1239|91061|186826|33958|2767893|1588;2|1239|91061|186826|33958|2742598|1598;2|976|200643|171549|2005473|1918540|1796646;2;2|74201|203494|48461;2|74201|203494;2|74201;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|186802|1392389;2|201174|1760|85004|31953|1678|165187,Complete,Svetlana up
bsdb:960/2/1,Study 960,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H, Zhang H, Hou B, Xu B, Ji L , Wu Y",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-M,Curcumin Medium-dose (CUR-M) group received a combination of both treatments in which curcumin (80 mg/kg),12,12,NA,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Fig 5 and Text,14 March 2024,MyleeeA,MyleeeA,Differential distribution of Specie in the gut Microbiota between MPTP and CUR-M.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DENB20,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__uncultured Streptococcus sp.",2|976|200643|171549|815|816|85831;2|1224|28216;2|1224|28216|80840|119060;2|201174|84998|1643822|1643826;2|201174|84998|1643822|1643826|580024;2|1239|186801|186802|186806|1730|290054;2|1239|186801|3085636|186803|1506553|2028282;2|976|200643|171549|2005473|2518497;2|976|200643|171549|2005473|2518497|2094151;2|976|200643|171549|171552;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|1231603;2|976|200643|171549|171550;2|201174|84998|1643822|1643826|580024;2|1239|91061|186826|1300|1301|83427,Complete,Svetlana up
bsdb:960/2/2,Study 960,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H, Zhang H, Hou B, Xu B, Ji L , Wu Y",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-M,Curcumin Medium-dose (CUR-M) group received a combination of both treatments in which curcumin (80 mg/kg),12,12,NA,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Fig 5 and Text,14 March 2024,MyleeeA,MyleeeA,Differential distribution of Specie in the gut Microbiota between MPTP and CUR-M.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus hilgardii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.",2|1239|186801|3085636|186803|1427378;2|1239|186801|3085636|186803|1427378|1872090;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958|2767893|1588;2|1239|91061|186826|33958|2742598|1598;2|1239|186801|186802|186806|1730|165185,Complete,Svetlana up
bsdb:960/3/1,Study 960,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H, Zhang H, Hou B, Xu B, Ji L , Wu Y",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-H,Curcumin High-dose (CUR-H) group received a combination of both treatments in which curcumin (160 mg/kg),12,12,NA,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Fig 5 and Text,14 March 2024,MyleeeA,MyleeeA,Differential distribution of Specie in the gut Microbiota between MPTP and CUR-H.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. L-YJ,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DENB20,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum|s__uncultured Allobaculum sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.",2|201174;2|1239|526524|526525|128827|174708;2|1239;2|201174|84998|84999;2|201174|84998;2|201174|84998|1643822|1643826;2|201174|84998|1643822|1643826|580024;2|1239|186801|186802|1392389;2|1239|91061|186826|33958|1578|215530;2|544448|31969;2|544448;2|976|200643|171549|2005473|2518497;2|976|200643|171549|2005473|2518497|2094151;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|1231603;2|201174|84998|1643822|1643826|580024;2|1239|186801|186802|1392389;2|1239|526524|526525|128827|174708|1187017;2|1239|186801|186802|216572|1508657|1757166,Complete,Svetlana up
bsdb:960/3/2,Study 960,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H, Zhang H, Hou B, Xu B, Ji L , Wu Y",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-H,Curcumin High-dose (CUR-H) group received a combination of both treatments in which curcumin (160 mg/kg),12,12,NA,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Fig 5 and Text,15 March 2024,MyleeeA,MyleeeA,Differential distribution of Specie in the gut Microbiota between MPTP and CUR-H.,decreased,"k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus hilgardii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",2|95818|2093818|2093825;2|95818|2093818;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186806|1730|290054;2|1239|526524|526525|128827|61170;2|1239|526524|526525|128827|61170|1468449;2|1239|91061|186826|33958|2767893|1588;2|1239|91061|186826|33958|2742598|1598;2;2|1239|186801|186802|543314|35518;2|95818|2093818|2093825|2171986|1331051;2|976|200643|171549|815|816|162156;2|1239|186801|186802|186806|1730|165185;2|95818|2093818|2093825|2171986|1331051,Complete,Svetlana up
bsdb:961/1/1,Study 961,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651963/,"Yang C, Wang W, Deng P, Wang X, Zhu L, Zhao L, Li C , Gao H",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Parkinson's disease,MONDO:0005180,Control (CON groups),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,None,16S,4,Ion Torrent,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,"Figure 5A, Text",13 March 2024,Fiddyhamma,Fiddyhamma,LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and CON groups (negative score).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|2005473;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|171552;2|976|200643|171549|171552|1283313;2|976|200643|171549|2005525;2|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:961/1/2,Study 961,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651963/,"Yang C, Wang W, Deng P, Wang X, Zhu L, Zhao L, Li C , Gao H",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Parkinson's disease,MONDO:0005180,Control (CON groups),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,None,16S,4,Ion Torrent,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,"Figure 5A, Text",13 March 2024,Fiddyhamma,Fiddyhamma,LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and CON groups (negative score).,decreased,"k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter mastomyrinus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|s__bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",2|95818|2093818|2093825|2171986|1331051;2|1239|186801;2|1239|186801|186802;2|29547|3031852|213849|72293|209|287948;2|1239|186801|3085636|186803;2|976|200643|1970189|1573805;2|544448|31969;2|544448;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572;2|1869227;2|1239|186801|186802|216572;2|544448|2790996|2790998|2129,Complete,Svetlana up
bsdb:961/2/1,Study 961,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651963/,"Yang C, Wang W, Deng P, Wang X, Zhu L, Zhao L, Li C , Gao H",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 2,China,Mus musculus,Colon,UBERON:0001155,Clinical treatment,EFO:0007056,FGF21 + MPTP mice (mice treated with Fibroblast growth factor 21 (FGF21)),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,None,16S,4,Ion Torrent,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 5C, Text",13 March 2024,Fiddyhamma,Fiddyhamma,LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and FGF21 groups (negative score).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus lentus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|1385;2|1239|91061|1385|90964|2803850|42858;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:961/2/2,Study 961,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651963/,"Yang C, Wang W, Deng P, Wang X, Zhu L, Zhao L, Li C , Gao H",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 2,China,Mus musculus,Colon,UBERON:0001155,Clinical treatment,EFO:0007056,FGF21 + MPTP mice (mice treated with Fibroblast growth factor 21 (FGF21)),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,None,16S,4,Ion Torrent,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 5C, Text",13 March 2024,Fiddyhamma,Fiddyhamma,LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and FGF21 groups (negative score).,decreased,"k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium papyrosolvens,k__Bacteria|s__bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|95818|2093818|2093825|2171986|1331051;2|1239|186801;2|28221;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|186801|186802|216572|1508657|29362;2|1869227;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:962/1/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 1,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Non-medicated control (CT) global data set,Antibiotic (Ab) global data set,"Piglets treated with antibiotics
Global data set involves both consistency and Day post weaning (dpw) factors",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, 5B and Text",20 April 2024,Fiddyhamma,Fiddyhamma,"Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",2|1239|909932|1843489|31977|906|907;2|1239|909932|1843489|31977|906;2|1239|909932;2|1239|909932|1843489|31977;2|1239|909932|1843489;2|1239|91061|186826|33958|2742598|1598,Complete,NA
bsdb:962/1/2,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 1,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Non-medicated control (CT) global data set,Antibiotic (Ab) global data set,"Piglets treated with antibiotics
Global data set involves both consistency and Day post weaning (dpw) factors",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5A, 5B and Text",20 April 2024,Fiddyhamma,Fiddyhamma,"Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera hexanoica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera stantonii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota",2|1239|909932|1843489|31977|39948|2161821;2|1224|1236|91347|543|561|562;2|1239|909932|909929|1843491|158846|158847;2|1239|909932|1843489|31977|906|1675036;2|1239|909932|1843489|31977|906|2144175;2|976|200643|171549|1853231|283168|28118;2|1239|909932|909929|1843491|970|971;2|1239|909932|909929|1843491|970|69823;2|1239|909932|909929;2|1239|909932|909929|1843491|970|1884263;2|1239|909932|909929|1843491;2|1224|1236|91347|543|561;2|1224|1236|91347|543;2|1224|1236|91347;2|1224,Complete,NA
bsdb:962/2/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 2,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Non-medicated control (CT) global data set,Therapeutic Zinc oxide (Zn) global data set,"Piglets treated with Therapeutic Zinc oxide
Global data set involves both consistency and Day post weaning (dpw) factors",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, 5B and Text",20 April 2024,Fiddyhamma,Fiddyhamma,"Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zoogleoformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium callanderi,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CT06,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Archaea|p__Candidatus Thermoplasmatota,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae",2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|2981780;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|290053;2|976|200643|171549|815|816|28113;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|28119;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|186802|186806|1730|53442;2|1239|186801|186802|216572|946234|292800;2157|2283796|183967|1235850|2517203|1291539|1291540;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|375288|2025876;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|376805;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|195950|28112;2|976|200643|171549|2005525|195950|712710;2|1239|186801|186802;2157|2283796;2157|2283796|183967|1235850;2|976|200643;2|976|200643|171549;2|976;2|976|200643|171549|815;2|976|200643|171549|2005525;2157|2283796|183967|1235850|2517203,Complete,NA
bsdb:962/2/2,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 2,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Non-medicated control (CT) global data set,Therapeutic Zinc oxide (Zn) global data set,"Piglets treated with Therapeutic Zinc oxide
Global data set involves both consistency and Day post weaning (dpw) factors",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5A, 5B and  Text",21 April 2024,Fiddyhamma,Fiddyhamma,"Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera hexanoica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera stantonii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales",2|1239|909932|1843489|31977|39948|2161821;2|1224|1236|91347|543|561|562;2|1239|909932|909929|1843491|158846|158847;2|1239|909932|1843489|31977|906|1675036;2|1239|909932|1843489|31977|906|2144175;2|976|200643|171549|1853231|283168|28118;2|1239|909932|909929|1843491|970|971;2|1239|909932|909929|1843491|970|1884263;2|1239|909932|909929|1843491|970|69823;2|1224;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1239|909932|909929|1843491;2|1239|909932|909929,Complete,NA
bsdb:962/3/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 3,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotics (AB) global data set,Therapeutic Zinc oxide (Zn) global data set,"Piglets treated with Therapeutic Zinc oxide
Global data set involves both consistency and Day post weaning (dpw) factors",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, 5B and Text",21 April 2024,Fiddyhamma,Fiddyhamma,"Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
	  
		  
		  
		  
		  
		  
		  
		  
		  
		  
	  
		  ",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zoogleoformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium callanderi,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CT06,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Archaea|p__Candidatus Thermoplasmatota,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota",2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|2981780;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|290053;2|976|200643|171549|815|816|28113;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|28119;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|186802|186806|1730|53442;2|1239|186801|186802|216572|946234|292800;2157|2283796|183967|1235850|2517203|1291539|1291540;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|375288|2025876;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|376805;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|195950|28112;2|976|200643|171549|2005525|195950|712710;2157|2283796|183967|1235850|2517203;2|1239|186801|186802;2157|2283796;2157|2283796|183967|1235850;2|976|200643|171549|2005525;2|976|200643|171549|815;2|976|200643|171549;2|976|200643;2|976,Complete,NA
bsdb:962/3/2,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 3,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotics (AB) global data set,Therapeutic Zinc oxide (Zn) global data set,"Piglets treated with Therapeutic Zinc oxide
Global data set involves both consistency and Day post weaning (dpw) factors",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5A, 5B and  Text",22 April 2024,Fiddyhamma,Fiddyhamma,"Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Negativicutes",2|1239|91061|186826|33958|2742598|1598;2|1239|909932|1843489|31977|906|907;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977;2|1239|909932|1843489;2|1239|909932,Complete,NA
bsdb:962/4/NA,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 4,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0 post weaning (0dpw),Day 7 post weaning (7dpw),"The dietary treatments were administered in the first two weeks post weaning and samplings were scheduled at days 0, 7 and 14 post weaning (0dpw, 7dpw, and 14dpw. respectively).",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:962/5/NA,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 5,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0 post weaning (0dpw),Day 14 post weaning (14dpw),"The dietary treatments were administered in the first two weeks post weaning and samplings were scheduled at days 0, 7 and 14 post weaning (0dpw, 7dpw, and 14dpw. respectively).",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:962/6/NA,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 6,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 7 post weaning (7dpw),Day 14 post weaning (14dpw),"The dietary treatments were administered in the first two weeks post weaning and samplings were scheduled at days 0, 7 and 14 post weaning (0dpw, 7dpw, and 14dpw. respectively).",NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:962/7/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 7,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_7dpw CT(no-medication) group,Diarrhoea_7dpw CT(no-medication) group,Diarrhoea samples collected at day 7 post weaning from piglets not treated with medication,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,decreased,decreased,NA,NA,Signature 1,"Fig 5E, Suppl fig 5 and text",22 April 2024,Fiddyhamma,Fiddyhamma,"Taxa associated with each dietary treatment in the analysis of Diarrhoea_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella megalosphaeroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",2|1224|28216;2|1224|28216|80840;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1224|1236;2|1224;2|1224|28216|80840|995019|40544|2494234;2|1224|28216|80840|995019,Complete,NA
bsdb:962/7/2,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 7,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_7dpw CT(no-medication) group,Diarrhoea_7dpw CT(no-medication) group,Diarrhoea samples collected at day 7 post weaning from piglets not treated with medication,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,decreased,decreased,NA,NA,Signature 2,"Fig 5C, Suppl fig 3B and text",24 April 2024,Fiddyhamma,Fiddyhamma,"Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio clariflavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio saccincola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium|s__Acetobacterium woodii,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus|s__Alkaliphilus oremlandii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila|s__Aminipila luticellarii,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BNL1100,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Bacteria|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae,k__Bacteria|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales,k__Bacteria|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae|g__Dehalococcoides|s__Dehalococcoides mccartyi,k__Bacteria|p__Chloroflexota|c__Dehalococcoidia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Hungateiclostridiaceae bacterium KB18,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family IV. Incertae Sedis|g__Mahella|s__Mahella australiensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella vaginalis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family IV. Incertae Sedis,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|186802|216572|35829|288965;2|1239|186801|186802|216572|35829|1677857;2|1239|186801|186802|186806|33951|33952;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|74201|203494|48461|1647988;2|1239|186801|3082720|3118656|114627|461876;2|1239|186801|3082720|3030910|2060094|2507160;2|1239|186801|3082768|990719|990721|1805714;2|1239|186801|3082768|990719;2|1239|186801|186802|31979|1485|755731;2|1239|186801|186802|31979|1485|84032;2|1239|186801|186802|186807|51514|51515;2|200795|301297|1202465|1202464;2|200795|301297|1202465;2|200795|301297|1202465|1202464|61434|61435;2|200795|301297;2|28221;2|200940|3031449|213115|194924|872|901;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350|1352;2|1239|186801|186802|543313;2|1239|186801|186802|216572|1834198;2|1239|186801|68295|543372|252965|252966;2|1239|186801|3082720|3030910|86331|114527;2|1239|1737404|1737405|1570339|1161127|1852373;2|201174|84998|84999|1643824|133925|712411;2|1239|186801|186802|186807;2|1239|1737404|1737405|1570339;2|1224;2|1239|186801|186802|216572|1263|1264;2|1239|186801|186802|216572|1263|3062497;2|1239|1737404|1737405|2992718;2|1239|909932|909929|1843490;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301|1307;2|1239|186801|68295;2|1239|186801|68295|543372;2|74201|203494|48461;2|74201;2|1239|186801|186802|216572,Complete,NA
bsdb:962/8/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 8,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_7dpw AB(antibiotics) group,Diarrhoea_7dpw AB(antibiotics) group,Diarrhoea samples collected at day 7 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,increased,increased,NA,NA,Signature 1,"Fig 5E, Suppl fig 5 and text",22 April 2024,Fiddyhamma,Fiddyhamma,"Taxa associated with each dietary treatment in the analysis of Diarrhoea_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",2|1239|91061;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|2742598|1598,Complete,NA
bsdb:962/8/2,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 8,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_7dpw AB(antibiotics) group,Diarrhoea_7dpw AB(antibiotics) group,Diarrhoea samples collected at day 7 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,increased,increased,NA,NA,Signature 2,"Fig 5C, Suppl fig 3B and text",22 April 2024,Fiddyhamma,Fiddyhamma,"Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena",2|1239|909932|1843489|31977|39948|2161821;2|1239|91061|186826|33958|2742598|1598;2|1239|909932|909929|1843491;2|1239|909932|909929;2|1239|909932|909929|1843491|970|69823,Complete,NA
bsdb:962/9/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 9,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_7dpw Zn(Zinc Oxide) group,Diarrhoea_7dpw Zn(Zinc Oxide) group,Diarrhoea samples collected at day 7 post weaning from piglets treated with Zinc Oxide,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,"Fig 5E, Suppl fig 5 and text",22 April 2024,Fiddyhamma,Fiddyhamma,"Taxa associated with each dietary treatment in the analysis of Diarrhoea_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|976|200643|171549|815|816|28116;2|1239|186801|186802|1392389|1297617;2|1239|186801|3082720|186804;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|821,Complete,NA
bsdb:962/9/2,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 9,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_7dpw Zn(Zinc Oxide) group,Diarrhoea_7dpw Zn(Zinc Oxide) group,Diarrhoea samples collected at day 7 post weaning from piglets treated with Zinc Oxide,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,"Fig 5C, Suppl fig 3B and text",22 April 2024,Fiddyhamma,Fiddyhamma,"Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila|s__Aminipila luticellarii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] sulci",2|1239|186801|3082720|3030910|2060094|2507160;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3082720|186804;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|821;2|1239|909932|909929|1843491|970|971;2|1239|909932|909929|1843491|970|1884263;2|1239|186801|186802|543314|143393,Complete,NA
bsdb:962/10/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 10,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_0dpw AB(antibiotics) group,Diarrhoea_0dpw AB(antibiotics) group,Diarrhoea samples collected at day 0 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Suppl fig 3A and text,22 April 2024,Fiddyhamma,Fiddyhamma,"Species associated with each dietary treatment in the analysis of Faecal_0dpw species data, according to LEfSe(Linear discriminant analysis Effect Size), most likely explaining the differences among dietary treatments.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,2|976|200643|171549|815|909656|376805,Complete,NA
bsdb:962/11/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 11,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_14dpw CT(no medication) group,Diarrhoea_14pw CT(no medication) group,Diarrhoea samples collected at day 14 post weaning from piglets not treated with medication,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig 5D, Suppl fig 4 and text",27 April 2024,Fiddyhamma,Fiddyhamma,"Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sporogenes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Intestinibaculum|s__Intestinibaculum porci,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera hexanoica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera stantonii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Methylomusa|s__Methylomusa anaerophila,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Pelosinus|s__Pelosinus fermentans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Petrocella|s__Petrocella atlantisensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|909932|1843488|909930|904|187327;2|1239|186801|186802|31979|1485|1509;2|200940|3031449|213115|194924|872|44742;2|1239|909932|1843489|31977|39948|2161821;2|1224|1236|91347|543|561|562;2|1239|526524|526525|128827|2679910|2487118;2|1239|91061|186826|33958|1578|1584;2|1239|909932|909929|1843491|158846|158847;2|1239|909932|1843489|31977|906|907;2|1239|909932|1843489|31977|906|1675036;2|1239|909932|1843489|31977|906|2144175;2|1239|909932|909929|1843490|2093783|1930071;2|1239|909932|909929|1843490|365348|365349;2|1239|186801|3085636|2603322|2603323|2173034;2|1239|186801|186802|216572|1263|3062497;2|1239|909932|909929|1843491|970|971;2|1239|909932|909929|1843491|970|1884263;2|1239|909932|909929|1843491|970|69823;2|200940|3031449|213115|194924|872|901;2|1224;2|1224|1236;2|28221;2|1224|1236|91347|543|561;2|1239|909932|1843489|31977|906;2|1239|909932;2|1239|909932|1843489;2|1239|909932|1843489|31977;2|1239|186801|3085636|2603322;2|1224|1236|91347;2|200940|3031449|213115;2|200940|3031449|213115|194924;2|1239|909932|909929|1843490;2|1239|909932|909929;2|1239|909932|909929|1843491;2|1224|1236|91347|543,Complete,NA
bsdb:962/12/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 12,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_14dpw AB(antibiotics) group,Diarrhoea_14dpw AB(antibiotics) group,Diarrhoea samples collected at day 14 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig 5D, Suppl fig 4 and text",27 April 2024,Fiddyhamma,Fiddyhamma,"Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SY8519,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1239|909932|1843488|909930|904|905;2|1239|186801|186802|31979|1485|1042156;2|1239|186801|3085636|186803|1766253|39491,Complete,NA
bsdb:962/13/1,Study 962,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM , Manzanilla EG",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 13,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Abnormal sample,EFO:0009655,Faecal_14dpw Zn(Zinc Oxide) group,Diarrhoea_14dpw Zn(Zinc Oxide) group,Diarrhoea samples collected at day 14 post weaning from piglets treated with Zinc Oxide,NA,NA,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig 5D, Suppl fig 4 and text",27 April 2024,Fiddyhamma,Fiddyhamma,"Description: Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Archaea|p__Candidatus Thermoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__Draconibacterium orientale,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Fermentimonas|s__Fermentimonas caenicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium|s__Ornithobacterium rhinotracheale,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter|s__Paludibacter propionicigenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",2|976|200643|171549|815;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|1796613;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|290053;2|976|200643|171549|815|816|28113;2|976|200643|171549|815|816|818;2157|2283796;2|1239|186801|3082720|186804|1870884|1496;2|976|200643|1970189|1471398|1471399|1168034;2|976|200643|171549|2005520|1784836|1562970;2|976|200643|1970189;2157|2283796|183967|1235850;2157|2283796|183967|1235850|2517203;2157|2283796|183967|1235850|2517203|1291539|1291540;2|976|117743|200644|2762318|28250|28251;2|976|200643|171549|2005523|346096|185300;2|976|200643|171549|2005523;2|976|200643|171549|2005525|375288|823;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|815|909656|376805;2|976|200643|1970189|1471398;2|976|200643|171549|2005525|195950|28112;2|976|200643|171549|2005525|195950|712710;2|976|200643|171549|2005525,Complete,NA
bsdb:963/1/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Pre-CT Stage I,Pre-CT Stage II/III,Breast cancer patients before chemotherapy with TNM Stage II/III,21,35,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1B,19 April 2024,Scholastica,Scholastica,Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Pre-CT TNM stage I (orange) compared to Pre-CT TNM stage II-III (blue),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05",2|976|200643|171549|815|816|820;2|1224|28216|80840|995019|1918598|1796652;2|1224|28216|80840|995019|577310|487175;2|1239|1262992;2|1239|91061|186826|1300|1357|1358;2|1239|91061|186826|1300|1301|1308;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|291645;2|1239|526524|526525|128827|1472649|1034346;2|201174|84998|1643822|1643826|84111|84112;2|1224|1236|135625|712|724|1608898,Complete,Svetlana up
bsdb:963/1/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Pre-CT Stage I,Pre-CT Stage II/III,Breast cancer patients before chemotherapy with TNM Stage II/III,21,35,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1B,19 April 2024,Scholastica,Scholastica,Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Pre-CT TNM stage I (orange) compared to Pre-CT TNM stage II-III (blue),decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides|s__Sanguibacteroides justesenii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:488,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. CAG:318,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger",2|1239|909932|909929|1843491|52225|52226;2|976|200643|171549|171551|1635148|1547597;2|1239|186801|186802|457421;2|256845|1313211|278082|255528|172900|172901;2|1239|1263000;2|1239|186801|3085636|186803|1506553|1965560;2|1239|186801|186802|216572|1263|1262959;2|1239|186801|186802|216572|2172004|2108523;2|200940|3031449|213115|194924|2049043;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|3342669|45851;2|1239|186801|186802|216572|1017280|1965576;2|976|200643|171549|815|816|1262739;2|201174|84998|84999|84107|1472762|1472761;2|1239|186801|3085636|186803|830|1262761;2|1239|186801|186802|216572|1263|1262958;2|1239|186801|186802|216572|1017280|106588;2|976|200643|171549|2005519|397864|487174;2|1239|186801|186802|3082771|1924093|1965604;2157|28890|183925|2158|2159|2172|2173;2|200940|3031449|213115|194924|872|901,Complete,Svetlana up
bsdb:963/2/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Post-CT Stage I,Post-CT Stage II/III,Breast cancer patients after chemotherapy with TNM Stage II/III,14,20,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1E,19 April 2024,Scholastica,Scholastica,Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Post-CT TNM stage I (orange) compared to Post-CT TNM stage II-III (blue),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA",2|201174|84998|1643822|1643826|644652|471189;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|1769710|1653434;2|1239|909932|1843488|909930|33024|626940;2|1239|186801|3085636|3118652|2039240|160404;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|820;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|3085636|186803|2719313|358743;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|2719313|1531;2|976|200643|171549|2005525|375288|46503;2|1239|186801|186802|216572|1892380|1849041;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|3085636|186803|1432051|1720294;2|1239|91061|186826|81852|1350|53345;2|1239|186801|3085636|186803|572511|33035;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|291645;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|31979|1485|1262777;2|1239|186801|3085636|186803|572511|1262756;2|1239|909932|1843489|31977|29465|1110546;2|1239|186801|186802|216572|1535;2|1239|186801|186802|186806|1730|1262882;2|1239|91061|186826|1300|1301|1308;2|1239|526524|526525|2810280|100883|100884;2|1239|186801|186802|457421,Complete,Svetlana up
bsdb:963/2/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Post-CT Stage I,Post-CT Stage II/III,Breast cancer patients after chemotherapy with TNM Stage II/III,14,20,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1E,20 April 2024,Scholastica,Scholastica,Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Post-CT TNM stage I (orange) compared to Post-CT TNM stage II-III (blue),decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:755,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. An31A,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus",2|1239|909932|909929|1843491|158846|158847;2|201174|84998|1643822|1643826|84108|572010;2|1239|1263000;2|1239|186801|186802|216572|459786|1262911;2|1239|186801|3085636|186803|1407607|1150298;2|976|200643|171549|815|816|674529;2|1239|1262988;2|1239|186801|3085636|186803|2316020|33039;2|976|200643|171549|815|816|246787;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|572511|40520;2|976|200643|171549|171552|838|1262935;2|1239|186801|186802|216572|946234|1965538;2|256845|1313211|278082|255528|172900|172901;2|1239|186801|186802|31979|1485|84024;2|976|200643|171549|171552|838|1262921;2|976|200643|171549|171550|239759|1965631;2|1224|1236|91347|543|561|1499973;2|976|200643|171549|815|816|1262739;2|201174|1760|2037|2049|1654|55565;2|1239|186801|186802|204475|745368;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|2974251|165179;2|1224|1236|135625|712|724|1608898;2|976|200643|171549|1853231|574697|544645;2|1239|186801|3085636|186803|28050|39485;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|216851|853;2|200940|3031449|213115|194924|872|901;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|33042|116085,Complete,Svetlana up
bsdb:963/3/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Pre-Chemo tumor size <pT1,Pre-Chemo tumor size >pT1,Breast cancer patients before chemotherapy with pathological tumor size greater than pT1,24,32,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S2B,20 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy with tumor size <pT1 versus tumor size >pT1,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|3085636|186803|207244|649756;2|976|200643|171549|815|816|871325;2|976|200643|171549|815|816|674529;2|976|200643|171549|815|816|371601;2|1239|186801|186802|31979|1485|29363;2|1239|909932|1843489|31977|39948|487173;2|201174|84998|1643822|1643826|84111|84112;2|1239|1262992;2|1224|1236|135625|712|724|729;2|1224|1236|135625|712|724|1608898;2|1239|186801|3082720|186804|1505657|261299;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|244366;2|1239|186801|3085636|186803|841|301302;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1308;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|3085636|186803|1506577|29361;2|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:963/3/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Pre-Chemo tumor size <pT1,Pre-Chemo tumor size >pT1,Breast cancer patients before chemotherapy with pathological tumor size greater than pT1,24,32,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S2B,20 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy with tumor size <pT1 versus tumor size >pT1,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas synergistica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. CAG:318,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides|s__Sanguibacteroides justesenii",2|1239|186801|186802|3082771|1924093|1965604;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|1262739;2|976|200643|171549|2005519|397864|487174;2|976|200643|171549|1853231|574697|544644;2|1239|186801|3085636|186803|830|1262761;2|200940|3031449|213115|194924|872|901;2|200940|3031449|213115|194924|2049043;2|1239|186801|3085636|186803|1432051|1720294;2|1239|1263005;2|508458|649775|649776|3029087|1434006|651822;2|1239|186801|186802|216572|2172004|2108523;2157|28890|183925|2158|2159|2172|2173;2|1239|186801|186802|216572|1263|1262958;2|976|200643|171549|171551|1635148|1547597,Complete,Svetlana up
bsdb:963/4/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Post-Chemo tumor size <pT1,Post-Chemo tumor size >pT1,Breast cancer patients after chemotherapy with pathological tumor size greater than pT1,13,21,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S2D,21 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy with tumor size <pT1 versus tumor size >pT1,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella|s__Rikenella microfusus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|371601;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802|3085642|580596|501571;2|1239|186801|186802|31979|1485|1502;2|1239|526524|526525|2810280|100883|100884;2|1239|186801|3085636|186803|2719313|1531;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|1892380|1849041;2|1239|186801|3082720|186804|1505657|261299;2|976|200643|171549|2005525|375288|46503;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|171552|838|1262924;2|976|200643|171549|171550|28138|28139;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|1769710|1653434;2|1239|91061|186826|1300|1301|1759399;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|1343;2|1239|526524|526525|2810280|3025755|29348;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|423477;2|1239|909932|1843489|31977|29465|1110546;2|1239|526524|526525|128827|1522;2|1239|186801|186802|216572|1535,Complete,Svetlana up
bsdb:963/4/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Post-Chemo tumor size <pT1,Post-Chemo tumor size >pT1,Breast cancer patients after chemotherapy with pathological tumor size greater than pT1,13,21,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S2D,21 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy with tumor size <pT1 versus tumor size >pT1,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An10,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|1239|186801|186802|3085642|2048137|1628085;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|626932;2|976|200643|171549|2005519|1348911|1099853;2|976|200643|171549|2005519|1348911|1501392;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|33042|410072;2|200940|3031449|213115|194924|872|901;2|1239|186801|186802|216572|946234|1965537;2|1239|186801|186802|216572|946234|1965538;2|1224|1236|135625|712|724|1608898;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|815|909656|821;2|1239|186801|3085636|186803|841|1262945;2|1239|186801|186802|216572|39492,Complete,Svetlana up
bsdb:963/5/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Tumor grading,OBI:0600002,SBR Gr1/2 Post-Chemo,SBR Gr3 Post-Chemo,Breast cancer patients after chemotherapy with Scarff Bloom & Richardson (SBR) grade Gr3,20,24,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S3C,21 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to tumor histological grade SBR; Gr1/2 compared to Gr3,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An10,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An14,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae",2|1239|186801|3085636|186803|33042|116085;2|976|200643|171549|171552|2974251|165179;2|1239|186801|186802|216572|39492;2|1239|186801|186802|216572|1892380|1849041;2|976|200643|171549|1853231|574697|544645;2|976|200643|171549|171550|239759|28117;2|200940|3031449|213115|194924|872|901;2|1239|186801|186802|3082771|1924093|1965604;2|1239|91061|186826|81852|1350|1351;2|1239|186801|186802|31979|1485|84024;2|1239|1262989;2|1239|1263006;2|1239|186801|186802|31979|1485|1262824;2|1798710|1906119|2137880;2|1239|186801|186802|216572|946234|1965537;2|1239|1262988;2|1239|1263011;2|976|200643|171549|171552|577309|454155;2|1239|1263005;2|976|200643|171549|815|816|1262739;2|200940|3031449|213115|194924|2049043;2|1239|186801|3085636|186803|1506553|1965562;2|1239|186801|3085636|186803|2719313|208479,Complete,Svetlana up
bsdb:963/5/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Tumor grading,OBI:0600002,SBR Gr1/2 Post-Chemo,SBR Gr3 Post-Chemo,Breast cancer patients after chemotherapy with Scarff Bloom & Richardson (SBR) grade Gr3,20,24,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S3C,21 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to tumor histological grade SBR; Gr1/2 compared to Gr3,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:144,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella hongkongensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae",2|976|200643|171549|815|816|1262736;2|1239|186801|3085636|186803|1432051|1432052;2|1239|186801|3085636|186803|1649459|154046;2|1239|186801|3082768|990719|990721|270498;2|1239|186801|3085636|186803|28050|706562;2|1239|186801|3085636|186803|1506553|1512;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|816|371601;2|976|200643|171549|815|816|246787;2|1239|909932|1843488|909930|33024|33025;2|1239|186801|3085636|186803|841|1262942;2|1239|186801|3085636|186803|1769710|1653434;2|976|200643|171549|2005525|375288|387661;2|1239|186801|3085636|186803|28050|28052;2|1239|91061|186826|1300|1301|1308;2|1239|186801|3085636|186803|33042|33043;2|201174|84998|1643822|1643826|644652|471189;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|2719313|358743,Complete,Svetlana up
bsdb:963/6/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 6,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- pre-Chemo,pN+ pre-Chemo,Breast cancer patients before chemotherapy with positive axillary lymph node involvement,30,26,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S4B,21 April 2024,Scholastica,Scholastica,"Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia alvei,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa",2|1239|186801|186802|216572|459786|1897011;2|976|200643|171549|2005519|1348911|1501392;2|1224|28216|80840|995019|577310|487175;2|1239|1262992;2|1224|28216|80840|995019|1918598|1796652;2|1239|186801|3085636|186803|2316020|33039;2|976|200643|171549|815|816|820;2|976|200643|171549|2005519|1348911|1099853;2|1239|909932|1843488|909930|33024|33025;2|200940|3031449|213115|194924|35832|35833;2|1224|1236|91347|1903412|568|569;2|1239|526524|526525|128827|1472649|1034346,Complete,Svetlana up
bsdb:963/6/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 6,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- pre-Chemo,pN+ pre-Chemo,Breast cancer patients before chemotherapy with positive axillary lymph node involvement,30,26,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S4B,21 April 2024,Scholastica,Scholastica,"Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:633,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:755,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. CAG:318,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An131,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger",2|976|200643|171549|815|816|1262744;2|1239|186801|186802|31979|1485|1262777;2|1239|526524|526525|2810280|3025755|29348;2|256845|1313211|278082|255528|172900|172901;2|1239|186801|3085636|186803|572511|1532;2|201174|1760|2037|2049|1654|55565;2|1224|1236|91347|543|544|133448;2|1224|1236|91347|543|544|546;2|1239|186801|186802|216572|1017280|1965576;2|1224|1236|91347|543|570|571;2|1239|909932|909929|1843491|158846|158847;2|1239|186801|186802|216572|1263|3062497;2|976|200643|171549|171552|838|1262935;2|1224|28216|80840|75682|846|847;2|201174|84998|84999|84107|1472762|1472761;2|976|200643|171549|815|816|1262739;2|1239|186801|3085636|186803|830|1262761;2|201174|84998|84999|84107|102106|147206;2|1239|186801|186802|216572|1263|1262958;2|1239|186801|3085636|186803|3342669|45851;2|1239|186801|3085636|186803|1506553|1965555;2|976|200643|171549|815|909656|387090;2|1239|909932|1843489|31977|29465|2027459;2|1239|186801|3085636|186803|572511|33035;2|1239|186801|3085636|186803|1506553|1965560;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|186806|1730|1262882;2|1239|186801|3085636|186803|1769710|1653434;2|1239|186801|186802|3082771|1924093|1965604;2|200940|3031449|213115|194924|872|901,Complete,Svetlana up
bsdb:963/7/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 7,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- post-Chemo,pN+ post-Chemo,Breast cancer patients after chemotherapy with positive axillary lymph node involvement,19,15,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S4D,22 April 2024,Scholastica,Scholastica,"Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:678,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile",2|976|200643|171549|171550|239759|328813;2|1239|186801|3085636|3118652|2039240|160404;2|1239|186801|3085636|186803|572511|33035;2|1239|186801|3085636|186803|572511|1262756;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|186802|3085642|580596|501571;2|1239|186801|186802|31979|1485|1262831;2|1239|186801|3085636|186803|189330|1262873;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|1432051|1720294;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|2719313|208479;2|1239|91061|186826|81852|1350|53345;2|1239|186801|186802|186806|1730|1262889;2|201174|84998|1643822|1643826|644652|471189;2|1239|186801|3082720|186804|1505657|261299;2|976|200643|171549|2005525|375288|46503;2|1224|1236|91347|1903414|583|584;2|201174|1760|85006|1268|32207|43675;2|1239|186801|3085636|186803|1769710|1653434;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1759399;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|1343;2|1239|526524|526525|2810280|3025755|1547;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|423477;2|1239|909932|1843489|31977|29465|1110546;2|1239|186801|186802|216572|1535;2|1239|186801|3085636|186803|1506577|29361,Complete,Svetlana up
bsdb:963/7/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 7,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- post-Chemo,pN+ post-Chemo,Breast cancer patients after chemotherapy with positive axillary lymph node involvement,19,15,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S4D,22 April 2024,Scholastica,Scholastica,"Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:251,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|28050|706562;2|976|200643|171549|171552|2974251|165179;2|1224|1236|135625|712|724|1608898;2|1239|186801|3085636|186803|572511|40520;2|201174|1760|85004|31953|196081|230143;2|1239|186801|3085636|186803|2569097|39488;2|1239|526524|526525|128827|1573534|39483;2|1239|909932|909929|1843491|158846|158847;2|1239|186801|3085636|186803|33042|410072;2|201174|1760|85004|31953|1678|1681;2|1239|186801|186802|186806|1730|1262886;2|1239|186801|3085636|186803|28050|39485;2|200940|3031449|213115|194924|872|901;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|1853231|283168|28118;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:963/8/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 8,"France,Italy",Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy volunteers,Breast cancer patients,Breast cancer patients enrolled in the CANTO study,336,76,None,WMS,NA,Ion Torrent,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A,22 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from breast cancer patients compared with healthy volunteers (HV) using LEfSe method,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. KLE 1755,k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Dhillonvirus|s__Dhillonvirus JL1,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Stephanstirmvirinae|g__Phapecoctavirus|s__Escherichia virus phAPEC8,k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Skunavirus|s__Skunavirus sv936,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Ceduovirus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Dhillonvirus|s__Dhillonvirus SO1,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",2|976|200643|171549|171550|239759|2585118;2|976|200643|171549|171550|239759|626932;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|291645;2|200940|3031449|213115|194924|35832|35833;2|1239|186801|186802|457421;2|1239|186801|186802|31979|1485|1226325;10239|2731360|2731618|2731619|1623289|1245890;2|1239|186801|3085636|186803|2719313|333367;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|2719313|1531;10239|2731360|2731618|2731619|2946646|2733124|2734131;10239|2731360|2731618|2731619|1623305|2845183;2|976|200643|171549|815|909656|376804;2|1239|186801|186802|216572|552398;2|200940|3031449|213115|194924|35832;10239|2731360|2731618|2731619|186532;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|976|200643|171549|815|816|28116;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|841|166486;2|976|200643|171549|171550|239759;2|976|200643|171549|2005525|375288|46503;2|1224|1236|91347|543|570|573;2|1239|186801|3085636|186803|28050|39485;2|976|200643|171549|2005519|397864|487174;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|816|817;10239|2731360|2731618|2731619|1623289|1954380;2|976|200643|171549|815|816|818;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|815|816|820,Complete,Svetlana up
bsdb:963/8/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 8,"France,Italy",Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy volunteers,Breast cancer patients,Breast cancer patients enrolled in the CANTO study,336,76,None,WMS,NA,Ion Torrent,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2A,22 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from breast cancer patients compared with healthy volunteers (HV) using LEfSe method,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. TW09276,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1745,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis",2|201174|1760|85004|31953|1678|1680;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|216572|1263|457412;2|201174|1760|85004|31953|1678|216816;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|2569097|39488;2157|28890|183925|2158|2159|2172|2173;2|1239|186801|3085636|186803|3342669|45851;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|189330|88431;2|976|200643|171549|815|816|46506;2|976|200643|171549|171552|2974265|363265;2|1239|186801|3085636|186803|572511|40520;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802|216572|39492;2|976|200643|171549|171551|836|501496;2|1239|909932|1843488|909930|33024|626940;2|1239|1737404|1737405|1570339|150022|1260;2|1239|186801|186802|31979|1485|411489;2|1239|526524|526525|2810280|135858|100886;2|203691|203692|136|2845253|157|167;2|201174|1760|85004|31953|1678|28026;2|201174|1760|85004|31953|1678|1686;2|1239|186801|3085636|186803|33042|116085;2|976|200643|171549|171552|2974257|28127;2|1239|186801|3085636|186803|33042|33043;2|201174|1760|85004|31953|1678|1683;2|1239|91061|186826|1300|1301|1304;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|815|816|329854;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|33958|2767887|1623;2|1239|186801|186802|186806|1730|39490;2|1239|186801|3082720|186804;2|1239|186801|186802|216572|1263|1161942;2|1239|91061|186826|1300|1301|1328;2|1239|1737404|1737405|1570339|165779|33037;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|547|550;2157|28890|183925|2158|2159|2172;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|1300|1301|102684;2|1224|1236|91347|543|561|754330;2|976|200643|171549|171551|836|322095;2|1239|186801|186802|216572|459786|1226323;2|1239|1737404|1737405|1570339|162289|54005;2|1239|186801|3085636|186803|1649459|154046;2|1239|1737404|1737405|1570339|165779|1287640;2|201174|84998|1643822|1643826|644652|471189;2|976|200643|171549|171551|836|281920,Complete,Svetlana up
bsdb:963/9/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 9,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant_pN-,Neoadjuvant_pN+,Breast cancer patients after neoadjuvant chemotherapy treatment with pathological lymph node involvement,8,2,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2D,23 April 2024,Scholastica,Scholastica,"Metagenomics analyses of stool samples from BC patients comparing species abundance according to the pathological lymph node involvement (no pathological lymph node involvement, pN-, orange; versus pathological lymph node involvement, pN+, blue) in stools collected after neoadjuvant CT (n = 10)",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis",2|976|200643|171549|815|816|818;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|1769710|1653434;2|1239|186801|3085636|186803|572511|418240;2|1239|186801|3085636|186803|1432051|1720294;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|3085636|186803|572511|1262756;2|1239|186801|3085636|186803|2719313|1531;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|186802|3082771|1924093|1965604;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|3085636|186803|2719313|358743;2|1239|186801|3085636|186803|2719313|358742,Complete,Svetlana up
bsdb:963/9/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 9,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant_pN-,Neoadjuvant_pN+,Breast cancer patients after neoadjuvant chemotherapy treatment with pathological lymph node involvement,8,2,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2D,23 April 2024,Scholastica,Scholastica,"Metagenomics analyses of stool samples from BC patients comparing species abundance according to the pathological lymph node involvement (no pathological lymph node involvement, pN-, orange; versus pathological lymph node involvement, pN+, blue) in stools collected after neoadjuvant CT (n = 10)",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|1239|186801|3085636|186803|572511|40520;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|3085636|186803|841|360807;2|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:963/10/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 10,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant stage post-Chemo (Stage 0),Neoadjuvant stage post-Chemo (Stage I/II),Breast cancer patients after neoadjuvant chemotherapy treatment who are pathological non-complete responders (stage I–II),5,5,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S3D,23 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early BC patients treated in a neoadjuvant setting comparing pathological complete responders (stage I) to non-complete responders (stage I–II),increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,2|1239|186801|3085636|186803|2719313|358743,Complete,Svetlana up
bsdb:963/10/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 10,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant stage post-Chemo (Stage 0),Neoadjuvant stage post-Chemo (Stage I/II),Breast cancer patients after neoadjuvant chemotherapy treatment who are pathological non-complete responders (stage I–II),5,5,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S3D,23 April 2024,Scholastica,Scholastica,Metagenomics analyses of stool samples from early BC patients treated in a neoadjuvant setting comparing pathological complete responders (stage I) to non-complete responders (stage I–II),decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",2|1239|91061|1385|539738|1378|84135;2|1239|91061|186826|1300|1301|28037;2|1239|186801|186802|186806|1730|39496,Complete,Svetlana up
bsdb:963/11/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 11,France,Homo sapiens,Feces,UBERON:0001988,Response to combination chemotherapy,EFO:0007965,Pre-Chemotherapy,Post-Chemotherapy,Breast cancer patients after Chemotherapy,45,45,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Fig. 3C,23 April 2024,Scholastica,Scholastica,Differentially significant abundant taxa in breast cancer patients pre-Chemotherapy compared to post-Chemotherapy,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",2|1239|526524|526525|128827|1573535|1735;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|189330|39486;2|1239|1263000;2157|28890|183925|2158|2159|2172|2173,Complete,Svetlana up
bsdb:963/11/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 11,France,Homo sapiens,Feces,UBERON:0001988,Response to combination chemotherapy,EFO:0007965,Pre-Chemotherapy,Post-Chemotherapy,Breast cancer patients after Chemotherapy,45,45,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Fig. 3C,23 April 2024,Scholastica,Scholastica,Differentially significant abundant taxa in breast cancer patients pre-Chemotherapy compared to post-Chemotherapy,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. OM08-24,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis",2|201174|84998|1643822|1643826|84111|84112;2|976|200643|171549|2005519|1348911|1099853;2|1239|909932|1843489|31977|29465|39777;2|1239|186801|3085636|186803|1432051|1432052;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|2719313|333367;2|1239|909932|1843489|31977|29465|29466;2|976|200643|171549|815|909656|821;2|1239|186801|186802|186806|1730|2292352;2|1239|186801|3085636|186803|841|166486;2|1239|186801|3085636|3118652|2039240|160404;2|201174|84998|1643822|1643826|644652|471189;2|1239|186801|186802|216572|244127|169435,Complete,Svetlana up
bsdb:963/12/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 12,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Pre-Chemo),Yes - increased BMI (Pre-Chemo),Breast cancer patients before Chemotherapy with increased Body Mass Index (BMI),30,34,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S6B,23 April 2024,Scholastica,Scholastica,Differentially significant abundant taxa in breast cancer patients before Chemotherapy with increased BMI compared to those without increased BMI,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185",2|976|200643|171549|815|816|46506;2|976|200643|171549|2005525|375288|46503;2|1239|186801|186802|3082771|1924093|1965604;2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|246787;2|1239|186801|186802|216572|1905344|1550024;2|201174|1760|85004|31953|1678|1686;2|1239|526524|526525|2810280|100883|100884;2|976|200643|171549|2005519|1348911|1501392;2|976|200643|171549|171552|838|28130;2|976|200643|171549|815|909656|821;2|1239|1262989;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|1853231|574697|544645;2|1239|186801|3085636|186803|572511|40520;2|201174|1760|85004|31953|1678|28025;2|1239|186801|186802|216572|1263|1262958;2|201174|84998|1643822|1643826|447020|446660;2|976|200643|171549|815|816|28111;2|1239|186801|186802|31979|1485|29363;2|1239|186801|186802|186806|1730|1262882;2|1239|1262988;2|1239|909932|1843489|31977|39948|487173;2|1239|186801|186802|216572|244127|1262700;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|457421;2|1798710|1906119|2137880;2|1239|186801|186802|216572|459786|1897011;2|201174|84998|1643822|1643826|447020|446660|394340;2|1239|186801|186802|31979|1485|84024;2|1239|526524|526525|2810280|3025755|1547;2|1239|186801|186802|216572|459786|1262911;2|1239|909932|909929|1843491|52225|187979;2|1239|526524|526525|128827|1472649|1034346;2|1239|909932|1843489|31977|29465|39777;2|1239|186801|186802|216572|946234|1965538;2|1224|28216|80840|995019|1918598|1796652;2|976|200643|171549|1853231|283168|28118;2|201174|1760|85004|31953|1678|1681;2|976|200643|171549|171552|838|1262921,Complete,Svetlana up
bsdb:963/12/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 12,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Pre-Chemo),Yes - increased BMI (Pre-Chemo),Breast cancer patients before Chemotherapy with increased Body Mass Index (BMI),30,34,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S6B,23 April 2024,Scholastica,Scholastica,Differentially significant abundant taxa in breast cancer patients before Chemotherapy with increased BMI compared to those without increased BMI,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:303,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PC13,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:251",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|1262739;2|508458|649775|649776|649777|508459|1197717;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107|102106|147207;2|1239|186801|3085636|186803|33042|33043;2|200940|3031449|213115|194924|872|901;2|1239|186801|3085636|186803|189330|1262873;2|1224|1236|91347|543|561|562;2|1239|909932|1843488|909930|33024|33025;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|310297;2|1239|186801|186802|216572|1017280|1965576;2|1239|186801|3085636|186803|841|1262942;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1318;2|1224|28216|80840|995019|40544|437898;2|1239|91061|186826|1300|1301|68892;2|1239|186801|186802|186806|1730|39490;2|1239|186801|3085636|186803|572511|53443;2|1239|186801|186802|216572|1263|40519;2|1239|186801|186802|3085642|580596|501571;2|1239|186801|3085636|186803|841|1262944;2|1239|909932|1843489|31977|29465|29466;2|1239|1263005;2|1239|186801|186802|216572|459786|1855299;2|201174|84998|84999|84107|1472762|1472761;2|1239|909932|1843489|31977|29465|39778;2|1239|91061|186826|1300|1301|1304;2|1239|186801|3085636|186803|3342669|45851;2|200940|3031449|213115|194924|2049043;2|976|200643|171549|2005525|375288|387661;2|1239|186801|186802|216572|1520815;2|1239|909932|1843489|31977|29465|2027459;2|976|200643|171549|815|816|820;2|1239|909932|1843489|31977|29465|1911679;2|1239|186801|3085636|186803|2719313|1531;2|1239|91061|186826|1300|1301|28037;2|1239|186801|3085636|186803|28050|706562;2|976|200643|171549|815|816|817;2|1239|186801|3085636|186803|1432051|1432052;2|1239|186801|3085636|186803|2316020|46228;2|1239|186801|3085636|186803|28050|28052;2|1239|91061|1385|539738|1378|84135;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|186806|1730|1262886,Complete,Svetlana up
bsdb:963/13/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 13,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Post-Chemo),Yes - increased BMI (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with increased Body Mass Index (BMI),15,24,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S6D,23 April 2024,Scholastica,Scholastica,Differentially significant abundant taxa in breast cancer patients 12 months after Chemotherapy with increased BMI compared to those without increased BMI,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An10,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An131,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus sanfranciscensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:678,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:755,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides galacturonicus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",2|976|200643|171549|171550|239759|1501391;2|1239|186801|186802|216572|244127|1262700;2|1239|186801|3085636|186803|2316020|46228;2|976|200643|171549|1853231|574697|544645;2|1239|186801|186802|216572|946234|1965537;2|1239|1262989;2|1239|186801|3085636|186803|841|1262948;2|1239|91061|186826|81852|1350|53345;2|1239|526524|526525|2810280|3025755|29348;2|1239|186801|3085636|186803|2316020|33039;2|1798710|1906119|2137880;2|1239|186801|186802|31979|1485|1262777;2|1224|28216|80840|995019|577310|487175;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|3085636|186803|1506553|1965560;2|1239|526524|526525|2810281|191303|154288;2|1239|186801|186802|31979|1485|84024;2|1239|186801|3085636|186803|1407607|1150298;2|1239|186801|186802|3082771|1924093|1965604;2|976|200643|171549|171550|239759|626932;2|1239|186801|3085636|186803|28050|28052;2|976|200643|171549|2005525|375288|46503;2|1224|28216|80840|995019|1918598|1796652;2|976|200643|171549|2005525|375288|823;2|201174|1760|85004|31953|1678|216816;2|1239|909932|1843489|31977|39948|218538;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|246787;2|1239|186801|3082768|990719|990721|626937;2|1239|186801|186802|216572|2172004|2108523;2|201174|1760|85004|31953|196081|230143;2|1239|186801|3085636|3118652|2039240|160404;2|976|200643|171549|815|816|338188;2|976|200643|171549|1853231|283168|28118;2|1239|186801|3085636|186803|1506553|1965555;2|976|200643|171549|2005519|1348911|1099853;2|976|200643|171549|815|816|371601;2|1239|186801|186802|216572|216851|853;2|1239|91061|186826|33958|2767881|1625;2|1239|186801|3082720|186804|1505657|261299;2|1239|526524|526525|128827|1472649|1034346;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|186802|31979|1485|1262831;2|1239|186801|186802|216572|1535;2|976|200643|171549|171552|577309|454154;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|186802|216572|1017280|1965576;2|976|200643|171549|171552|838|1262935;2|1239|186801|186802|216572|946234|1965538;2|1239|91061|186826|1300|1301|1759399;2|976|200643|171549|2005519|397864|487174;2|201174|84998|1643822|1643826|84108|572010;2|1239|186801|3085636|186803|572511|40520;2|976|200643|171549|815|816|384639;2|1239|909932|1843488|909930|904|187327;2|976|200643|171549|171550|239759|328813;2|1239|526524|526525|128827|1573535|1735,Complete,Svetlana up
bsdb:963/13/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 13,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Post-Chemo),Yes - increased BMI (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with increased Body Mass Index (BMI),15,24,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S6D,23 April 2024,Scholastica,Scholastica,Differentially significant abundant taxa in breast cancer patients 12 months after Chemotherapy with increased BMI compared to those without increased BMI,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:5226,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella|s__Allisonella histaminiformans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1092,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",2|1239|186801|186802|216572|1263|40518;2|1239|909932|909929|1843491|52225|187979;2|1239|91061|186826|1300|1301|1303;2|201174|1760|85006|1268|32207|43675;2|1239|186801|3085636|186803|841|166486;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|31979|1485|1502;2|1239|186801|186802|216572|1520815;2|1239|91061|186826|1300|1301|28037;2|1239|909932|909929|1843491|52225|52226;2|201174|1760|2037|2049|1654|55565;2|1239|91061|186826|1300|1301|1343;2|1239|186801|186802|204475|745368;2|1239|91061|1385|539738|1378|84135;2|976|200643|171549|171552|2974265|363265;2|976|200643|171549|171552|838|1262930;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85004|31953|1678|1689;2|1239|909932|1843489|31977|29465|1911679;2|976|200643|171549|171552|838|1262929;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|209879|209880;2|1239|186801|3085636|186803|1432051|1432052;2|976|200643|171549|815|909656|357276;2|1239|909932|1843489|31977|29465|39777;2|1239|186801|186802|31979|1485|1262785;2|976|200643|171549|815|816|818;2|1239|186801|3085636|186803|841|301301;2|976|200643|171549|171552|838|1262919;2|1239|186801|3085636|186803|28050|39485;2|976|200643|171549|815|816|291644;2|1239|91061|186826|1300|1301|1318;2|1239|186801|3085636|186803|1649459|154046;2|1239|91061|186826|1300|1301|68892;2|976|200643|171549|815|816|817;2|1239|186801|3085636|186803|1766253|39491;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|3085636|186803|2719313|1531,Complete,Svetlana up
bsdb:963/14/NA,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 14,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - constipation (Post-Chemo),Yes - constipation (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with constipation,27,15,None,WMS,NA,Ion Torrent,NA,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:963/15/NA,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 15,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - diarrhea (Post-Chemo),Yes - diarrhea (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with diarrhea,33,9,None,WMS,NA,Ion Torrent,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:963/16/NA,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 16,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - hot flashes (Post-Chemo),Yes - hot flashes (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with hot flashes,21,21,None,WMS,NA,Ion Torrent,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:963/17/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 17,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,Without neurotoxicity (Post-Chemo),With neurotoxicity (Post-Chemo),Breast cancer patients with neurotoxicity evaluated 12 months after Chemotherapy,12,30,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4B,24 April 2024,Scholastica,Scholastica,Differentially abundant taxa in breast cancer patients 12 months after Chemotherapy with neurotoxicity compared to those without neurotoxicity,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans",2|976|200643|171549|815|816|820;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|216572|244127|169435;2|1239|186801|3085636|186803|1506553|1512;2|201174|84998|1643822|1643826|84111|84112;2|1239|526524|526525|2810280|3025755|29348;2|1239|186801|3085636|186803|2719313|358743;2|976|200643|171549|815|816|818;2|1239|186801|186802|216572|1905344|1550024;2|1239|526524|526525|2810280|3025755|1547;2|1239|526524|526525|128827|1472649|1034346;2|1239|186801|186802|1392389|1297617;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|3085636|186803|207244|649756;2|1239|186801|3085636|186803|2719313|208479;2|1239|186801|186802|3082771|1924093|1965604;2|1239|186801|3085636|186803|2719313|333367;2|1239|91061|186826|81852|1350|53345,Complete,Svetlana up
bsdb:963/17/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 17,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,Without neurotoxicity (Post-Chemo),With neurotoxicity (Post-Chemo),Breast cancer patients with neurotoxicity evaluated 12 months after Chemotherapy,12,30,None,WMS,NA,Ion Torrent,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4B,24 April 2024,Scholastica,Scholastica,Differentially abundant taxa in breast cancer patients 12 months after Chemotherapy with neurotoxicity compared to those without neurotoxicity,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:5226,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1224|28216|80840|995019|40544|437898;2|1239|186801|186802|31979|1485|1262777;2|1239|909932|1843489|31977|29465|1911679;2|976|200643|171549|171552|838|1262930;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|33042|410072;2|1239|91061|186826|1300|1301|1318;2|201174|1760|85006|1268|32207|43675;2|1239|186801|186802|216572|459786|1897011;2|976|200643|171549|171552|577309|454155;2|976|200643|171549|171552|838|1262929;2|1239|1263005;2|1239|1263011;2|976|200643|171549|1853231|574697|544645;2|1239|186801|186802|216572|1263|40519;2|976|200643|171549|171550|239759|28117;2|1239|186801|3085636|186803|2316020|33039;2|1239|1263000;2|200940|3031449|213115|194924|2049043;2|1239|186801|3085636|186803|3342669|45851;2|976|200643|171549|2005519|397864|487174;2|1239|91061|186826|1300|1301|1343;2|1239|186801|186802|216572|244127|1262700;2|1224|1236|135625|712|724|729;2|1239|186801|186802|3085642|2048137|1628085;2|976|200643|171549|171552|2974265|363265;2|200940|3031449|213115|194924|872|901;2|1239|91061|186826|1300|1301|68892;2|976|200643|171549|815|816|1262739;2|1239|186801|186802|216572|459786|1262911;2|976|200643|171549|815|816|674529;2|1239|909932|1843488|909930|33024|33025;2|1239|1262988;2|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:963/18/1,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 18,France,Mus musculus,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Heathy mice,Breast cancer mice,Mice “humanized” by fecal microbial transplantation (FMT) from breast cancer patients,7,5,None,WMS,NA,Ion Torrent,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5D,24 April 2024,Scholastica,Scholastica,"LEfSe differentiating breast cancer (BC) and healthy volunteers (HV), describing the 14 most discriminant species in 5 early BC pre-CT versus 7 HV stools used for FMT in AT3 tumor bearing mice",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium JC118,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis",2|1239|909932|1843489|31977|29465|39777;2|1239|91061|186826|1300|1357|1358;2|1239|186801|186802|31979|1070699;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|2719313|333367,Complete,Svetlana up
bsdb:963/18/2,Study 963,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S , Zitvogel L",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 18,France,Mus musculus,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Heathy mice,Breast cancer mice,Mice “humanized” by fecal microbial transplantation (FMT) from breast cancer patients,7,5,None,WMS,NA,Ion Torrent,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5D,24 April 2024,Scholastica,Scholastica,"LEfSe differentiating breast cancer (BC) and healthy volunteers (HV), describing the 14 most discriminant species in 5 early BC pre-CT versus 7 HV stools used for FMT in AT3 tumor bearing mice",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|171550|239759|1470347;2|1239|186801|186802|216572|459786;2|201174|1760|85004|31953|1678|216816;2|976|200643|171549|171550|239759|626932;2|201174|84998|84999|84107|102106|74426;2|201174|1760|2037|2049|2529408|1660;2|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:964/1/1,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 0,PCOS patients at Zeitgeber (ZT) 0,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 0",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3A,20 April 2024,Idiaru angela,Idiaru angela,Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT0 vs. PCOS.ZT0,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium human oral taxon HOT-345",2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848|860;2|363464;2|363464;2|221235|1226342;2|221235|1540874,Complete,Svetlana up
bsdb:964/1/2,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 0,PCOS patients at Zeitgeber (ZT) 0,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 0",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3A,20 April 2024,Idiaru angela,Idiaru angela,Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT0 vs. PCOS.ZT0,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",2|201174;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|838|470565,Complete,Svetlana up
bsdb:964/2/1,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 6,PCOS patients at Zeitgeber (ZT) 6,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 6",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3B,20 April 2024,Idiaru angela,Idiaru angela,Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT6 vs. PCOS.ZT6,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875",2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|860;2|221235|1226342,Complete,Svetlana up
bsdb:964/3/1,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 12,PCOS patients at Zeitgeber (ZT) 12,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 12",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3C,20 April 2024,Idiaru angela,Idiaru angela,Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT12 vs. PCOS.ZT12,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848|860,Complete,Svetlana up
bsdb:964/3/2,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 12,PCOS patients at Zeitgeber (ZT) 12,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 12",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3C,20 April 2024,Idiaru angela,Idiaru angela,Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT12 vs. PCOS.ZT12,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|838|470565,Complete,Svetlana up
bsdb:964/4/1,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 18,PCOS patients at Zeitgeber (ZT) 18,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 18",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3D,20 April 2024,Idiaru angela,Idiaru angela,Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT18 vs. PCOS.ZT18,increased,"k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Gracilibacteria",2|221235|1226342;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848|860;2|1239|186801|186802;2|1239|186801;2|976|117743|200644;2|1239|186801|186802|216572;2|363464;2|363464,Complete,Svetlana up
bsdb:964/4/2,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 18,PCOS patients at Zeitgeber (ZT) 18,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 18",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3D,21 April 2024,Idiaru angela,Idiaru angela,Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT18 vs. PCOS.ZT18,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1224|28216|206351|481|482|34026;2|1117;2|1117;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552,Complete,Svetlana up
bsdb:964/5/1,Study 964,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N, Li Y, Qian C, Liu Q, Cao W, Ma M, He R, Chen R, Geng R , Liu Y",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy controls,PCOS Patients,"PCOS patients who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries",10,10,use of antibiotics within 3 months,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental Figure 5E,21 April 2024,Idiaru angela,Idiaru angela,The microbiota that showed significant differences between the two groups as analysed by LEfSe with an LDA score threshold of 4.0.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",2|1239|186801|3085636|186803|572511;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301|1308;2|201174|1760|85004|31953|1678|1680,Complete,Svetlana up
bsdb:965/1/1,Study 965,prospective cohort,NA,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L, Del Chierico F, Pane S, Ristori MV, Pirona I, Guarrasi V, Cotugno N, Bernardi S, Lancella L, Perno CF, Rossi P, Villani A, Campana A, Palma P",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,NA,NA,Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,healthy controls,COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",59,71,none,16S,34,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3,14 March 2024,Ndruscilla,"Ndruscilla,Ayibatari,Joan Chuks",Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients VS Control (CTRL) groups,increased,"k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|200795|292625|292629|292628|233189;2|1239|91061|1385|186817|1386;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060;2|976|117743|200644|49546|1016;2|1239|91061|186826|186828;2|1224|28216|206351|1499392;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539738;2|1224|28216|206351|1499392|397456;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|201174|1760|85006|1268;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1239|909932;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|201174|1760|85006|1268|32207;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,ChiomaBlessing
bsdb:965/1/2,Study 965,prospective cohort,NA,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L, Del Chierico F, Pane S, Ristori MV, Pirona I, Guarrasi V, Cotugno N, Bernardi S, Lancella L, Perno CF, Rossi P, Villani A, Campana A, Palma P",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,NA,NA,Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,healthy controls,COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",59,71,none,16S,34,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 3,14 March 2024,Ndruscilla,"Ndruscilla,Ayibatari,Joan Chuks",Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs Control (CTRL) groups,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|3085636|186803|1766253;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|976|200643|171549|815;2|976|200643|171549|815|816;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3082768|424536;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1918511;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|292632,Complete,ChiomaBlessing
bsdb:965/2/1,Study 965,prospective cohort,NA,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L, Del Chierico F, Pane S, Ristori MV, Pirona I, Guarrasi V, Cotugno N, Bernardi S, Lancella L, Perno CF, Rossi P, Villani A, Campana A, Palma P",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,NA,NA,Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,NO COVID-19 (Patients with diagnosis different from COVID-19),COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",7,71,none,16S,34,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S4,11 April 2024,Joan Chuks,Joan Chuks,Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs NO COVID-19 (Patients with diagnosis different from COVID-19),increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,2|1239|909932|1843489|31977|39948,Complete,ChiomaBlessing
bsdb:965/2/2,Study 965,prospective cohort,NA,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L, Del Chierico F, Pane S, Ristori MV, Pirona I, Guarrasi V, Cotugno N, Bernardi S, Lancella L, Perno CF, Rossi P, Villani A, Campana A, Palma P",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,NA,NA,Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,NO COVID-19 (Patients with diagnosis different from COVID-19),COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",7,71,none,16S,34,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure S4,11 April 2024,Joan Chuks,"Joan Chuks,ChiomaBlessing",Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs NO COVID-19 (Patients with diagnosis different from COVID-19),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,s__unidentified,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|976|200643|171549|171552|1283313;2|1224|28211;2|1224|28211|356|45404;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1224|28216|80840|119060|47670;2|1224|1236|2887326|468;2|1224|28211|204455|31989;2|1224|28211|204455|31989|265;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224|28211|204455;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687;32644;2|1224|1236|72274|135621|286,Complete,ChiomaBlessing
bsdb:966/1/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 1,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Household Control,Parkinson's diease (PD) patients,PD patients on standard therapies,74,74,1 month,16S,34,Illumina,"ANOVA,T-Test",0.05,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,"Result, Figure 2",13 March 2024,Bolanle,Bolanle,Differentially abundant  taxa between the PD and HC groups across the three timepoints; bacteria that produce short chain fatty-acids in PD patients compared to healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803,Complete,NA
bsdb:966/2/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 2,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Patients with Slow progressing Parkinson's disease,Patients with Faster progressing Parkinson's disease,Patients with faster progressing parkinson's disease over a 12 month period,40,34,All participants had not received antibiotics supplements for at least 1 month prior sample collection,16S,34,Illumina,"ANOVA,T-Test",0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 4,13 March 2024,Bolanle,Bolanle,"Differential abundance of taxa between faster progressing and slower progressing PD patients within 12 months, specifically at two-time intervals(t=0, t=12)",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,2|976|200643|171549|2005519,Complete,NA
bsdb:966/3/NA,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 3,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy),DBS(deep brain stimulation),initiation of DBS therapy on parkinson's disease patients at 0 month,74,9,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:966/4/NA,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 4,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy) PD patients,LCIG(Levodopa-Carbidopa Intestinal Gel),initiation of LCIG therapy on parkinson's disease patients at 0 month,74,10,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:966/5/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 5,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Household Control,Parkinson's diease patients at 6 months,PD patients on standard therapies at 6months,74,74,1 month,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 2 text,18 March 2024,Bolanle,Bolanle,There was statistically significant underrepresentation of the bacterial signatures in the gut microbiota of PD patients at 6months time point compared to healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|1766253;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|1263031;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|216572|1263,Complete,NA
bsdb:966/5/2,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 5,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Household Control,Parkinson's diease patients at 6 months,PD patients on standard therapies at 6months,74,74,1 month,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 7 text,18 March 2024,Bolanle,Bolanle,There was statistically significant overrepresentation of the bacterial signatures in the gut microbiota of PD patients at 6months time point compared to healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1224|1236|91347|543;2|1239|91061|186826|33958,Complete,NA
bsdb:966/6/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 6,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Household Control,Parkinson's diease patients at 12 months,Parkinson's disease patients samples collected at 12months,74,74,1 month,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 2 text,18 March 2024,Bolanle,Bolanle,There was statistically significant overrepresentation of the bacterial signatures in the gut microbiota of PD patients at 12months time point compared to healthy control,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|3085642,Complete,NA
bsdb:966/6/3,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 6,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Household Control,Parkinson's diease patients at 12 months,Parkinson's disease patients samples collected at 12months,74,74,1 month,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 3,Figure 2 text,18 March 2024,Bolanle,Bolanle,There was statistically significant overrepresentation of the bacterial signatures in the gut microbiota of PD patients at 12months time point compared to healthy control,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,NA
bsdb:966/7/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 7,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy),DBS(deep brain stimulation),initiation of DBS therapy on parkinson's disease patients at 6 month,74,9,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,figure 7,16 March 2024,Bolanle,Bolanle,the most differentially abbundant taxa after the initiation of DS therapy at 0-6months timepoint included overrepresentation of the geus level,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:966/8/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 8,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy),DBS(deep brain stimulation),initiation of DBS therapy on parkinson's disease patients at 12 month,74,9,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 7,16 March 2024,Bolanle,Bolanle,DBS therapy patients showed overrepresentation of these taxa (t=12moths),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|1224|1236|91347|543|544;2|1239|526524|526525|128827|1573536;2157|28890|183925|2158|2159;2157|28890|183925|2158|2159|2172;2|1224|1236|91347|1903414|581;2|976|200643|171549|171552|838;2|203691|203692|136|137;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:966/8/2,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 8,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy),DBS(deep brain stimulation),initiation of DBS therapy on parkinson's disease patients at 12 month,74,9,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 7,16 March 2024,Bolanle,Bolanle,DBS therapy patients showed uderrepresentation of these taxa after 12 months initiation,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella",2|1239|186801|186802|216572|258514;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|241189;2|1239|186801|186802|404402,Complete,NA
bsdb:966/9/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 9,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy) PD patients,LCIG(Levodopa-Carbidopa Intestinal Gel),initiation of LCIG therapy on parkinson's disease patients at 6 month,74,10,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 7,16 March 2024,Bolanle,Bolanle,Gut microbiome compositional differences in response to the initiation and continuation Levodopa-Carbidopa Intestinal gel (LCIG) therapies at 6months,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:966/9/2,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 9,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy) PD patients,LCIG(Levodopa-Carbidopa Intestinal Gel),initiation of LCIG therapy on parkinson's disease patients at 6 month,74,10,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 7,16 March 2024,Bolanle,Bolanle,Gut microbiome compositional differences in response to the initiation and continuation Levodopa-Carbidopa Intestinal gel (LCIG) therapies at 6months,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",2|1239|186801|186802|216572|258514;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|644652;2|1239|186801|3085636|186803|241189;2|1239|526524|526525|128827|61170,Complete,NA
bsdb:966/10/1,Study 966,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 10,Australia,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Parkinson's disease,MONDO:0005180,Pre DAT(device assisted therapy) PD patients,LCIG(Levodopa-Carbidopa Intestinal Gel),initiation of LCIG therapy on parkinson's disease patients at 12 month,74,10,1 month,16S,34,Illumina,ANOVA,0.01,TRUE,NA,NA,"age,constipation,diet,sex",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 7,16 March 2024,Bolanle,Bolanle,Gut microbiome compositional differences in response to the initiation and continuation Levodopa-Carbidopa Intestinal gel (LCIG) therapies at 12months,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|91061|1385|186817|1386;2|976|200643|171549|171552|838,Complete,NA
bsdb:967/1/1,Study 967,case-control,37208728,10.1186/s12974-023-02782-1,NA,"Yu J, Meng J, Qin Z, Yu Y, Liang Y, Wang Y , Min D",Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease,Journal of neuroinflammation,2023,"Dysbiosis of gut microbiota, Fecal microbiota transplantation, NMNAT2, Neurobehavioral symptoms, Oxidative stress response, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy,Parkinson's Disease (PD)-patients,Individuals with early-stage Parkinson's disease,28,31,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Figure 2B,13 March 2024,Barrakat,Barrakat,Difference in gut microbiota composition between Parkinson's Disease (PD)-patients and healthy individuals,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",2|201174|84998|1643822|1643826|447020;2|201174|84998|1643822|1643826|447020|446660;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|2030927;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461;2|74201;2|976|200643|171549,Complete,Svetlana up
bsdb:967/1/2,Study 967,case-control,37208728,10.1186/s12974-023-02782-1,NA,"Yu J, Meng J, Qin Z, Yu Y, Liang Y, Wang Y , Min D",Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease,Journal of neuroinflammation,2023,"Dysbiosis of gut microbiota, Fecal microbiota transplantation, NMNAT2, Neurobehavioral symptoms, Oxidative stress response, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy,Parkinson's Disease (PD)-patients,Individuals with early-stage Parkinson's disease,28,31,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Figure 2B,13 March 2024,Barrakat,"Barrakat,Scholastica",Difference in gut microbiota composition between Parkinson's Disease (PD)-patients and healthy individuals,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55_1",2|1239|909932|1843488|909930;2|201174|1760|2037;2|1239|91061;2|1239|526524|526525|2810280|135858|100886;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1224|1236;2|1239|526524|526525|128827|1573535|1735;2|1239|186801|3085636|186803;2|1239|91061|186826;2|976|200643|171549|171552|2974265|363265;2|1239|909932;2|976|200643|171549|171552|577309;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171552|2974251|165179;2|1239|909932|909929;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1308;2|1239|909932|1843489|31977|29465|39777;2|1239|186801|186802|216572|1535;2|1239|526524|526525|128827;2|976|200643|171549|171552|577309;2|1239|526524|526525|2810280|135858;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803|33042|2710826,Complete,Svetlana up
bsdb:968/1/1,Study 968,case-control,36068280,10.1038/s41598-022-19393-0,NA,"Kaiyrlykyzy A, Kozhakhmetov S, Babenko D, Zholdasbekova G, Alzhanova D, Olzhayev F, Baibulatova A, Kushugulova AR , Askarova S",Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan,Scientific reports,2022,NA,Experiment 1,Kazakhstan,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy senior group,Alzheimer's group,Patients with Alzheimer's disease,43,41,None,16S,NA,Illumina,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,"Supplementary Table 1a,b,c",13 March 2024,EniolaAde,"EniolaAde,Scholastica",Differentially abundant taxa in healthy control versus Alzheimer's disease group determined using MaAsLin2,increased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Acidobacteriota|c__Blastocatellia,k__Bacteria|p__Candidatus Latescibacterota,k__Bacteria|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales|f__Chthoniobacteraceae|g__Candidatus Udaeobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Dinghuibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Gemmatimonadota|c__Longimicrobiia|o__Longimicrobiales|f__Longimicrobiaceae|g__Longimicrobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylotenera,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Niastella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Parasegetibacter,k__Bacteria|p__Planctomycetota|c__Phycisphaerae,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Solitalea,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae|g__Thioalkalivibrio,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Acidobacteriota|c__Vicinamibacteria|o__Vicinamibacterales|f__Vicinamibacteraceae|g__Vicinamibacter,s__metagenome,s__uncultured organism,k__Bacteria|s__uncultured soil bacterium,k__Bacteria|p__Bacillota",2|201174|84992;2|57723;2|74201|203494|48461|1647988|239934;2|57723|1562566;2|74015;2|74201|134549|1836787|1836792|1921511;2|508458|649775|649776|649777|508459;2|201174|1760|85007|1653|1716;2|976|1853228|1853229|563835|1795363;2|1239|186801|186802|186806|1730;2|976|117743|200644|49546|237;2|142182|1804991|1804992|1804993|1804994;2|1224|28216|32003|32011|359407;2|976|1853228|1853229|563835|354354;2|1224|28216|80840|75682|846;2|976|1853228|1853229|563835|1004302;2|203682|666505;2|203682;2|1224|28216|80840|80864|52972;2|976|200643|171549|171552|838;2|976|117747|200666|84566|929509;2|508458|649775;2|508458;2|1224|1236|135613|72276|106633;2|74201|203494;2|74201;2|57723|1813735|2910145|2211325|1847386;256318;155900;2|164851;2|1239,Complete,Svetlana up
bsdb:968/1/2,Study 968,case-control,36068280,10.1038/s41598-022-19393-0,NA,"Kaiyrlykyzy A, Kozhakhmetov S, Babenko D, Zholdasbekova G, Alzhanova D, Olzhayev F, Baibulatova A, Kushugulova AR , Askarova S",Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan,Scientific reports,2022,NA,Experiment 1,Kazakhstan,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy senior group,Alzheimer's group,Patients with Alzheimer's disease,43,41,None,16S,NA,Illumina,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,"Supplementary Table 1a,b,c",13 March 2024,EniolaAde,"EniolaAde,Scholastica",Differentially abundant taxa in healthy control versus Alzheimer's disease group determined using MaAsLin2,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Nitrosococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,s__gut metagenome,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|201174;2|201174|1760|85004|31953|1678;2|1224|28216|80840|506|359336;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|2767842;2|1239|91061|186826|33958|2767885;2|1239|91061|186826|33958|2767886;2|1239|186801|3085656|3085657|2039302;2|1224|1236|135613|1046|1227;2|1224|28211|356|69277|28100;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1506577;2|1239|909932|1843489|31977|29465;749906;2|1239|186801|244328;2|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:968/2/1,Study 968,case-control,36068280,10.1038/s41598-022-19393-0,NA,"Kaiyrlykyzy A, Kozhakhmetov S, Babenko D, Zholdasbekova G, Alzhanova D, Olzhayev F, Baibulatova A, Kushugulova AR , Askarova S",Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan,Scientific reports,2022,NA,Experiment 2,Kazakhstan,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy senior group,Alzheimer's disease group,Patients with Alzheimer's disease,43,41,None,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 3c,18 March 2024,EniolaAde,"EniolaAde,Ayibatari,Scholastica",Significantly different enrichment of bacteria taxa in the Alzheimer’s disease (AD) group (purple) compared to the control group (green),increased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,s__gut metagenome,k__Bacteria|p__Bacteroidota|s__uncultured Bacteroidetes bacterium,s__uncultured organism,k__Bacteria|s__uncultured soil bacterium,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|s__uncultured Terriglobales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",2|201174|84992;2|57723;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171552|1283313;2|1239;2;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3082768|990719;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186806|1730|290054;2|1224|28211|356;2|1239|186801|186802|216572;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;749906;2|976|152509;155900;2|164851;2|57723|204432|204433|190530;2|1239|186801|244328,Complete,Svetlana up
bsdb:968/2/2,Study 968,case-control,36068280,10.1038/s41598-022-19393-0,NA,"Kaiyrlykyzy A, Kozhakhmetov S, Babenko D, Zholdasbekova G, Alzhanova D, Olzhayev F, Baibulatova A, Kushugulova AR , Askarova S",Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan,Scientific reports,2022,NA,Experiment 2,Kazakhstan,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy senior group,Alzheimer's disease group,Patients with Alzheimer's disease,43,41,None,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 3c,19 March 2024,EniolaAde,"EniolaAde,Scholastica",Significantly different enrichment of bacteria taxa in the Alzheimer’s disease (AD) group (purple) compared to the control group (green),decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes sp. ES-JQ-2,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,s__gut metagenome,s__uncultured organism,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|201174;2|1224|28216|80840|506|507|588454;2|1239|91061;2|1239;2|976|200643|171549;2|976|200643|171549|815|816;2|1239|186801;2|1224|1236|91347;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1224|1236;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803;2|1239|186801|3085636;2|1239|91061|186826|33958|2767842|1590;2|1239|91061|186826|33958|2767886;2|1239|186801|3085656|3085657|2039302;2|1239|186801|3085636|186803|1506577;2|1239|909932|1843489|31977|29465;749906;155900;2|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:969/1/1,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),PD (Parkinson's Disease),This group consists of 30 Parkinson's disease subjects.,17,30,12 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Supplementary figure 2 and Supplementary table 10 & 11.,18 March 2024,Idiat,"Idiat,Victoria",Nasal microbial differences between rHC and PD subjects. Differential abundance differences were measured using DESeq2 within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus yunnanensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brenneri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mandelii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Methylophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Geopsychrobacteraceae|g__Desulfuromusa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1239|1737404|1737405|1570339|165779|33029;2|201174|1760|85007|1653|1716|43769;2|1224|28216|80840|80864|80865|180282;2|201174|1760|85006|1268|1269|566027;2|1224|1236|2887326|468|475|480;2|1224|1236|72274|135621|286|129817;2|1224|1236|72274|135621|286|75612;2|1224|28216|80840|119060|48736|190721;2|1239|91061|1385|90964|1279|1282;2|1224|1236|2887326|468|475;2|1224|1236|72273|135616|40222;2|201174|1760|85006|85020|36739;2|1224|28216|80840|80864|80865;2|1224|28216|80840|119060|48736;2|200940|3031651|69541|3031659|37817;2|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:969/1/2,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),PD (Parkinson's Disease),This group consists of 30 Parkinson's disease subjects.,17,30,12 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Supplementary figure 2 and Supplementary table 10 & 11.,19 March 2024,Idiat,"Idiat,Ayibatari,Victoria","Nasal microbial differences between rHC and PD subjects. Differential abundance
differences were measured using DESeq2 within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.",decreased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminiphilaceae|g__Aminiphilus|s__Aminiphilus circumscriptus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum palatum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides denticanum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia mallei,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia multivorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia vietnamiensis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter canadensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium acetoacidophilum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium doosanense,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium massiliense,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium ulceribovis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter gracilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter lanceolatus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium modestum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia kunjamensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Alismatales|f__Araceae|s__Gymnostachydoideae|g__Gymnostachys|s__Gymnostachys anceps,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria rosea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia caviae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium paludicola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium chitae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides|s__Myroides odoratus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia bryophila,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia kururiensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phenoliruptrix,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus methioninivorax,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus olsenii,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus tyrrelliae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus hauseri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania|s__Qipengyuania aquimaris,k__Bacteria|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|g__Rhodothermus|s__Rhodothermus clarus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia naturae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hyicus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas pavanii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces danangensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas|s__Tolumonas auensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia pestis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|s__[Actinobacillus] rossii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lampyridae|s__Luciolinae|g__Serratia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Erythrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|g__Rhodothermus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminiphilaceae|g__Aminiphilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacteria|p__Acidobacteriota|c__Holophagae|o__Holophagales|f__Holophagaceae|g__Geothrix,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter",2|508458|649775|649776|3029090|290731|290732;2|1224|28211|204441|2829815|191|561521;2|976|200643|171549|815|816|266833;2|1239|186801|3085636|186803|572511|418240;2|1224|28216|80840|119060|32008|13373;2|1224|28216|80840|119060|32008|87883;2|1224|28216|80840|119060|32008|101571;2|1224|28216|80840|119060|32008|60552;2|29547|3031852|213849|72294|194|449520;2|201174|1760|85007|1653|1716|38285;2|201174|1760|85007|1653|1716|191610;2|201174|1760|85007|1653|1716|1121358;2|201174|1760|85007|1653|1716|441501;2|201174|1760|85007|1653|1716|598660;2|201174|1760|85007|1653|1716|487732;2|1224|28216|80840|80864|281915|230310;2|1224|28216|80840|80864|281915|86182;2|201174|1760|85009|31957|1912216|2559073;2|201174|1760|85007|85029|37914|322509;2|1224|1236|91347|543|561|208962;2759|33090|35493|3398|16360|4454|284549|4466|4467;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|43994|43995;2|201174|1760|85006|1268|57493|1275;2|1239|186801|3085636|186803|28050|28052;2|1224|1236|135625|712|75984|879276;2|201174|1760|85006|85023|33882|300019;2|201174|1760|85007|1762|1866885|1792;2|976|117743|200644|49546|76831|256;2|976|200643|171549|2005525|375288|328812;2|1224|28216|80840|119060|1822464|420952;2|1224|28216|80840|119060|1822464|984307;2|1224|28216|80840|119060|1822464|252970;2|1239|1737404|1737405|1570339|162289|907224;2|1239|1737404|1737405|1570339|162289|411570;2|1239|1737404|1737405|1570339|162289|755171;2|1224|1236|91347|1903414|583|183417;2|1224|28211|204457|335929|1855416|255984;2|1853220|1853222|1853224|563843|29548|374811;2|1224|28216|80840|2975441|93681|304;2|201174|1760|2037|2049|2529408|52773;2|201174|1760|2037|2049|2529408|635203;2|1239|909932|909929|1843491|970|135080;2|1239|91061|1385|90964|1279|1284;2|1224|1236|135614|32033|40323|487698;2|201174|1760|85011|2062|1883|248040;2|1224|1236|135624|84642|43947|43948;2|1224|1236|91347|1903411|629|419257;2|1224|1236|91347|1903411|629|632;2|1224|1236|135625|712|123820;2|201174|1760|85007|85029|37914;2|1224|28216|80840|119060|32008;2|1224|28216|80840|2975441|93681;2|1239|91061|1385|186820|1637;2759|33208|6656|50557|7041|7049|433515|2985502;2|1239|91061|1385|186817|1386;2|1224|28211|204457|335929|1041;2|1224|1236|91347|1903411|629;2|1239|186801|3082720|3118656|114627;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|28050;2|1853220|1853222|1853224|563843|29548;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|43994;2|1224|1236|91347|543|158851;2|1224|28216|206389|2008795|73029;2|508458|649775|649776|3029090|290731;2|1224|28211|204441|2844866|168934;2|1224|28216|80840|80864|665874;2|1224|1236|91347|1903412|635;2|1239|526524|526525|2810281|191303;2|142182|219685|219686|219687|173479;2|57723|533205|574975|574976|44675;2|1224|28216|80840|80864|281915,Complete,Svetlana up
bsdb:969/2/1,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),PD (Parkinson's Disease),This group consists of 30 Parkinson's disease subjects.,17,30,12 weeks,16S,4,Illumina,ANCOM,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Supplementary table 10 & 11.,20 August 2024,Victoria,Victoria,Nasal microbial differences between rHC and PD subjects. The differential abundance differences were measured using ANCOM within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Geopsychrobacteraceae|g__Desulfuromusa",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|106649;2|200940|3031651|69541|3031659|37817,Complete,Svetlana up
bsdb:969/3/1,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,12 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure 1 and Supplementary table 6 & 7.,20 August 2024,Victoria,Victoria,Nasal microbial differences between rHC and SpHC subjects. The differential abundance differences were measured using DESeq2 within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium paucivorans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus yunnanensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brenneri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mandelii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces nanchangensis",2|1239|1737404|1737405|1570339|165779|33029;2|201174|1760|85006|85019|1696|170994;2|201174|1760|85007|1653|1716|156978;2|1224|28216|80840|80864|80865;2|1224|28216|80840|80864|80865|180282;2|201174|1760|85006|85020|36739;2|201174|1760|85006|1268|1269|566027;2|1224|1236|72274|135621|286|129817;2|1224|1236|72274|135621|286|75612;2|1239|91061|1385|90964|1279|1282;2|201174|1760|85011|2062|1883|204925,Complete,Svetlana up
bsdb:969/3/2,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,12 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Figure 1 and Supplementary table 6 & 7.,20 August 2024,Victoria,Victoria,Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using DESeq2 within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas terrae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia vietnamiensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium acetoacidophilum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter lanceolatus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella|s__Dyella ginsengisoli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Acidobacteriota|c__Holophagae|o__Holophagales|f__Holophagaceae|g__Geothrix,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus|s__Lentibacillus kapialis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium paludicola,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides|s__Myroides odoratus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia bryophila,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia kururiensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phenoliruptrix,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phytofirmans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia sabiae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia terrae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia tuberum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus hauseri,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania|s__Qipengyuania aquimaris,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia detusculanense,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus opacus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Segetibacter|s__Segetibacter aerophilus,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lampyridae|s__Luciolinae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia entomophila,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces danangensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella|s__Trabulsiella odontotermitis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora|s__Salinispora tropica",2|1239|91061|1385|186817|1386;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|418240;2|1224|28211|204458|76892|41275|363631;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060|32008|101571;2|1224|28216|80840|119060|32008|60552;2|201174|1760|85007|1653|1716|38285;2|1224|28216|80840|80864|281915;2|1224|28216|80840|80864|281915|86182;2|1224|1236|135614|1775411|231454|363848;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|208962;2|57723|533205|574975|574976|44675;2|1239|91061|186826|33958|1578;2|1239|91061|1385|186817|175304;2|1239|91061|1385|186817|175304|340214;2|1224|28216|80840|80864|665874;2|201174|1760|85006|85023|33882|300019;2|976|117743|200644|49546|76831;2|976|117743|200644|49546|76831|256;2|1239|186801|186802|216572|119852;2|1224|28216|80840|119060|1822464|420952;2|1224|28216|80840|119060|1822464|984307;2|1224|28216|80840|119060|1822464|252970;2|1224|28216|80840|119060|1822464|261302;2|1224|28216|80840|119060|1822464|273251;2|1224|28216|80840|119060|1822464|311230;2|1224|28216|80840|119060|1822464|157910;2|1224|28216|80840|119060|1822464|36873;2|1224|1236|91347|1903414|583|183417;2|1224|28211|204457|335929|1855416|255984;2|1224|28216|80840|119060|48736;2|1224|28216|80840|119060|48736|148618;2|1224|28216|80840|119060|48736|190721;2|201174|1760|85007|85025|1827|37919;2|1224|28216|80840|2975441|93681;2|1224|28216|80840|2975441|93681|304;2|201174|1760|85008|28056|168694;2|976|1853228|1853229|563835|460073|670293;2759|33208|6656|50557|7041|7049|433515|2985502;2|1224|1236|91347|1903411|613|42906;2|201174|1760|85011|2062|1883|248040;2|1224|1236|91347|1903411|629|419257;2|1224|1236|91347|543|158851|379893;2|201174|1760|85008|28056|168694|168695,Complete,Svetlana up
bsdb:969/4/1,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,12 weeks,16S,4,Illumina,ANCOM,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary table 6 & 7.,21 August 2024,Victoria,Victoria,Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using ANCOM within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1224|1236|2887326|468|469|106649;2|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:969/4/2,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,12 weeks,16S,4,Illumina,ANCOM,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary table 6 & 7.,21 August 2024,Victoria,Victoria,Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using ANCOM within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans,2|1224|28216|80840|119060|1822464|36873,Complete,Svetlana up
bsdb:969/5/1,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,SpHC (Spousal household Healthy Control),SpPD (Spousal household Parkinson's Disease),This group consists of Parkinson's Disease subjects living in the same household as their healthy control spouses.,11,11,12 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary table 13 and Fig. 2b,21 August 2024,Victoria,Victoria,Significant differential abundance analysis values of the microbial profiles between spousal household (SpHC) healthy control subjects and their corresponding household PD (SpPD) subjects. At the genus and species taxonomic level.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Chromobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium bovis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis",2|1224|28216|206351|1499392|535;2|1224|1236|2887326|468|475;2|201174|1760|85007|1653|1716|36808;2|1224|1236|2887326|468|475|480,Complete,Svetlana up
bsdb:969/5/2,Study 969,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G, Ramirez V, Engen PA, Naqib A, Forsyth CB, Green SJ, Mahdavinia M, Batra PS, Tajudeen BA , Keshavarzian A",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,SpHC (Spousal household Healthy Control),SpPD (Spousal household Parkinson's Disease),This group consists of Parkinson's Disease subjects living in the same household as their healthy control spouses.,11,11,12 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary table 13 and Fig. 2b,21 August 2024,Victoria,Victoria,Significant differential abundance analysis values of the microbial profiles between spousal household (SpHC) healthy control subjects and their corresponding household PD (SpPD) subjects. At the genus and species taxonomic level.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Nitrospirota|c__Thermodesulfovibrionia|o__Thermodesulfovibrionales|f__Thermodesulfovibrionaceae|g__Thermodesulfovibrio,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus chromogenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus fryi,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia frederiksenii",2|201174|1760|85006|145357|57495;2|1239|91061|1385|90964|1279;2|40117|2811502|2811503|2811504|28261;2|1239|1737404|1737405|1570339|165779|33034;2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|46126;2|1239|91061|1385|90964|1279|29382;2|1239|91061|1385|90964|1279|1282;2|1239|91061|186826|1300|1301|661498;2|1239|91061|186826|1300|1301|68892;2|1224|1236|91347|1903411|629|29484,Complete,Svetlana up
bsdb:970/1/1,Study 970,laboratory experiment,35619714,10.3389/fimmu.2022.900132,NA,"Zhang B, Chen T, Cao M, Yuan C, Reiter RJ, Zhao Z, Zhao Y, Chen L, Fan W, Wang X, Zhou X , Li C",Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity,Frontiers in immunology,2022,"alzheimer's disease, fecal microbiota transplantation, gut- brain axis, melatonin, microbiota dysbiosis, obesity, systemic inflammation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease biomarker measurement,EFO:0006514,Wild type (WT) mice,Endogenous melatonin reduction (EMR) mice,"Mice that exhibited a pan-metabolic disorder, with significant transcriptome changes in 11 organs, serum metabolome alterations as well as microbiota dysbiosis.",NA,NA,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4C,24 March 2024,Shulamite,"Shulamite,Deacme,Scholastica",Distinct gut microbiota identified by LEfSe in endogenous melatonin reduction (EMR) versus  wild type (WT) mice with biomarkers at all levels,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paenarthrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|201174;2|1224|28211;2|1239|526524|526525|128827|2749267;2|1239|91061;2|95818|2093818|2093825|2171986;2|95818|2093818|2093825;2|95818|2093818;2|95818|2093818|2093825|2171986|1331051;2|201174|84998|84999;2|201174|84998;2|201174|84998|1643822|1643826;2|201174|84998|1643822|1643826|580024;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268;2|201174|1760|85006;2|201174|1760|85006|1268|1742992;2|1239|186801|186802|216572|100175;2;2|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:970/1/2,Study 970,laboratory experiment,35619714,10.3389/fimmu.2022.900132,NA,"Zhang B, Chen T, Cao M, Yuan C, Reiter RJ, Zhao Z, Zhao Y, Chen L, Fan W, Wang X, Zhou X , Li C",Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity,Frontiers in immunology,2022,"alzheimer's disease, fecal microbiota transplantation, gut- brain axis, melatonin, microbiota dysbiosis, obesity, systemic inflammation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease biomarker measurement,EFO:0006514,Wild type (WT) mice,Endogenous melatonin reduction (EMR) mice,"Mice that exhibited a pan-metabolic disorder, with significant transcriptome changes in 11 organs, serum metabolome alterations as well as microbiota dysbiosis.",NA,NA,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4C,25 March 2024,Shulamite,"Shulamite,Deacme,Scholastica",Distinct gut microbiota identified by LEfSe in endogenous melatonin reduction (EMR) versus  wild type (WT) mice with biomarkers at all levels,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota",2|976|200643|171549;2|976|200643;2|976|200643|171549|2005473;2|1239|186801|186802|216572|3068309;2|976|200643|171549;2|976|200643|171549|2005473;2|976,Complete,Svetlana up
bsdb:971/1/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with Parkinson's Disease.,25,34,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients and Healthy Controls.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:971/1/2,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with Parkinson's Disease.,25,34,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients and Healthy controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607,Complete,Peace Sandy
bsdb:971/2/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Male Parkinson's disease Patients,Female Parkinson's disease Patients,Female Patients with Parkinson's disease,23,11,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Parkinson's disease Patients and Female Parkinson's disease Patients.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:971/2/2,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Male Parkinson's disease Patients,Female Parkinson's disease Patients,Female Patients with Parkinson's disease,23,11,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Parkinson's Disease Patients and Female Parkinson's Disease Patients.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:971/3/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin Negative Controls,Parkinson's Disease Patients with elevated Calprotectin levels,Parkinson's Disease Patients with elevated levels of Fecal Calprotectin,22,14,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with elevated levels of fecal Calprotectin and Calprotectin Negative Healthy Controls.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:971/3/2,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin Negative Controls,Parkinson's Disease Patients with elevated Calprotectin levels,Parkinson's Disease Patients with elevated levels of Fecal Calprotectin,22,14,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with elevated levels of fecal Calprotectin  and Calprotectin Negative Healthy Controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607,Complete,Peace Sandy
bsdb:971/4/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin positive Parkinson's Disease Patients,Parkinson's Disease Patients with normal Calprotectin levels,Patients with Parkinson's disease that had normal Calprotectin levels..,14,NA,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with normal Calprotectin levels and Calprotectin positive Parkinson's Disease Patients',increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:971/4/2,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin positive Parkinson's Disease Patients,Parkinson's Disease Patients with normal Calprotectin levels,Patients with Parkinson's disease that had normal Calprotectin levels..,14,NA,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with normal Calprotectin levels and Calprotectin positive Parkinson's Disease Patients.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:971/5/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Male Healthy Controls,Female Healthy Controls,Healthy Control persons who were of the female gender,11,14,Not Aplicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Healthy Controls and Female Healthy Controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:971/6/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Female Parkinson's Disease Patients,Male Parkinson's Disease Patients,Parkinson's Disease Patients of the Male Gender,11,23,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Parkinson's disease Patients and Female Parkinson's disease Patients.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,Peace Sandy
bsdb:971/7/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 7,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Normal Calprotectin levels Parkinson's Disease Patients,Parkinson's disease Patients with Normal Calprotectin levels.,25,14,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with normal Calprotectin levels and Healthy Controls.,increased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,2|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:971/8/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 8,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients treated with L-dopa,Parkinson's disease Patients who were treated with L-dopa.,25,24,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients treated with L-dopa and Healthy Controls.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|91061|186826|81852;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:971/8/2,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 8,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients treated with L-dopa,Parkinson's disease Patients who were treated with L-dopa.,25,24,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients treated with L-dopa and Healthy Controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263|438033,Complete,Peace Sandy
bsdb:971/9/NA,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 9,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients not treated with L-dopa,Parkinson's disease Patients who were not treated with L-dopa.,25,10,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:971/10/NA,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 10,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease Patients treated with L-dopa,Parkinson's Disease Patients not treated with L-dopa,Parkinson's disease Patients who were not treated with L-dopa.,24,10,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:971/11/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 11,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients treated with entacapone,Parkinson's disease patients who were treated with entacapone.,25,11,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients treated with entacapone and Healthy Controls.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy",2|1239|1737404|1737405|1570339|165779;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803|1769710;2|1239|186801|186802|543314|35517,Complete,Peace Sandy
bsdb:971/11/2,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 11,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients treated with entacapone,Parkinson's disease patients who were treated with entacapone.,25,11,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients treated with entacapone and Healthy Controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263|438033,Complete,Peace Sandy
bsdb:971/12/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 12,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HR Phenotype,Parkinson's disease Patients with a Hypokinetic-rigid phenotype.,25,15,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hypokinetic-rigid [HR] Phenotype and Healthy Controls.,increased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,2|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:971/12/2,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 12,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HR Phenotype,Parkinson's disease Patients with a Hypokinetic-rigid phenotype.,25,15,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hypokinetic-rigid [HR] Phenotype and Healthy Controls.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:971/13/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 13,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with Tremor dominant Phenotype,Parkinson's disease Patients with Tremor dominant [T] phenotype.,25,6,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Tremor dominant [T] Phenotype and Healthy Controls.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:971/14/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 14,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HY Stage of 1 to 2.5,Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 1 to 2.5.,25,18,Not Applicable,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 1 to 2.5 and Healthy Controls.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1239|186801|186802|216572|216851;2|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:971/15/1,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 15,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HY Stage of 3 to 4,Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 3 to 4.,25,16,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,Peace Sandy",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hoehn-Yahr [HY] Stage 3 to 4 and Healthy Controls.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|1737404|1737405|1570339|162289;2|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:971/16/NA,Study 971,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 16,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease Patients with HY Stage of 1 to 2.5,Parkinson's disease Patients with HY Stage of 3 to 4,Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 3 to 4.,18,16,Not Applicable.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:972/3/1,Study 972,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian XH, Liu XL, Chen G, Chen SD , Tang HD",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Sham-operated group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 3 (I - N),15 March 2024,Flo,"Flo,Scholastica",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the phosphate-buffered saline (PBS) sham-operated group,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|28138,Complete,Svetlana up
bsdb:972/3/2,Study 972,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian XH, Liu XL, Chen G, Chen SD , Tang HD",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Sham-operated group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 3 (I - N),15 March 2024,Flo,"Flo,Scholastica",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the phosphate-buffered saline (PBS) sham-operated group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|1283313;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:972/6/1,Study 972,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian XH, Liu XL, Chen G, Chen SD , Tang HD",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Control group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 3 (I - N),13 March 2024,Flo,"Flo,Scholastica",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the control group,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|28138,Complete,Svetlana up
bsdb:972/6/2,Study 972,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian XH, Liu XL, Chen G, Chen SD , Tang HD",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Control group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 3 (I - N),13 March 2024,Flo,"Flo,Scholastica",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the control group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|1283313;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:973/1/1,Study 973,case-control,34776854,10.3389/fnins.2021.756951,NA,"Kenna JE, Chua EG, Bakeberg M, Tay A, McGregor S, Gorecki A, Horne M, Marshall B, Mastaglia FL , Anderton RS",Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson's Disease Cohort,Frontiers in neuroscience,2021,"16S, KEGG, Parkinson’s disease, gut bacteria, gut microbiome",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,People with Parkinson's Disease (PWP),People with Parkinson's Disease from multiple Movement Disorders Clinics,47,87,3 Months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,18 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Significantly different taxa in the gut microbiome of controls compared to people with Parkinson's disease (PwP) following 16S rRNA sequencing.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Synergistota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1224|1236|91347|543;2|1224|1236;2|508458|649775;2|1224;2|508458;2|1224|1236|91347,Complete,Svetlana up
bsdb:973/1/2,Study 973,case-control,34776854,10.3389/fnins.2021.756951,NA,"Kenna JE, Chua EG, Bakeberg M, Tay A, McGregor S, Gorecki A, Horne M, Marshall B, Mastaglia FL , Anderton RS",Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson's Disease Cohort,Frontiers in neuroscience,2021,"16S, KEGG, Parkinson’s disease, gut bacteria, gut microbiome",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,People with Parkinson's Disease (PWP),People with Parkinson's Disease from multiple Movement Disorders Clinics,47,87,3 Months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,18 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Significantly different taxa in the gut microbiome of controls compared to people with Parkinson's disease (PwP) following 16S rRNA sequencing.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|186802|3085642|2048137;2|1239|186801|186802|1898207;2|1239|186801|186802|1980681;2|1239|186801|3082720|186804|1505657;2|1239|186801|3085636|186803|2163168;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801;2|1239|186801|186802,Complete,Svetlana up
bsdb:974/1/1,Study 974,"cross-sectional observational, not case-control",36975828,10.1128/spectrum.03549-22,NA,"Sheng D, Yue K, Li H, Zhao L, Zhao G, Jin C , Zhang L",The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer,Microbiology spectrum,2023,"gynecological, microbiome, ovarian cancer, prognostic biomarkers, tumor microenvironment",Experiment 1,China,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Immune-enriched subtype (clust2),Immune-deficient subtype (clust1),Patients with the ovarian cancer subtype which is characterized by the lack of immune infiltration and high tumor purity,191,182,None,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3C,25 March 2024,Scholastica,Scholastica,Significant differentially abundant taxonomic biomarkers between immune-deficient subtype (clust1) and immune-enriched subtype (clust2) identified by LEfSe,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas dhakensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella|s__Coxiella endosymbiont of Amblyomma nuttalli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium modestum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus|s__Dermacoccus nishinomiyaensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Halopseudomonas|s__Halopseudomonas phragmitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Halopseudomonas|s__Halopseudomonas sabulinigri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides|s__Mycobacteroides chelonae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum|s__Nitrospirillum amazonense,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas asplenii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas campi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas cavernae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas citronellolis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas congelans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas cremoricolorata,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas furukawaii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas glycinae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas iranensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas marincola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas promysalinigenes,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. 02C 26,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. B10,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DR 5-09,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DY-1,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. LPB0260,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. R3-18-08,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. R84,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. S11A 273,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. St316,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. Z003-0.4C(8344-21),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas syringae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas vanderleydeniana,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viciae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas xanthosomatis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas zeae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium meliloti,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. CFSAN084952,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. A214,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. OST1909,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella|s__Legionella longbeachae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. St29,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas tensinigenes",2|1224|1236|135624|84642|642|196024;2|1239|91061|1385|186817|1386|1423;2|1224|1236|118969|118968|776|2749996;2|201174|1760|85009|31957|1912216|2559073;2|1224|28216|80840|80864|80865|80866;2|201174|1760|85006|145357|57495|1274;2|32066|203490|203491|203492|848|851;2|1224|1236|72274|135621|2901189|1931241;2|1224|1236|72274|135621|2901189|472181;2|201174|1760|85007|1762|670516|1774;2|1224|28211|204441|2829815|1543705|28077;2|1224|1236|72274|135621|286|53407;2|1224|1236|72274|135621|286|2731681;2|1224|1236|72274|135621|286|2320867;2|1224|1236|72274|135621|286|53408;2|1224|1236|72274|135621|286|200452;2|1224|1236|72274|135621|286|157783;2|1224|1236|72274|135621|286|1149133;2|1224|1236|72274|135621|286|1785145;2|1224|1236|72274|135621|286|2745503;2|1224|1236|72274|135621|286|437900;2|1224|1236|72274|135621|286|1392877;2|1224|1236|72274|135621|286|485898;2|1224|1236|72274|135621|286|2054914;2|1224|1236|72274|135621|286|118613;2|1224|1236|72274|135621|286|1534110;2|1224|1236|72274|135621|286|1755504;2|1224|1236|72274|135621|286|2614442;2|1224|1236|72274|135621|286|1173283;2|1224|1236|72274|135621|286|1573712;2|1224|1236|72274|135621|286|2866277;2|1224|1236|72274|135621|286|2678257;2|1224|1236|72274|135621|286|1855380;2|1224|1236|72274|135621|286|317;2|1224|1236|72274|135621|286|2745495;2|1224|1236|72274|135621|286|2505979;2|1224|1236|72274|135621|286|2842356;2|1224|1236|72274|135621|286|2745510;2|1224|28211|356|82115|28105|382;2|1239|91061|1385|90964|1279|29388;2|1239|91061|186826|1300|1301|28037;2|1224|1236|72274|135621|286|2664899;2|1224|1236|72274|135621|286|1855331;2|1224|1236|72274|135621|286|2777367;2|1224|1236|118969|444|445|450;2|1224|1236|72274|135621|286|1500687;2|1224|1236|72274|135621|286|2745511,Complete,Svetlana up
bsdb:974/1/2,Study 974,"cross-sectional observational, not case-control",36975828,10.1128/spectrum.03549-22,NA,"Sheng D, Yue K, Li H, Zhao L, Zhao G, Jin C , Zhang L",The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer,Microbiology spectrum,2023,"gynecological, microbiome, ovarian cancer, prognostic biomarkers, tumor microenvironment",Experiment 1,China,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Immune-enriched subtype (clust2),Immune-deficient subtype (clust1),Patients with the ovarian cancer subtype which is characterized by the lack of immune infiltration and high tumor purity,191,182,None,PCR,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 3C,25 March 2024,Scholastica,Scholastica,Significant differentially abundant taxonomic biomarkers between immune-deficient subtype (clust1) and immune-enriched subtype (clust2) identified by LEfSe,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga|s__Hydrogenophaga sp. NH-16,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio anguillarum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas thiooxydans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. C27(2019),k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter woluwensis,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Aquisphaera|s__Aquisphaera giovannonii",2|1224|1236|72274|135621|286|287;2|1224|1236|2887326|468|469|470;2|1224|28216|80840|80864|47420|2184519;2|1224|1236|2887326|468|469|40215;2|1224|1236|135623|641|662|55601;2|1224|28216|80840|80864|283|363952;2|1224|28216|80840|119060|32008|101571;2|1224|1236|72274|135621|286|2604941;2|1224|28216|80840|119060|106589|119219;2|201174|1760|85006|1268|1663|156980;2|203682|203683|2691356|1763524|1511635|406548,Complete,Svetlana up
bsdb:975/1/1,Study 975,case-control,38229613,10.4103/aian.aian_460_23,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10789430/,"Pavan S, Gorthi SP, Prabhu AN, Das B, Mutreja A, Vasudevan K, Shetty V, Ramamurthy T , Ballal M",Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India,Annals of Indian Academy of Neurology,2023,"16S rRNA gene sequencing, Parkinson's disease, dysbiosis, gut microbiota, neurodegenerative disease, stool",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease from India,13,23,4 weeks,16S,NA,Nanopore,LEfSe,0.01,TRUE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 5,18 March 2024,Kaycee,"Kaycee,Peace Sandy","The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.",increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801;2|1239|186801|3082768|424536;2|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:975/1/2,Study 975,case-control,38229613,10.4103/aian.aian_460_23,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10789430/,"Pavan S, Gorthi SP, Prabhu AN, Das B, Mutreja A, Vasudevan K, Shetty V, Ramamurthy T , Ballal M",Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India,Annals of Indian Academy of Neurology,2023,"16S rRNA gene sequencing, Parkinson's disease, dysbiosis, gut microbiota, neurodegenerative disease, stool",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease from India,13,23,4 weeks,16S,NA,Nanopore,LEfSe,0.01,TRUE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 5,18 March 2024,Kaycee,"Kaycee,Peace Sandy","The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.",decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",2|201174|84998|84999|84107;2|1239|186801|3085636|186803;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1898203,Complete,Peace Sandy
bsdb:976/1/1,Study 976,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D , Roy S",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Ileum,Colon","UBERON:0002116,UBERON:0001155",Response to antiviral drug,EFO:0010123,Intestinal samples of Healthy Control,Intestinal samples of HIV Positive Patients,"All intestinal samples (colon brush, colon wash, terminal ileum brush, and terminal ileum wash) of HIV-positive individuals on antiretroviral therapy",12,5,30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 1C,14 March 2024,Eve10111,"Eve10111,Scholastica",Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between gut samples from HIV-positive compared to HIV-negative patients.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter",2|74201|203494|48461|1647988|239934;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|3030910|86331;2|1239|186801|3082720|186804|1257;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|1224|1236|135624|83763|83770;2157|28890|183925|2158|2159|2172,Complete,Svetlana up
bsdb:976/1/2,Study 976,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D , Roy S",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Ileum,Colon","UBERON:0002116,UBERON:0001155",Response to antiviral drug,EFO:0010123,Intestinal samples of Healthy Control,Intestinal samples of HIV Positive Patients,"All intestinal samples (colon brush, colon wash, terminal ileum brush, and terminal ileum wash) of HIV-positive individuals on antiretroviral therapy",12,5,30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig. 1C,14 March 2024,Eve10111,"Eve10111,Scholastica",Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between gut samples from HIV-positive compared to HIV-negative patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:976/2/1,Study 976,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D , Roy S",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 2,United States of America,Homo sapiens,Colon,UBERON:0001155,Response to antiviral drug,EFO:0010123,Colon wash samples of Healthy Control,Colon wash samples of HIV Positive Patients,Colon wash samples of HIV-positive individuals on antiretroviral therapy,12,5,30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 3C,27 May 2024,Scholastica,Scholastica,Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between colon wash samples from HIV-positive compared to HIV-negative patients.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",2|1224|1236|135624|83763|83770;2|1224|1236|135625|712|416916,Complete,Svetlana up
bsdb:976/3/1,Study 976,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D , Roy S",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 3,United States of America,Homo sapiens,Colon,UBERON:0001155,Response to antiviral drug,EFO:0010123,Colon brush samples of Healthy Control,Colon brush samples of HIV Positive Patients,Colon brush samples of HIV-positive individuals on antiretroviral therapy,12,5,30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 4C,27 May 2024,Scholastica,Scholastica,Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between colon brush samples from HIV-positive compared to HIV-negative patients.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",2|1239|909932|1843489|31977|906;2|201174|84998|1643822|1643826|84108,Complete,Svetlana up
bsdb:976/4/1,Study 976,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D , Roy S",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 4,United States of America,Homo sapiens,Ileum,UBERON:0002116,Response to antiviral drug,EFO:0010123,Terminal ileum wash samples of Healthy Control,Terminal ileum wash samples of HIV Positive Patients,Terminal ileum (TI) wash samples of HIV-positive individuals on antiretroviral therapy,12,5,30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 5C,27 May 2024,Scholastica,Scholastica,Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between terminal ileum (TI) samples from HIV-positive compared to HIV-negative patients.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",2|976|200643|171549|171552|838;2|1239|186801|3082720|3030910|86331;2|1239|909932|909929|1843491|52225;2|1224|1236|135625|712|416916,Complete,Svetlana up
bsdb:977/1/1,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 1,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,COVID-19 patients,Hospitalized COVID-19 patients,76,76,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Fig 2A,14 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients versus local controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838;2|1239|526524|526525|128827|123375;2|1224|28211|204457|41297|13687;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:977/1/2,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 1,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,COVID-19 patients,Hospitalized COVID-19 patients,76,76,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Fig 2A,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients versus local controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1224|1236|135625|712|713;2|1224|28216|206351|481|194195;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|976|117743|200644|49546|1016;2|1239|186801|3085636|186803|43996;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|3118655|44259;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1357;2|1224|28216|80840|119060|47670;2|201174|1760|85007|2805586|1847725;2|976|200643|171549|1840213|1840214;2|1239|186801|3082720|3030910|86331;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572|1263;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:977/2/1,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 2,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Abnormality of the respiratory system,HP:0002086,local controls,Non-Covid-19 Patients,Hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses.,76,69,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig 2B,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized non-COVID-19 patients versus local controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|186828|29393;2|1239|91061|186826|33958|2759736;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2767887;2|1239|91061|186826|33958|2742598;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:977/2/2,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 2,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Abnormality of the respiratory system,HP:0002086,local controls,Non-Covid-19 Patients,Hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses.,76,69,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig 2B,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized non-COVID-19 patients versus local controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1224|1236|135625|712|713;2|1224|28216|206351|481|194195;2|1239|186801|3082720|3030910|2060094;2|1239|91061|1385|186817|1386;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|3085636|186803|43996;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|216851;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|201174|1760|85007|2805586|1847725;2|976|200643|171549|1840213|1840214;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|186804|1257;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964|1279;2|1239|186801|3085636|186803|1213720;2|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:977/3/1,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 3,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,non-Covid-19 patients,Covid-19 patients,Hospitalised Covid-19 patients.,69,76,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 2C,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 versus non-COVID-19 patients.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus",2|976|200643|171549|171552|1283313;2|976|117743|200644|2762318|59735;2|29547|3031852|213849|72294|194;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|3085636|186803|43996;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|201174|1760|85007|2805586|1847725;2|1224|1236|2887326|468|475;2|1239|186801|3082720|186804|1257;2|1239|526524|526525|128827|123375;2|95818|2093818|2093819|2093822|2093823|2093824,Complete,Svetlana up
bsdb:977/3/2,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 3,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,non-Covid-19 patients,Covid-19 patients,Hospitalised Covid-19 patients.,69,76,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 2C,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 versus non-COVID-19 patients.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|1239|909932|1843489|31977|156454;2|1239|91061|186826|33958|2759736;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2767887;2|1239|91061|186826|33958|2742598;2|1239|186801|3082720|3030910|86331;2759|33090|35493|3398|72025|3803|3814|508215,Complete,Svetlana up
bsdb:977/4/1,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 4,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Pneumonia,EFO:0003106,Covid-19 with no Pneumonia,Covid-19 with Pneumonia,Hospitalized COVID-19 patients with Pneumonia,38,38,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,21 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with pneumonia compared to those with no pneumonia.,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,2|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:977/4/2,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 4,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Pneumonia,EFO:0003106,Covid-19 with no Pneumonia,Covid-19 with Pneumonia,Hospitalized COVID-19 patients with Pneumonia,38,38,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A,21 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with pneumonia compared to those with no pneumonia.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1224|1236|2887326|468|475;2|1239|1737404|1737405|1570339|162289,Complete,Svetlana up
bsdb:977/5/1,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 5,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Viral load,EFO:0010125,viral load (≤7.5),viral load (>7.5),COVID-19 patients with viral load greater than 7.5,33,35,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with viral load ≤7.5 versus viral load >7.5.,increased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum",2|544448|31969|186329|2146|2147;2|976|200643|171549|815|816;2|976|200643|171549|171551|836;2|1239|186801|186802|543314|35518,Complete,Svetlana up
bsdb:977/5/2,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 5,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Viral load,EFO:0010125,viral load (≤7.5),viral load (>7.5),COVID-19 patients with viral load greater than 7.5,33,35,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6B,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with viral load ≤7.5 versus viral load >7.5.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia caballeronis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1239|91061|186826|81852|1350;2|1239|91061|1385|539738|1378;2|1224|28216|80840|119060|1822464|416943;2|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:977/6/1,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 6,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,Hospitalized patients,"Hospitalized COVID and non-COVID patients,",76,145,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4A,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized (COVID-19 and non-COVID-19) patients versus local controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|909932|909929|1843491|82202;2|1239|91061|186826|33958|2767887;2|1239|91061|186826|33958|2742598;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838;2|1239|526524|526525|128827|123375;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:977/6/2,Study 977,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS , Chen Z",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 6,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,Hospitalized patients,"Hospitalized COVID and non-COVID patients,",76,145,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4A,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized (COVID-19 and non-COVID-19) patients versus local controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1224|1236|135625|712|713;2|1224|28216|206351|481|194195;2|1239|186801|3082720|3030910|2060094;2|1239|91061|1385|186817|1386;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|43996;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|216851;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|28216|80840|119060|47670;2|201174|1760|85007|2805586|1847725;2|976|200643|171549|1840213|1840214;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964|1279;2|1239|186801|3085636|186803|1213720;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:978/1/1,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Non-responders to anti–PD-1/PD-L1 immunotherapy,Responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,29,45,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3A, Supp. Table S6",15 March 2024,Hamza,"Hamza,Scholastica",Differential abundance between responders and non-responders to  Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|28050;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|297314;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:978/1/2,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Non-responders to anti–PD-1/PD-L1 immunotherapy,Responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,29,45,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3A, Supp. Table S6",15 March 2024,Hamza,"Hamza,Scholastica",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|815|816;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|1649459;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:978/2/1,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (colorectal cancer - CRC),Responders (colorectal cancer - CRC),Patients with colorectal cancer (CRC) who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,7,12,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3B, Supp. Table S7",29 March 2024,Scholastica,Scholastica,Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Colorectal Cancer (CRC),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|976|200643|171549|815|816;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|28050;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|3068309;2|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:978/2/2,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (colorectal cancer - CRC),Responders (colorectal cancer - CRC),Patients with colorectal cancer (CRC) who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,7,12,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3B, Supp. Table S7",29 March 2024,Scholastica,Scholastica,Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Colorectal Cancer (CRC),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|1506553;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|292632,Complete,Folakunmi
bsdb:978/3/1,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Esophageal carcinoma,EFO:0002916,Non-responders (esophageal carcinoma),Responders (esophageal carcinoma),Patients with esophageal carcinoma who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,6,8,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3C, Supp. Table S8",30 March 2024,Scholastica,Scholastica,Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in esophageal carcinoma cancer patients,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|976|200643|171549|815|816;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|877420;2|976|200643|171549|171552|577309;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:978/3/2,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Esophageal carcinoma,EFO:0002916,Non-responders (esophageal carcinoma),Responders (esophageal carcinoma),Patients with esophageal carcinoma who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,6,8,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3C, Supp. Table S8",30 March 2024,Scholastica,Scholastica,Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in esophageal carcinoma cancer patients,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|1649459;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|248744;2|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:978/4/1,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Non-responders (gastric cancer),Responders (gastric cancer),Patients with gastric cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,8,15,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3D, Supp. Table S9",30 March 2024,Scholastica,Scholastica,Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|28050;2|976|200643|171549|815|816;2|1239|186801|186802|216572|3068309;2|1239|186801|3085636|186803|1766253,Complete,Folakunmi
bsdb:978/4/2,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Non-responders (gastric cancer),Responders (gastric cancer),Patients with gastric cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,8,15,None,16S,34,Illumina,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3D, Supp. Table S9",30 March 2024,Scholastica,Scholastica,Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|1239|186801|3085636|186803|1766253;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|976|200643|171549|1853231|574697;2|1239|909932|909929|1843491|158846;2|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:978/5/1,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Responders to anti–PD-1/PD-L1 immunotherapy,Non-responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who did not achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,25,15,None,WMS,NA,Illumina,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supp. Table S10,30 March 2024,Scholastica,Scholastica,"Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Gastrointestinal Cancer (Responders, n=25; Non-responders, n=15)",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus curvatus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",2|1239|91061|186826|33958|2767885|28038;2|1239|526524|526525|2810280|135858|100886;2|1239|909932|1843489|31977|39948|487173;2|1224|1236|91347|1903411|629,Complete,Folakunmi
bsdb:978/5/2,Study 978,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z, Cheng S, Kou Y, Wang Z, Jin R, Hu H, Zhang X, Gong JF, Li J, Lu M, Wang X, Zhou J, Lu Z, Zhang Q, Tzeng DTW, Bi D, Tan Y , Shen L",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Responders to anti–PD-1/PD-L1 immunotherapy,Non-responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who did not achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,25,15,None,WMS,NA,Illumina,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supp. Table S10,30 March 2024,Scholastica,Scholastica,"Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Gastrointestinal Cancer (Responders, n=25; Non-responders, n=15)",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|186802|31979|1485|1502;2|1239|186801|186802|186806|1730|39490;2|1239|91061|186826|33958|2742598|97478;2|976|200643|171549|2005525|375288|823;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|186828|117563;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|189330|88431;2|1239|526524|526525|128827|469614;2|74201|203494|48461|1647988|239934|239935,Complete,Folakunmi
bsdb:979/1/1,Study 979,"cross-sectional observational, not case-control",37502423,10.3389/fnagi.2023.1148546,NA,"Zhang M, Zhai Z, Yang B, He L, Wang J, Dai W, Xue L, Yang X, Feng Y , Wang H",Exploring the alteration of gut microbiota and brain function in gender-specific Parkinson's disease based on metagenomic sequencing,Frontiers in aging neuroscience,2023,"Parkinson’s disease, fMRI, gender, gut microbiota, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Female Parkinson’s disease (PD_F) patients,Male Parkinson’s disease (PD_M) patients,Male patients with Parkinson’s disease (PD) diagnosed according to the primary Parkinson’s disease diagnostic criteria.,11,13,History of antibiotic use in the last month,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,body weight",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Fig. 2C, 2E",14 March 2024,Keamy,"Keamy,Scholastica",Significantly differential taxa identified between male and female Parkinson’s disease (PD) patients,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Alsobacteraceae|g__Alsobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Bacillota|c__Tissierellia|g__Dethiosulfatibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halocella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Leminorella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae|g__Propionivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermosediminibacterales|f__Thermosediminibacteraceae|g__Thermosediminibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|74201|203494|48461|1647988;2|1224|28211|356|2792775|1502180;2|1239|186801|186802|1470353;2|1239|1737404|448125;2|1239|186801|53433|972|46466;2|1224|1236|91347|1903416|82980;2|1224|28216|206389|75787|83766;2|1239|186801|2770089|2770093|291988;2|74201|203494|48461;2|74201|203494;2|74201;2;2|976|117743|200644|49546,Complete,Svetlana up
bsdb:979/1/2,Study 979,"cross-sectional observational, not case-control",37502423,10.3389/fnagi.2023.1148546,NA,"Zhang M, Zhai Z, Yang B, He L, Wang J, Dai W, Xue L, Yang X, Feng Y , Wang H",Exploring the alteration of gut microbiota and brain function in gender-specific Parkinson's disease based on metagenomic sequencing,Frontiers in aging neuroscience,2023,"Parkinson’s disease, fMRI, gender, gut microbiota, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Female Parkinson’s disease (PD_F) patients,Male Parkinson’s disease (PD_M) patients,Male patients with Parkinson’s disease (PD) diagnosed according to the primary Parkinson’s disease diagnostic criteria.,11,13,History of antibiotic use in the last month,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,body weight",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Fig. 2C, 2E",14 March 2024,Keamy,"Keamy,Scholastica",Significantly differential taxa identified between male and female Parkinson’s disease (PD) patients,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Propionicicella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|33042;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|3085636|186803;2|201174|1760|85009|85015|348581;2|1239|186801|3085636|186803|841|166486;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|1262953;2|1239|186801|3085636|186803|2316020|33039;2|1224|1236|91347|543|561;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:980/1/1,Study 980,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J, Shi M, Zhao C, Liang G, Li C, Ge X, Pei C, Kong Y, Li D, Yang W, Cao B, Fu L, Yan Y, Wu J, Zhou J, Fang Y, Meng X, Li Y , Wang L",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy controls,Non-alcoholic fatty liver disease (NAFLD),Pediatric patients with non-alcoholic fatty liver disease (NAFLD) whose body mass index (BMI) was higher than the 95th percentile and defined through a clinical evaluation and liver ultrasonography,35,79,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 3,14 March 2024,Scholastica,Scholastica,Multiple bacterial species with significantly different abundance found in the intestinal flora of patients with non-alcoholic fatty liver disease (NAFLD) versus healthy controls (HCs),increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|28216|80840|506;2|1239|91061;2;2|1224|28216;2|1224|28216|80840;2|1239|186801|186802|3085642|580596;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|946234;2|32066|203490|203491;2|32066|203490;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|2316020|33038;2|1224;2|1239|186801|3085636|186803|1506577;2|1239|186801|3085636|186803|1506577|2053632;2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:980/1/2,Study 980,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J, Shi M, Zhao C, Liang G, Li C, Ge X, Pei C, Kong Y, Li D, Yang W, Cao B, Fu L, Yan Y, Wu J, Zhou J, Fang Y, Meng X, Li Y , Wang L",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy controls,Non-alcoholic fatty liver disease (NAFLD),Pediatric patients with non-alcoholic fatty liver disease (NAFLD) whose body mass index (BMI) was higher than the 95th percentile and defined through a clinical evaluation and liver ultrasonography,35,79,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 3,14 March 2024,Scholastica,"Scholastica,Ayibatari",Multiple bacterial species with significantly different abundance found in the intestinal flora of patients with non-alcoholic fatty liver disease (NAFLD) versus healthy controls (HCs),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Archaea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Archaea|p__Euryarchaeota|c__Methanobacteria,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae sp. B_A14,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|s__uncultured bacterium",2|1239|186801|3085636|186803|207244;2157;2|976|200643|171549|2005519|397864;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|186801|3082768|424536;2|1239|186801|3082768|990719;2|1224|28216|80840|80864;2|1224|28216|80840|80864|283;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|39496;2157|28890;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1224|1236|135625|712|724;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2157|28890|183925;2157|28890|183925|2158|2159;2157|28890|183925|2158;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572;2|976|200643|171549|171552|577309;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3082720|3120161|1481960;2|1239|186801|3082720|186804;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|1486938;2|976|200643|171549|171552;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|3023528;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977;2|1239|526524|526525|128827|331630;2|1239|186801|186802|216572|707003;2|77133,Complete,Svetlana up
bsdb:980/2/1,Study 980,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J, Shi M, Zhao C, Liang G, Li C, Ge X, Pei C, Kong Y, Li D, Yang W, Cao B, Fu L, Yan Y, Wu J, Zhou J, Fang Y, Meng X, Li Y , Wang L",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,NAFL (Non-alcoholic fatty liver) patients,NASH (Non-alcoholic steatohepatitis) patients,Non-alcoholic fatty liver disease (NAFLD) patients with the presence of hepatic steatosis with necroinflammation and hepatocellular injury with or without fibrosis,5,8,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,increased,NA,increased,Signature 1,"Fig 4C, Fig 4D",15 March 2024,Scholastica,Scholastica,Differential diversity and multiple bacterial species with significantly different abundance found in the intestinal flora of patients with NAFL (Non-alcoholic fatty liver) compared to NASH (Non-alcoholic steatohepatitis),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|976|200643|171549|815|816|820;2|1239|186801|186802|186806|1730|39496;2|1239|186801|3085636|186803|658087;2|1239|186801|3085636|186803|841;2|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:980/2/2,Study 980,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J, Shi M, Zhao C, Liang G, Li C, Ge X, Pei C, Kong Y, Li D, Yang W, Cao B, Fu L, Yan Y, Wu J, Zhou J, Fang Y, Meng X, Li Y , Wang L",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,NAFL (Non-alcoholic fatty liver) patients,NASH (Non-alcoholic steatohepatitis) patients,Non-alcoholic fatty liver disease (NAFLD) patients with the presence of hepatic steatosis with necroinflammation and hepatocellular injury with or without fibrosis,5,8,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,increased,NA,increased,Signature 2,"Fig 4C, Fig 4D",15 March 2024,Scholastica,Scholastica,Differential diversity and multiple bacterial species with significantly different abundance found in the intestinal flora of patients with NAFL (Non-alcoholic fatty liver) compared to NASH (Non-alcoholic steatohepatitis),decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,2|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:981/1/1,Study 981,case-control,35645785,10.3389/fnagi.2022.881872,NA,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease,Frontiers in aging neuroscience,2022,"Parkinson’s disease, biomarker, dysbiosis, gastrointestinal microbiome, gut microbiota, medication, prediction model",Experiment 1,Australia,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,Patients with a clinical diagnosis of idiopathic PD according to the UK Parkinson’s Disease Society Brain Bank Diagnostic Criteria,81,103,All participants did not receive antibiotics or probiotic supplements for at least 1-month prior to sample collection.,16S,34,Illumina,ANOVA,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,15 March 2024,Assel,Assel,Gastrointestinal microbiota compositional differences between Parkinson’s Disease patients and Household Controls.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea|s__Candidatus Soleaferrea sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|201174|1760|85004|31953|1678;2|976|200643|171549|1853231|574697;2|1239|186801|186802|1470353|2856521;2|1239|186801|186802|216572|216851|1946507;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|1263|41978,Complete,Peace Sandy
bsdb:981/1/2,Study 981,case-control,35645785,10.3389/fnagi.2022.881872,NA,"Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL , Sue CM",Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease,Frontiers in aging neuroscience,2022,"Parkinson’s disease, biomarker, dysbiosis, gastrointestinal microbiome, gut microbiota, medication, prediction model",Experiment 1,Australia,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,Patients with a clinical diagnosis of idiopathic PD according to the UK Parkinson’s Disease Society Brain Bank Diagnostic Criteria,81,103,All participants did not receive antibiotics or probiotic supplements for at least 1-month prior to sample collection.,16S,34,Illumina,ANOVA,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 3,15 March 2024,Assel,"Assel,Ayibatari",Gastrointestinal microbiota compositional differences between Parkinson’s Disease patients and Household Controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium ND3006,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum",2|1239|186801|3085636|186803|1766253;2|1239|186801|186802|3085642|580596;2|1239|526524|526525|128827|2049044;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|1410629;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|186806|1730|39497,Complete,Peace Sandy
bsdb:982/1/1,Study 982,laboratory experiment,31837420,https://doi.org/10.1016/j.nbd.2019.104704,NA,"Yang D, Zhao D, Shah SZA, Wu W, Lai M, Zhang X, Li J, Guan Z, Zhao H, Li W, Gao H, Zhou X , Yang L",Implications of gut microbiota dysbiosis and metabolic changes in prion disease,Neurobiology of disease,2020,"Metabolomics, Microbiome, Multi-omics analysis, Prion infection, Short chain fatty acids",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Prion disease,EFO:0004720,Healthy Control (C),Prion-infected mice (R),Prion-infected mice,25,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Fig. 2B,18 March 2024,Ikehdarlington,"Ikehdarlington,Scholastica",Differentially abundant bacterial taxa in prion-infected groups versus healthy control groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota",2|1239|91061;2|29547|3031852|213849;2|29547|3031852;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1224,Complete,Svetlana up
bsdb:982/1/2,Study 982,laboratory experiment,31837420,https://doi.org/10.1016/j.nbd.2019.104704,NA,"Yang D, Zhao D, Shah SZA, Wu W, Lai M, Zhang X, Li J, Guan Z, Zhao H, Li W, Gao H, Zhou X , Yang L",Implications of gut microbiota dysbiosis and metabolic changes in prion disease,Neurobiology of disease,2020,"Metabolomics, Microbiome, Multi-omics analysis, Prion infection, Short chain fatty acids",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Prion disease,EFO:0004720,Healthy Control (C),Prion-infected mice (R),Prion-infected mice,25,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Fig. 2B,18 March 2024,Ikehdarlington,"Ikehdarlington,Scholastica",Differentially abundant bacterial taxa in prion-infected groups versus healthy control groups.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|1283313;2|95818;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|186802|216572;2|1239|186801|186802|216572|707003;2|976|200643|171549|171552,Complete,Svetlana up
bsdb:983/1/1,Study 983,case-control,23335968,10.1371/journal.pone.0053653,https://pubmed.ncbi.nlm.nih.gov/23335968/,"McCoy AN, Araújo-Pérez F, Azcárate-Peril A, Yeh JJ, Sandler RS , Keku TO",Fusobacterium is associated with colorectal adenomas,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal adenoma,EFO:0005406,Non-adenoma,Adenoma,Patients with colorectal adenoma,67,48,None,16S,123,Roche454,T-Test,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,14 March 2024,Uhabiba14,"Uhabiba14,Scholastica",Abundance of Fusobacterium in rectal mucosal biopsies from adenoma cases versus non-adenoma controls,increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,2|32066|203490|203491|203492|848,Complete,Svetlana up
bsdb:984/1/1,Study 984,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH , Egert M",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease,Patients with Parkinson's Disease.,25,34,Not Reported,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2,14 March 2024,FaithAlexander,FaithAlexander,16S rRNA analysis showing the differences in the relative abundance of microbiota composition between PD and Healthy controls.,increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|1737404|1737405|1570339|165779;2|201174|1760|85004|31953;2|1239|91061|186826|81852;2|1239|186801|186802|216572|216851;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3085636|186803|1769710;2|1239|186801|186802|543314|35517;2|1239|186801|3082720|186804,Complete,NA
bsdb:985/1/1,Study 985,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen TH, Cheng CY, Huang CK, Ho YH , Lin JC",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic Kidney Disease,Chronic kidney disease patients,60,105,NA,16S,NA,Nanopore,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,21 March 2024,PreciousMike,"PreciousMike,Ayibatari",Classification of operational taxonomy unit (OTU) with long-read sequencing in healthy participants and enrolled CKD patients.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Culturomica|s__Culturomica massiliensis",2|976|200643|171549|815|816|46506;2|1224|1236|91347|543|561|1499973;2|32066|203490|203491|203492|848|850;2|1239|91061|186826|33958|2742598|97478;2|1239|91061|186826|1300|1301|197614;2|1239|186801|186802|216572|292632|214851;2|976|200643|171549|1853231|1926651|1841857,Complete,Svetlana up
bsdb:985/1/2,Study 985,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen TH, Cheng CY, Huang CK, Ho YH , Lin JC",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic Kidney Disease,Chronic kidney disease patients,60,105,NA,16S,NA,Nanopore,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,21 March 2024,PreciousMike,"PreciousMike,Ayibatari",Classification of operational taxonomy unit (OTU) with long-read sequencing in healthy participants and enrolled CKD patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera indica",2|1239|186801|3085636|186803|207244|649756;2|1239|909932|909929|1843491|970|971;2|1239|909932|909929|1843491|52225|187979;2|1239|909932|1843489|31977|906|879612,Complete,Svetlana up
bsdb:985/2/NA,Study 985,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen TH, Cheng CY, Huang CK, Ho YH , Lin JC",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,NC-CKD,Chronic kidney disease patients without comorbidities,60,40,NA,16S,NA,Nanopore,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:985/3/NA,Study 985,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen TH, Cheng CY, Huang CK, Ho YH , Lin JC",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,H-CKD,Hypertensive chronic kidney disease patients,60,26,NA,16S,NA,Nanopore,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:985/4/NA,Study 985,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen TH, Cheng CY, Huang CK, Ho YH , Lin JC",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,D-CKD,Diabetic chronic kidney disease patients,60,39,NA,16S,NA,Nanopore,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:987/1/1,Study 987,case-control,35900092,https://doi.org/10.1128/spectrum.01676-22,NA,"Yang X, Pan X, Li M, Zeng Z, Guo Y, Chen P, Liang X, Chen P , Liu G",Interaction between Cervical Microbiota and Host Gene Regulation in Caesarean Section Scar Diverticulum,Microbiology spectrum,2022,"cesarean section scar diverticulum, gene regulation, host-microbiota interaction, microbiome",Experiment 1,China,Homo sapiens,"Endometrium,Uterine cervix","UBERON:0001295,UBERON:0000002",Cesarean section,EFO:0009636,Control,Cesarean section scar diverticulum (CSD),"Women with cesarean section scar diverticulum (CSD), a complication that can occur following a cesarean section (C-section) delivery.",24,28,1 Month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,figure 2,17 March 2024,Eve10111,"Eve10111,Scholastica",Differential genera between cesarean section scar diverticulum (CSD) and control group based on linear discriminant analysis (LDA),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|815|816;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|201174|1760|85004|31953|2701;2|976|200643|171549|2005473;2|976|200643|171549|171552|838;2|1224|28216|80840|119060|48736;2|1224|28211|204457|41297|13687;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:987/1/2,Study 987,case-control,35900092,https://doi.org/10.1128/spectrum.01676-22,NA,"Yang X, Pan X, Li M, Zeng Z, Guo Y, Chen P, Liang X, Chen P , Liu G",Interaction between Cervical Microbiota and Host Gene Regulation in Caesarean Section Scar Diverticulum,Microbiology spectrum,2022,"cesarean section scar diverticulum, gene regulation, host-microbiota interaction, microbiome",Experiment 1,China,Homo sapiens,"Endometrium,Uterine cervix","UBERON:0001295,UBERON:0000002",Cesarean section,EFO:0009636,Control,Cesarean section scar diverticulum (CSD),"Women with cesarean section scar diverticulum (CSD), a complication that can occur following a cesarean section (C-section) delivery.",24,28,1 Month,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,figure 2,17 March 2024,Eve10111,"Eve10111,Scholastica",Differential genera between cesarean section scar diverticulum (CSD) and control group based on linear discriminant analysis (LDA),decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|526524|526525|128827|1729679;2|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:988/1/1,Study 988,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,"Mycobacterium tuberculosis,Lung cancer","NCBITAXON:1773,MONDO:0008903",Healthy Control Group (HCG),Untreated TB Group (UTG) and lung cancer patient group (LCG),"This group consists of patients who have untreated pulmonary tuberculosis group (UTG; 5 males, 7 females) and lung cancer patient group (LCG; 5 males, 2 females)",8,19,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3C,17 March 2024,BSpac126,"BSpac126,Victoria,Scholastica",Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus",2|1224|28216|80840|119060|48736|329;2|1239|91061|1385|90964|1279|1283,Complete,Svetlana up
bsdb:988/2/1,Study 988,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Mycobacterium tuberculosis,NCBITAXON:1773,Healthy Control Group (HCG) and Lung Cancer Group (LCG),Untreated TB Group (UTG),This group consists of patients who have Untreated Pulmonary Tuberculosis and are not taking any antibiotics.,15,12,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3C,20 March 2024,BSpac126,"BSpac126,Victoria",Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia solanacearum",2|1224|1236|135625|712|745|747;2|1239|91061|1385|90964|1279|1280;2|1224|28216|80840|119060|48736|305,Complete,Svetlana up
bsdb:988/3/1,Study 988,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Lung cancer,MONDO:0008903,Healthy Control Group (HCG) and Untreated TB Group (UTG),Lung cancer patient group (LCG),Patients with lung cancer,20,7,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4D,22 March 2024,BSpac126,"BSpac126,Victoria,Scholastica",Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. ICC4",2|976|200643|171549|171552|838|28131;2|201174|1760|85011|2062|1883|2099584,Complete,Svetlana up
bsdb:988/4/1,Study 988,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 4,China,Homo sapiens,Throat,UBERON:0000341,Mycobacterium tuberculosis,NCBITAXON:1773,Treated pulmonary TB group (TTG) and cured pulmonary TB group (CTG),Untreated pulmonary TB group (UTG),This group consists of patients who have Untreated Pulmonary Tuberculosis and are not taking any antibiotics.,26,12,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4D,31 July 2024,Scholastica,Scholastica,Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",2|1224|1236|135625|712|745|747;2|1239|91061|1385|90964|1279|1280,Complete,Svetlana up
bsdb:989/1/1,Study 989,laboratory experiment,36943054,https://doi.org/10.1128/spectrum.03330-22,NA,"Zhou C, Wang Y, Li C, Xie Z , Dai L",Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids,Microbiology spectrum,2023,"bacterial consortium, colitis, gut microbiome, metabolomics, secondary bile acids, targeted metabolomics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,DSS Group (Day 7),DSS + BAC Group (Day 7),Mice were given dextran sulfate sodium (DSS) to induce Colitis and then treated with Bile Acid Consortium (BAC).,7,7,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,15 March 2024,Victoria,Victoria,Bacterial taxa identified as differentially abundant between the untreated group (DSS) and the BAC treatment group (DSS + BAC) by LEfSe. Green indicates bacterial taxa whose abundance was higher in the DSS + BAC group; red indicates otherwise.,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus",2|1239|91061;2|976|200643|171549;2|976|200643|171549|815|816|28116;2|976|200643;2|976;2|976|200643|171549|2005519|397864|397865;2|976|200643|171549|2005519;2|201174|1760|85004|31953|1678|28025;2|1239|91061|186826;2|976|200643|171549|2005473;2|976|200643|171549|2005473|1918540|1796646;2|1239|91061|186826|33958;2|1239|91061|186826|33958|2767887|1622,Complete,Svetlana up
bsdb:989/1/2,Study 989,laboratory experiment,36943054,https://doi.org/10.1128/spectrum.03330-22,NA,"Zhou C, Wang Y, Li C, Xie Z , Dai L",Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids,Microbiology spectrum,2023,"bacterial consortium, colitis, gut microbiome, metabolomics, secondary bile acids, targeted metabolomics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,DSS Group (Day 7),DSS + BAC Group (Day 7),Mice were given dextran sulfate sodium (DSS) to induce Colitis and then treated with Bile Acid Consortium (BAC).,7,7,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,15 March 2024,Victoria,Victoria,Bacterial taxa identified as differentially abundant between the untreated group (DSS) and the BAC treatment group (DSS + BAC) by LEfSe. Green indicates bacterial taxa whose abundance was higher in the DSS + BAC group; red indicates otherwise.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium YL45,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phocaeense,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|328814;2|1239;2|1224|28216;2|201174|1760|85004|31953|1678|1694;2|1224|28216|80840|1834205;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|2109688;2|1239|186801|3082720|186804|1870884|1496;2|1239|186801|3085636|186803|2719313|208479;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|216572|216851|853;2|1239|526524|526525|128827|1729679|1702221;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|1392389|1297617;2|1239|186801|3085636|186803|1506553|1871021;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|2109691;2|1239|186801|186802|216572|459786|2109687;2|1239|186801|3082720|186804;2|1239|186801|186802|216572|1017280;2|1224;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841|301301;2|1224|1236|91347|543|590|28901;2|1239|186801|186802;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:990/1/1,Study 990,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F, Li Q, Wang S, Dong M, Xiao G, Bai J, Wang J , Sun X",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Tumor control group (CK),Living bacteria group (LB),"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,none,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 3g,17 March 2024,Manisha28,"Manisha28,Svetlana up",Effects of administration of Lactobacillus on living bacteria group(LB). The gut microbiota with the capacity of producing antitumor compounds are increased in living bacteria group.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|s__bacterium AF12",2|1224|1236|135624;2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061;2|1239;2|1239|186801;2|1224|1236|135622|267889;2|1239|186801|3085636|186803|33042;2|1224|1236|91347|543|547;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1239|186801|186802;2|1224|1236;2|1239|186801|3085636|186803;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|2818505|32015|29;2|1239|186801|186802|216572|119852;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|1729795,Complete,Svetlana up
bsdb:990/1/2,Study 990,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F, Li Q, Wang S, Dong M, Xiao G, Bai J, Wang J , Sun X",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Tumor control group (CK),Living bacteria group (LB),"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,none,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 3g,17 March 2024,Manisha28,"Manisha28,Svetlana up",Effects of administration of Lactobacillus on living bacteria group(LB). Some gut microbiota are decreased in living bacteria group.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta",2|976|200643|171549;2|976|200643|171549|1853231|574697;2|1117;2|976|200643|171549|171550;2|1224|28211|204457|41297;2|1224|28211|204457|41297|13687;2759|33090|35493,Complete,Svetlana up
bsdb:990/2/1,Study 990,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F, Li Q, Wang S, Dong M, Xiao G, Bai J, Wang J , Sun X",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Tumor control group (CK),Inactivated bacteria group (IB),"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of inactivated Lactobacillus bacteria.",30,30,none,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 3g,17 March 2024,Manisha28,"Manisha28,Svetlana up","Effects of administration of inactive Lactobacillus on inactivated bacteria group(IB). 
The abundance of microbial flora in inactivated bacteria group was significantly higher than that of the tumor control group (P < 0.001).",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239;2|1224|28211|204458|76892;2|1239|186801;2|1239|186801|3085636|186803|33042;2|1239|186801|186802,Complete,Svetlana up
bsdb:990/2/2,Study 990,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F, Li Q, Wang S, Dong M, Xiao G, Bai J, Wang J , Sun X",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Tumor control group (CK),Inactivated bacteria group (IB),"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of inactivated Lactobacillus bacteria.",30,30,none,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 3g,17 March 2024,Manisha28,"Manisha28,Svetlana up","Effects of administration of inactive Lactobacillus on inactivated bacteria group(IB). The abundance of microbial flora in inactivated bacteria group was significantly higher than that of the tumor control group (P < 0.001). However, some bacteria groups decreased.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Svetlana up
bsdb:990/3/1,Study 990,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F, Li Q, Wang S, Dong M, Xiao G, Bai J, Wang J , Sun X",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Inactivated bacteria group,Living bacteria group,"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,none,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3g,6 April 2024,Svetlana up,Svetlana up,LEfSe results of Inactivated vs Living Bacteria group,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1224|28211;2|1117;2|1239|186801|186802|216572|2485925;2|1224|28211|766;2|976|200643|171549|171550,Complete,Svetlana up
bsdb:990/3/2,Study 990,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F, Li Q, Wang S, Dong M, Xiao G, Bai J, Wang J , Sun X",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Inactivated bacteria group,Living bacteria group,"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,none,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3g,6 April 2024,Svetlana up,Svetlana up,LEfSe results of Inactivated vs Living Bacteria group,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:991/1/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 1,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma surface of pigs with with melanoma regression,Melanoma surface of pigs with Melanoma progression,Melanoma surface samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 4A,1 April 2024,Snehhumann,"Snehhumann,Idiaru angela",Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium canine oral taxon 260",2|201174|1760|2037|2049|1654;2|976|200643|171549|815|816;2|29547|3031852|213849|72294|194;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848;2|1239|91061|186826|186827|13075;2|1239|1737404|1737405|1570339|31983;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|201174|1760|2037|2049|1069494;2|1239|186801|186802|1151637,Complete,Svetlana up
bsdb:991/1/2,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 1,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma surface of pigs with with melanoma regression,Melanoma surface of pigs with Melanoma progression,Melanoma surface samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 4A,1 April 2024,Snehhumann,"Snehhumann,Idiaru angela",Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|g__Aerosphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",2|1239|91061|186826|137460;2|1239|91061|186826|186828|292480;2|1239|186801|3085636|186803|572511;2|201174|1760|85006|85020|43668;2|200940|3031449|213115|194924|872;2|201174|1760|85007|85029|37914;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186827|66831;2|1239|186801|186802|216572|216851;2|1239|91061|186826|186827|89092;2|1239|91061|186826|186828|1470540;2|1239|91061|1385|90964|227979;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|1269;2|1224|28216|80840|506|90243;2|1224|1236|2887326|468|497;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|3068309;2|1239|186801|3082720|186804|1505652;2|1239|526524|526525|2810281|191303;2|1239|91061|186826|33958|46255;2|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:991/2/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 2,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma tissue of pigs with with melanoma regression,Melanoma tissue of pigs with Melanoma progression,Melanoma tissue samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 4B,8 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma tissue in melanoma progression and melanoma regression,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__Coriobacteriales bacterium DNF00809,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales bacterium S5-A14a",2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|31983;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2759|33090|35493|3398|72025|3803|3814|508215;2|201174|1760|2037|2049|1069494;2|201174|84998|84999|1588753;2|1239|186801|186802|543314|1230734,Complete,Svetlana up
bsdb:991/2/2,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 2,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma tissue of pigs with with melanoma regression,Melanoma tissue of pigs with Melanoma progression,Melanoma tissue samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 4B,8 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma tissue in melanoma progression and melanoma regression,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Eukaryota|k__Metazoa|p__Mollusca|c__Gastropoda|o__Neogastropoda|f__Buccinidae|g__Colubraria|s__Colubraria reticulata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",2|1224|1236|2887326|468|469;2|1224|1236|135625|712|713;2|1239|91061|1385|186817|1386;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|49082;2|201174|84998|84999|84107|102106;2759|33208|6447|6448|6479|37796|604271|604273;2|201174|1760|85009|31957|1912216;2|1239|186801|3085636|186803|189330;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851;2|1239|91061|186826|33958|1578;2|1224|28211|356|69277|68287;2|1224|28211|356|119045|407;2|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:991/3/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 3,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma surface from black pigs,cutaneous melanoma surface samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 1,Supplementary figure 5,8 April 2024,Idiaru angela,Idiaru angela,"Differential abundance calculated using linear discriminant analysis (LDA) effect size
(LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|g__Aerosphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Kurthia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",2|1224|1236|2887326|468|469;2|1239|91061|186826|137460;2|1239|91061|186826|186828|292480;2|1239|186801|3085636|186803|572511;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|201174|1760|85007|1653|1716;2|201174|1760|85007|85029|37914;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186827|66831;2|1239|186801|186802|216572|216851;2|1239|91061|186826|186827|89092;2|1239|91061|186826|186828|1470540;2|1239|91061|1385|90964|227979;2|201174|1760|85006|1268|57493;2|1239|91061|1385|186818|1649;2|1239|91061|186826|33958|1578;2|1224|28216|80840|75682|149698;2|1224|28216|80840|506|90243;2|1224|1236|72274|135621|286;2|1224|1236|2887326|468|497;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1224|28211|204457|41297|13687;2|1239|186801|3082720|186804|1505652;2|1239|526524|526525|2810281|191303;2|1239|91061|186826|33958|46255;2|1239|186801|186802|216572|3068309;2|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:991/3/2,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 3,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma surface from black pigs,cutaneous melanoma surface samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 2,Supplementary figure 5,8 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|31983;2|1224|1236|2887326|468|475;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:991/4/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 4,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma tissue from black pigs,cutaneous melanoma tissue samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 1,Supplementary figure 6,9 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma tissue.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|g__Aerosphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Frigoribacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Kurthia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",2|1224|1236|2887326|468|469;2|1239|91061|186826|137460;2|1239|909932|909929|1843491|82373;2|1239|91061|186826|186828|292480;2|1239|186801|3085636|186803|572511;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|201174|1760|85007|85029|37914;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186827|66831;2|1239|186801|186802|216572|216851;2|976|117743|200644|49546|237;2|201174|1760|85006|85023|96492;2|1239|91061|186826|186827|89092;2|201174|1760|85006|85021|53457;2|1239|91061|186826|186828|1470540;2|1239|91061|1385|90964|227979;2|201174|1760|85006|1268|57493;2|1239|91061|1385|186818|1649;2|1239|91061|186826|33958|1578;2|1224|28216|80840|75682|149698;2|201174|1760|85006|1268|1269;2|1224|1236|2887326|468|475;2|1224|28216|80840|506|90243;2|1224|1236|72274|135621|286;2|1224|1236|2887326|468|497;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|3068309;2|1224|28211|204457|41297|13687;2|1239|186801|3082720|186804|1505652;2|1239|526524|526525|2810281|191303;2|1239|91061|186826|33958|46255;2|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:991/4/2,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 4,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma tissue from black pigs,cutaneous melanoma tissue samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 2,Supplementary figure 6,9 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma tissue.,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium",2|32066|203490|203491|203492|848;2|1239|91061|1385|90964|1279;2|201174|1760|2037|2049|1069494;2|1239|186801|3082720|186804|1257;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|543311;2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|201174|1760|85009|31957|1912216,Complete,Svetlana up
bsdb:991/5/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 5,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Cutaneous melanoma,EFO:0000389,controls without melanoma and melanoma regression,Melanoma progression,samples collected from piglets undergoing melanoma progression.,24,10,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 7,9 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",2|976|200643|171549|815|816;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|31983;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|216851|1946507,Complete,Svetlana up
bsdb:991/6/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 6,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Cutaneous melanoma,EFO:0000389,controls without melanoma and melanoma progression,melanoma regression,samples collected from piglets undergoing melanoma regression,20,14,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 7,10 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,2|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:991/7/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 7,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Cutaneous melanoma,EFO:0000389,Controls without melanoma,Melanoma progression and regression,samples collected from piglets undergoing melanoma regression and progression,10,24,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 7,10 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",2|976|200643|171549|171552|1283313;2|1239|909932|909929|1843491|82373;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:991/8/1,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 8,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Breed,EFO:0005238,Crossbreed between MeLiM and white piglets,Homogenous breed MeLiM piglets,MeLiM piglets whose parents are both MeLiM black pigs,14,20,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 8,10 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between crossbred and MeLiM piglets,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI001,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|976|200643|171549|815|816;2|204428|204429|51291|809|810;2|1239|186801|186802|1780378;2|201174|84998|84999|84107|102106;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|1506553;2|1224|1236|135614|32033|83614;2|1224|1236|135625|712|75984;2|1224|1236|135625|712|745;2|1239|1737404|1737405|1570339|162289;2|1224|1236|72274|135621|286;2|1239|186801|3082720|186804|1501226;2|1239|91061|1385|90964|1279;2|201174|1760|2037|2049|1069494;2|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:991/8/2,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 8,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Breed,EFO:0005238,Crossbreed between MeLiM and white piglets,Homogenous breed MeLiM piglets,MeLiM piglets whose parents are both MeLiM black pigs,14,20,NA,16S,45,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary figure 8,10 April 2024,Idiaru angela,Idiaru angela,Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between crossbred and MeLiM piglets.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171552|1283313;2|1239|909932|909929|1843491|82373;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|52225;2|1239|186801|186802|216572|459786;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|3068309;2|1239|186801|3085636|186803|177971;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|877420;2|1239|526524|526525|128827|331630;2|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:991/9/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 9,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Sample splitting,EFO:0030016,melanoma surface,melanoma tissue,melanoma inner tissue samples collected from piglets with melanoma,24,24,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/10/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 10,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,skin samples from white piglets,skin samples from crossbred piglets,skin samples from Black crossbred piglets.,10,4,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,unchanged,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/11/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 11,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,samples from white piglets,samples from MeLiM piglets,samples from piglets gotten through Homogenous breeding of two Black MeLiM pigs.,10,20,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/12/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 12,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Breed,EFO:0005238,Black crossbred between white and MeLiM piglets,Homogenous breed Black MeLiM piglets,samples from piglets gotten through Homogenous breeding of two Black MeLiM pigs.,4,20,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/13/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 13,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Age at assessment,EFO:0008007,melanoma regression at age 8 weeks,melanoma regression at age 12 weeks,samples gotten from piglets undergoing melanoma regression at age 12 weeks,14,14,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,increased,increased,unchanged,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/14/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 14,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Age at assessment,EFO:0008007,melanoma regression at age 10 weeks,melanoma regression at age 12 weeks,samples gotten from piglets undergoing melanoma regression at age 12 weeks,14,14,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/15/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 15,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Age at assessment,EFO:0008007,melanoma regression at age 8 weeks,melanoma regression at age 10 weeks,samples gotten from piglets undergoing melanoma regression at age 10 weeks,14,14,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,increased,increased,increased,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/16/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 16,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Age at assessment,EFO:0008007,melanoma regression at age 8 weeks,melanoma regression at age 10 weeks,samples gotten from piglets undergoing melanoma regression at age 10 weeks,14,14,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,increased,increased,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:991/17/NA,Study 991,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V , Mrazek J",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 17,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Breed,EFO:0005238,crossbred piglets undergoing regression,MeLiM piglets undergoing regression,samples gotten from Black MeLiM piglets undergoing regression,4,10,NA,16S,45,Ion Torrent,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:992/1/1,Study 992,case-control,34795317,10.1038/s41531-021-00244-0,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8602383/,"Weis S, Meisner A, Schwiertz A, Unger MM, Becker A, Faßbender K, Schnell S, Schäfer KH , Egert M",Association between Parkinson's disease and the faecal eukaryotic microbiota,NPJ Parkinson's disease,2021,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease patients (PD),Patients suffering from Parkinson's disease,25,34,3 months.,18S,NA,Illumina,ANCOM,0.05,TRUE,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 1,29 March 2024,Samreen-19,Samreen-19,Taxa differing significantly between PD samples and controls.,increased,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum candidum,2759|4751|4890|3239873|3243772|34353|43987|1173061,Complete,Svetlana up
bsdb:992/1/2,Study 992,case-control,34795317,10.1038/s41531-021-00244-0,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8602383/,"Weis S, Meisner A, Schwiertz A, Unger MM, Becker A, Faßbender K, Schnell S, Schäfer KH , Egert M",Association between Parkinson's disease and the faecal eukaryotic microbiota,NPJ Parkinson's disease,2021,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease patients (PD),Patients suffering from Parkinson's disease,25,34,3 months.,18S,NA,Illumina,ANCOM,0.05,TRUE,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 1,29 March 2024,Samreen-19,Samreen-19,Taxa differing significantly between PD samples and controls.,decreased,"k__Eukaryota|p__Cercozoa|s__Cercozoa sp. B134,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Malpighiales|f__Linaceae|g__Linum|s__Linum usitatissimum,k__Eukaryota|p__Cercozoa|o__Cercomonadida|f__Cercomonadidae|g__Paracercomonas|s__Paracercomonas sp.,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium roqueforti,k__Eukaryota|c__Synurophyceae|o__Ochromonadales|f__Ochromonadaceae|g__Poterioochromonas|s__Poterioochromonas malhamensis",2759|136419|983299;2759|33090|35493|3398|3646|4004|4005|4006;2759|136419|188941|45108|372085|1979800;2759|4751|4890|147545|5042|1131492|5073|5082;2759|33859|98652|88165|88166|88167,Complete,Svetlana up
bsdb:993/1/1,Study 993,"prospective cohort,time series / longitudinal observational",38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB , Arrieta MC",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,3 months,12 months,infants when they are 12 months of age,99,99,exposure prior to 3 months,16S,4,Illumina,DESeq2,0.001,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig 3C,23 March 2024,Tayk26,"Tayk26,Svetlana up",Comparison of bacterial growth  at 3 and 12 months,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|820;2|976|200643|171549|171552|2974251|165179;2|976|200643|171549|171550,Complete,Svetlana up
bsdb:993/1/2,Study 993,"prospective cohort,time series / longitudinal observational",38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB , Arrieta MC",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,3 months,12 months,infants when they are 12 months of age,99,99,exposure prior to 3 months,16S,4,Illumina,DESeq2,0.001,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig 3C,23 March 2024,Tayk26,"Tayk26,Svetlana up",Comparison of bacterial growth at 3 and 12 months,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:993/2/1,Study 993,"prospective cohort,time series / longitudinal observational",38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB , Arrieta MC",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,3 months,12 months,infants when they are 12 months of age,95,95,before 3 months,ITS / ITS2,NA,Illumina,DESeq2,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig 3F,23 March 2024,Tayk26,"Tayk26,Svetlana up",Comparison of differential fungal growth in 3 and 12 months,decreased,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,2759|4751|4890|3239874|2916678|766764|5475|5480,Complete,Svetlana up
bsdb:993/2/2,Study 993,"prospective cohort,time series / longitudinal observational",38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB , Arrieta MC",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,3 months,12 months,infants when they are 12 months of age,95,95,before 3 months,ITS / ITS2,NA,Illumina,DESeq2,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig 3F,23 March 2024,Tayk26,"Tayk26,Svetlana up",Comparison of differential fungal growth in 3 and 12 months,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera|s__Cyberlindnera jadinii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae",2759|4751|4890|4891|3243778|115784|604195|4903;2759|4751|4890|4891|4892|4893|4930|4932,Complete,Svetlana up
bsdb:994/1/1,Study 994,case-control,22622349,10.1038/ismej.2012.43,https://pubmed.ncbi.nlm.nih.gov/22622349/,"Sanapareddy N, Legge RM, Jovov B, McCoy A, Burcal L, Araujo-Perez F, Randall TA, Galanko J, Benson A, Sandler RS, Rawls JF, Abdo Z, Fodor AA , Keku TO",Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans,The ISME journal,2012,NA,Experiment 1,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal adenoma,EFO:0005406,Adenoma-free (controls),Adenoma patients (cases),Patients who have colorectal adenoma,38,33,"Subjects were asked if they used antibiotics in the last 3 months before colonoscopy. In all, 33 subjects (11 controls and 22 cases) answered the question. Among these subjects, one case subject (4.55%) and one control subject (9.09%) reported antibiotics use.",16S,12,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Supplementary Table 1 and 2,1 May 2024,Rahila,"Rahila,Scholastica",Wilcoxon-tests on log-normalized abundances of of all phyla and genera in cases (33 subjects) versus controls (38 subjects).,increased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Azonexus,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|57723;2|1224|28216|80840|80864|12916;2|1224|1236|2887326|468|469;2|976|117743|200644|2762318|501783;2|1224|28211|356|82115|357;2|74201|203494|48461|1647988|239934;2|1224|28216|80840|92793;2|1224|28216|206389|2008795|146936;2|1117;2|1224|28216|206389|2008795|73029;2|1224|28216|80840|80864|80865;2|29547|3031852|213849|72293|209;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|1239|186801|3085636|186803|248744;2|1224|28211|204457|41297|165695;2|1224|1236|135614|32033|40323;2|1224|1236|135624|83763|83770;2|1239|526524|526525|2810281|191303;2|74201;2|1239|91061|186826|33958|46255,Complete,ChiomaBlessing
bsdb:995/1/1,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 1,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP Group,"Mice were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 1,Figure 4G,16 March 2024,Mariposa,Mariposa,Differences in bacterial taxa abundance in the MPTP Group (Mice treated with MPTP) VS Control group.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",2|1224|28216;2|1224|28216|80840;2|1239|526524|526525|128827|1729679;2|1239|526524|526525|128827|1729679|1702221;2|1239|186801|186802|216572|1892380;2|1239|186801|186802|216572|1892380|1849041;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1224|28216|80840|995019|577310|487175;2|1239|186801|186802|216572|1263|1161942;2|1224|28216|80840|995019;2|976|200643|171549|2005525,Complete,ChiomaBlessing
bsdb:995/1/2,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 1,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP Group,"Mice were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 2,Figure 4G and 4F,16 March 2024,Mariposa,Mariposa,Differences in bacterial taxa abundance in the MPTP group (mice treated with MPTP) vs. the control group.,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium",2|1239|526524|526525|128827|2749846|31971;2|1239|526524|526525|128827|2749267,Complete,ChiomaBlessing
bsdb:995/3/1,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 3,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP + Acu Group,Mice treated with MPTP received acupuncture.,6,9,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 4G and 4F,23 March 2024,Mariposa,Mariposa,Differences in bacterial taxa abundance in the MPTP + Acu (Mice treated with MPTP that received Acupuncture) vs. Control group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora xylanisolvens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora aerotolerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Vallitalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Vallitalea|s__Vallitalea pronyensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae",2|976|200643|171549|171550|239759;2|1239|186801|186802|31979|1485|84032;2|1239|186801|3085636|186803|2719231|384636;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|2719231|36832;2|1239|186801|186802|216572|2304693;2|976|200643|171549|171550;2|1239|186801|3085636|186803|841|301302;2|1239|186801|3085636|2603322|1348611;2|1239|186801|3085636|2603322|1348611|1348613;2|1239|186801|3085636|2603322,Complete,ChiomaBlessing
bsdb:995/3/2,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 3,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP + Acu Group,Mice treated with MPTP received acupuncture.,6,9,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 4G and 4F,23 March 2024,Mariposa,Mariposa,Differences in bacterial taxa abundance in the MPTP + Acu (Mice treated with MPTP that received Acupuncture) vs. Control group,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",2|1239|526524|526525|128827|2749846;2|1239|526524|526525|128827|2749846|31971,Complete,ChiomaBlessing
bsdb:995/4/NA,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 4,South Korea,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,MPTP + Acu Group,MPTP + Non Acu Group,Mice treated with MPTP did not receive acupuncture,9,5,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,decreased,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:995/5/1,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 5,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP group,"Mice that were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,N/A,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 1,Fig 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,Mariposa,ChiomaBlessing",Bacterial genera with significant differences in the gut microbiota of MPTP group VS Control group.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae|g__Aestuariispira,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Rhodospirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1224|28211|204441|597359|1647175;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|872;2|1239|526524|526525|128827|1729679;2|1239|186801|3085636|186803|1918511;2|1239|186801|186802|216572|1892380;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|248744;2|976|200643|171549|171552|577309;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|1224|28211|204441|41295|1081;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239|526524|526525|2810280|3025755;2|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:995/5/2,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 5,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP group,"Mice that were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,N/A,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 2,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,Mariposa,ChiomaBlessing",Bacterial genera with significant differences in the gut microbiota of MPTP group VS Control group.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfitobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans",2|1239|186801|186802|3082771|1918385;2|1239|186801|186802|216572|244127;2|976|200643|171549|1853231|574697;2|1239|186801|186802|2937909|36853;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|1918454;2|1239|186801|186802|541019|342658;2|1239|186801|186802|216572|3028852;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1200657,Complete,ChiomaBlessing
bsdb:995/6/1,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 6,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",6,9,N/A,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,ChiomaBlessing",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS Control group.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Vallitalea,k__Bacteria|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio",2|976|200643|171549|815|816;2|1239|186801|186802|216572|2304693;2|1239|186801|3085636|2603322|1348611;2|1798710|3118680|2211217|213484,Complete,ChiomaBlessing
bsdb:995/6/2,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 6,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",6,9,N/A,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,ChiomaBlessing",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS Control group.,decreased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium,2|1239|526524|526525|128827|2749267,Complete,ChiomaBlessing
bsdb:995/7/1,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 7,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,MPTP group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",10,9,N/A,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,Mariposa,ChiomaBlessing",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS MPTP group.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Alkalibacter,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfitobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor",2|1239|186801|3085636|186803|1427378;2|1239|186801|186802|3082771|1918385;2|976|200643|171549|171550|239759;2|1239|186801|186802|186806|274470;2|544448|31969|186332|186333|2086;2|1239|186801|3085636|186803|653683;2|976|200643|171549|1853231|574697;2|1239|186801|3082768|990719|990721;2|1239|186801|186802|2937909|36853;2|1239|186801|186802|216572|946234;2|1239|186801|186802|1918454;2|1239|186801|186802|541019|342658;2|1239|186801|3085636|186803|2163168;2|1239|186801|3085636|186803|1506553;2|1239|186801|186802|216572|3028852;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1017280,Complete,ChiomaBlessing
bsdb:995/7/2,Study 995,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang JH, Yeom MJ, Ahn S, Oh JY, Ji S, Kim TH , Park HJ",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 7,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,MPTP group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",10,9,N/A,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,ChiomaBlessing",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS MPTP group.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae|g__Aestuariispira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Rhodospirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1224|28211|204441|597359|1647175;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|200940|3031449|213115|194924|872;2|1239|186801|3085636|186803|1918511;2|1239|526524|526525|128827|61170;2|1239|186801|3085636|186803|248744;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|1224|28211|204441|41295|1081;2|1239|186801|186802|216572|44748;2|1239|526524|526525|2810280|3025755;2|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:996/1/1,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal mucosa samples),IBS-D patients (Duodenal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,37,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",2|1239|91061|1385|186817|1386;2|1239|91061|186826|186828|2747;2|1224|28211|356|118882|528;2|1239|91061|186826|1300|1357;2|201174|1760|85006|1268|1269;2|201174|1760|85009|31957|1743;2|1224|28211|356|119045|407;2|201174|1760|85006|85023|33882;2|1239|91061|1385|186822|44249;2|201174|1760|85007|1653|1716;2|1224|28216|80840|80864|80865;2|1224|28211|204458|76892|41275;2|201174|1760|85007|1762|1763,Complete,Svetlana up
bsdb:996/1/2,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal mucosa samples),IBS-D patients (Duodenal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,37,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",2|1224|1236|2887326|468|469;2|1224|28216|80840|506|222,Complete,Svetlana up
bsdb:996/2/1,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 2,China,Homo sapiens,Lumen of duodenum,UBERON:0016512,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal lumen samples),IBS-D patients (Duodenal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),19,43,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|526524|526525|128827|118747;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|29465;2|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:996/2/2,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 2,China,Homo sapiens,Lumen of duodenum,UBERON:0016512,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal lumen samples),IBS-D patients (Duodenal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),19,43,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium",2|976|200643|171549|171551|836;2|1224|28211|204457|41297|13687;2|1224|28211|204457|41297|165695;2|976|117743|200644|49546|237,Complete,Svetlana up
bsdb:996/3/1,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal mucosa samples),IBS-D patients (Rectal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,53,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",2|976|200643|171549|815|816;2|1224|28211|356|212791;2|1297|188787|68933|188786|270,Complete,Svetlana up
bsdb:996/3/2,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal mucosa samples),IBS-D patients (Rectal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,53,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|976|200643|171549|171552|838;2|1224|28211|204455|31989|265;2|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:996/4/1,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 4,China,Homo sapiens,Rectal lumen,UBERON:0009670,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal lumen samples),IBS-D patients (Rectal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),17,74,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:996/4/2,Study 996,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K , Hou X",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 4,China,Homo sapiens,Rectal lumen,UBERON:0009670,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal lumen samples),IBS-D patients (Rectal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),17,74,Within one month before the start of this study,16S,123,Roche454,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,Aleru Divine,Site-specific biomarkers detected by LEfSe.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus",2|1239|186801|186802|216572|216851;2|1297|188787|118964|183710|1298,Complete,Svetlana up
bsdb:997/1/1,Study 997,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S , Wu X",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 1,"China,Singapore,Turkey",Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Healthy group,Mild cognitive impairment (MCI) and Alzheimer’s disease (AD),Patients with mild cognitive impairment (MCI) and Alzheimer’s disease (AD),125,244,None,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3A,16 March 2024,Samreen-19,"Samreen-19,Scholastica",Linear discriminant analysis (LDA) scores of the bacteria at the genus level significantly different in healthy group versus mild cognitive impairment (MCI) and Alzheimer’s disease (AD),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656;2|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:997/2/1,Study 997,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S , Wu X",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 2,"China,Singapore,Turkey",Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy group and mild cognitive impairment (MCI),Alzheimer’s disease (AD),Patients with Alzheimer’s disease (AD),266,103,None,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,16 March 2024,Samreen-19,"Samreen-19,Scholastica",Linear discriminant analysis (LDA) scores of the bacteria at the genus level significantly different in healthy group and mild cognitive impairment (MCI) versus Alzheimer’s disease (AD),increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,2|1224|1236|91347|543|561,Complete,Svetlana up
bsdb:997/3/1,Study 997,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S , Wu X",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 3,"China,Singapore,Turkey",Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Healthy group and Alzheimer's Disease (AD),Mild Cognitive Impairment (MCI),Patients with mild cognitive impairment (MCI),228,141,None,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,16 March 2024,Samreen-19,"Samreen-19,Scholastica",Linear discriminant analysis (LDA) scores of the bacteria at the genus level significantly different in healthy group and mild cognitive impairment (MCI) versus Alzheimer’s disease (AD),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:997/4/1,Study 997,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S , Wu X",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 4,South Korea,Rattus norvegicus,Feces,UBERON:0001988,Memory impairment,EFO:0001072,Normal health group,Positive and memory deficit (MD) group,Rats divided into the positive group (n = 10) given intraperitoneal scopolamine plus donepezil injection and those belonging to the memory deficit (MD) group (n = 10) given intraperitoneal scopolamine injection,10,20,None,16S,34,"Illumina,Roche454",LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6F,16 March 2024,Samreen-19,"Samreen-19,Scholastica",LDA scores of the bacteria at the species level significantly different in normal health group versus positive and memory deficit (MD) group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|976|200643|171549|171550|239759|626932;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|815|816|820;2|1239|186801|3085636|186803|2719313|358742;2|1239|186801|3085636|186803|2719313|460384;2|1239|91061|186826|81852|1350|37734;2|1239|186801|186802|216572|216851|853;2|1239|91061|186826|33958|2742598|1633;2|976|200643|171549|2005525|375288|574930;2|1239|186801|186802|216572|1263|438033;2|1239|91061|1385|90964|1279|1280;2|1239|186801|3085636|186803|1506553|1512;2|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:997/5/1,Study 997,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S , Wu X",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 5,South Korea,Rattus norvegicus,Feces,UBERON:0001988,Memory impairment,EFO:0001072,Normal health group and memory deficit (MD) group,Positive group,Rats in the positive group (n = 10) given intraperitoneal scopolamine plus donepezil injection,20,10,None,16S,34,"Illumina,Roche454",LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6F,16 March 2024,Samreen-19,"Samreen-19,Scholastica",LDA scores of the bacteria at the species level significantly different in positive group  versus normal health and memory deficit (MD) group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile",2|976|200643|171549|815|816|338188;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|1694;2|201174|84998|84999|84107|102106|74426;2|1239|91061|186826|33958|2742598|1598;2|1239|186801|186802|216572|292632|214851,Complete,Svetlana up
bsdb:997/6/1,Study 997,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S , Wu X",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 6,South Korea,Rattus norvegicus,Feces,UBERON:0001988,Memory impairment,EFO:0001072,Normal health group and positive group,Memory deficit (MD) group,Rats in the memory deficit (MD) group (n = 10) given intraperitoneal scopolamine injection,20,10,None,16S,34,"Illumina,Roche454",LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6F,30 June 2024,Scholastica,Scholastica,LDA scores of the bacteria at the species level significantly different in memory deficit (MD) group versus normal health and positive group,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus|s__Anaerorhabdus furcosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor|s__Lactonifactor longoviformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",2|1239|526524|526525|128827|118966|118967;2|976|200643|171549|815|816|674529;2|976|200643|171549|815|816|28116;2|1239|186801|186802|31979|1485|36834;2|1239|186801|186802|31979|1485|1502;2|1239|186801|3085636|186803|2719313|358743;2|1224|1236|91347|543|561|562;2|1239|186801|186802|31979|420345|341220;2|1239|91061|186826|33958|2742598|97478;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572|459786|1263547;2|976|200643|171549|2005525|375288|823;2|1239|526524|526525|2810280|3025755|1547,Complete,Svetlana up
bsdb:998/1/1,Study 998,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X, Tang P, Hou C, Chong L, Zhang X, Liu P, Chen L, Liu Y, Zhang L , Li R","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 1,"Japan,United States of America,Denmark,Finland,Germany,China,Italy",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,1028,1441,NA,16S,NA,"Illumina,Roche454",DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Supplementary Tables 4 and 5,27 March 2024,Leenaa,Leenaa,Significantly changed genera and species between PD patients and controls,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus",2|1239|91061|186826|186827|46123|46125;2|1239|909932|1843488|909930|904;2|1239|186801|186802|186806|264995;2|1239|186801|186802|216572|244127;2|29547|3031852|213849|72294|194;2|1224|1236|91347|543|544;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|186807|51514;2|1239|186801|186802|186806|1730;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162290;2|1224|1236|135619|28256|2745;2157|28890|183925|2158|2159|2172;2157|2283796|183967|1235850|1577788|1080709;2|1239|186801|3082720|3030910|86331;2|1239|91061|186826|33958|1253;2|1239|1737404|1737405|1570339|162289;2|1224|1236|91347|1903414|583;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|100132|507843;2|508458|649775|649776|649777|2753;2|1239|526524|526525|2810281|191303;2|201174|1760|2037|2049|184869;2|1239|91061|186826|33958|1253,Complete,NA
bsdb:998/1/2,Study 998,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X, Tang P, Hou C, Chong L, Zhang X, Liu P, Chen L, Liu Y, Zhang L , Li R","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 1,"Japan,United States of America,Denmark,Finland,Germany,China,Italy",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,1028,1441,NA,16S,NA,"Illumina,Roche454",DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Supplementary Tables 4 and 5,27 March 2024,Leenaa,Leenaa,Significantly changed genera between PD patients and controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|28050;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:998/2/1,Study 998,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X, Tang P, Hou C, Chong L, Zhang X, Liu P, Chen L, Liu Y, Zhang L , Li R","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,90,90,NA,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary Table 6,27 March 2024,Leenaa,Leenaa,Significantly changed genera in the blood samples between PD patients and controls,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330;2|1297|188787|68933|188786|65551;2|201174|1760|85006|1268|57494,Complete,NA
bsdb:998/3/1,Study 998,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X, Tang P, Hou C, Chong L, Zhang X, Liu P, Chen L, Liu Y, Zhang L , Li R","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 3,"United States of America,Israel,Netherlands",Homo sapiens,Brain,UBERON:0000955,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,119,150,NA,NA,NA,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,27 March 2024,Leenaa,Leenaa,Significantly changed genera in the brain between PD patients and controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rathayibacter,k__Bacteria|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae|g__Syntrophobacter",2|1224|1236|91347|543|413496;2|201174|1760|85009|85015|1839;2|203682|203683|112|126|118;2|201174|1760|85006|85023|33886;2|200940|3024408|213462|213465|29526,Complete,NA
bsdb:998/3/2,Study 998,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X, Tang P, Hou C, Chong L, Zhang X, Liu P, Chen L, Liu Y, Zhang L , Li R","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 3,"United States of America,Israel,Netherlands",Homo sapiens,Brain,UBERON:0000955,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,119,150,NA,NA,NA,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3,27 March 2024,Leenaa,Leenaa,Significantly changed genera in the brain between PD patients and controls,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Erythrobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacteria|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|976|117743|200644|2762318|308865;2|1224|28211|204457|335929|1041;2|1239|1737404|1737405|1570339|150022;2|1224|1236|135619|28256|2745;2|201174|1760|85010|2070|1847;2|1239|186801|68295|186814|28895,Complete,NA
bsdb:999/1/1,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 1,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous sulfate (FS) treated pups (PD 15),Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2–14 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.,28,27,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 2d + Figure 3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",2|1239|186801|3085636|186803|1427378;2|1239|91061|186826|186827|1375;2|544448|31969|186332|186333|2086;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827|1729679;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|1892380;2|544448;2|1239|186801|186802|216572|100175;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|1506577;2|1239|186801|244328;2|1239|186801|186802|216572|216851|1946507,Complete,NA
bsdb:999/1/2,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 1,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous sulfate (FS) treated pups (PD 15),Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2–14 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.,28,27,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 2d + Figure 3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,k__Bacteria|s__uncultured bacterium,s__uncultured organism",2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|201174|1760|85004|31953|1678;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1239|186801|3085636|186803|830;2|1239|186801|186802|1470353;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186827|66831;2|1239|91061|1385|90964|227979;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|248744;2|1239|186801|186802|216572|2895461;2|1224|28216|80840|995019|577310;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|201174|1760|85006|1268|225447;2|77133;155900,Complete,NA
bsdb:999/2/1,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 2,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.",28,29,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 2d + Figure 3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Glorious",Taxa Differing in Abundance Between ferrous bis-glycinate chelate (FC) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|1239|526524|526525|128827|174708;2|1239|526524|526525|128827|1937008;2|1239|186801|186802|216572|100175;2|1239|186801|186802|216572|1263|438033;2|1239|186801|3085636|186803|1506577;2|74201,Complete,NA
bsdb:999/2/2,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 2,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.",28,29,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 2d + Figure 3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Glorious",Taxa Differing in Abundance Between ferrous bis-glycinate chelate (FC) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacteria|s__uncultured bacterium,s__uncultured organism,s__unidentified,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",2|1239|186801|3085636|186803|1427378;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|1239;2|976;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|830;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1432051;2|1239|91061|186826|81852|1350;2|1239|186801|186802|186806|1730|39497;2|1239|91061|186826|186827|66831;2|1239|91061|1385|90964|227979;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|877420;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|248744;2|1239|186801|186802|216572|2895461;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|841;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|201174|1760|85006|1268|225447;2|976|200643|171549|194843;2|976|200643|171549|2005519|397864|584861;2|77133;155900;32644;2|1239|186801|186802|31979|1485|59620,Complete,NA
bsdb:999/3/1,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 3,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated pups (PD 15),Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) 2-14 and samples collected from 4–6 hours-fasted animals on postnatal day (PD) 15",27,29,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure S3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Ferrous bis-glycinate chelate (FC) treated pups (PD 15) as determined by DESeq2,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|526524|526525|128827|174708;2|1239|186801|186802|1470353;2|1239|526524|526525|128827|1937008;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:999/3/2,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 3,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated pups (PD 15),Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) 2-14 and samples collected from 4–6 hours-fasted animals on postnatal day (PD) 15",27,29,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure S3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Ferrous bis-glycinate chelate (FC) treated pups (PD 15) as determined by DESeq2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacteria|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacteria|s__uncultured bacterium,s__uncultured organism,s__unidentified",2|1239|186801|3085636|186803|1427378;2|1239|91061|186826|186827|1375;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1432051;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|216851|1946507;2|1224|1236|135625|712|724;2|1239|186801|186802|216572|1892380;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|877420;2|544448;2|976|200643|171549|2005525|375288;2|1239|186801|3085636|186803|841;2|976|200643|171549|194843;2|976|200643|171549|2005519|397864|584861;2|1239|186801|244328;2|1239|186801|186802|31979|1485|59620;2|77133;155900;32644,Complete,NA
bsdb:999/4/1,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 4,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult (YA) rats,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 58 +/- 4.",23,23,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 5d and 6  +Figure S6 + Table S7 and S8,19 March 2024,Keamy,"Keamy,Glorious",Taxa Differing in Abundance Between Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) and Vehicle control-supplemented (CON) as determined by DESeq2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fournierella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|s__uncultured Firmicutes bacterium,k__Bacteria|s__uncultured bacterium,s__unidentified",2|1239|186801|3085636|186803|1427378;2|201174|84998|1643822|1643826|580024;2|1239|186801|186802|216572|1940255;2|976|200643|171549|2005525|375288;2|201174|1760|85006|1268|32207;2|1239|344338;2|77133;32644,Complete,NA
bsdb:999/4/2,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 4,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult (YA) rats,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 58 +/- 4.",23,23,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 5d,6 and S6 + Table S7and S8",19 March 2024,Keamy,"Keamy,Glorious",Taxa Differing in Abundance Between fYoung Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS). and Vehicle control-supplemented (CON),decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|s__uncultured bacterium,s__unidentified,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis",2|1224|1236|2887326|468|469;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803|2005359|290055;2|1239|91061|186826|33958|1578;2|1224;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|77133;32644;2|1239|186801|186802|216572|2895461;2|1239|186801|186802|216572|3028852,Complete,NA
bsdb:999/5/1,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 5,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult rats,Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5d +  Figure 6 + Figure S6 + Table s7 +Table s8,19 March 2024,Keamy,"Keamy,Joan Chuks",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4) and Vehicle control-supplemented (CON) young Adult rats as determined by DESeq2.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Caldicoprobacteraceae|g__Caldicoprobacter,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sufflavum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,s__uncultured organism,k__Bacteria|s__uncultured rumen bacterium,k__Bacteria|s__unidentified rumen bacterium RF32",2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1239|186801|186802|715221|715222;2|1117;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|100175;2;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|1508657|396504;2|1239|186801|3085636|186803|1506577;2|74201;2|201174|1760|85006|1268|225447;155900;2|136703;2|60675,Complete,NA
bsdb:999/5/2,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 5,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult rats,Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 5d +  Figure 6 + Figure S6 + Table s7 +Table s8,20 March 2024,Keamy,"Keamy,Joan Chuks",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4) and Vehicle control-supplemented (CON) young Adult rats as determined by DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Mycoplasmatota,k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,s__unidentified",2|1239|186801|3085636|186803|1427378;2|1239|186801|3085636|186803|31980;2|1224|1236|2887326|468|469;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330;2|201174|84998|1643822|1643826|580024;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|841;2|1239|526524|526525|2810281|191303;2|976|200643|171549|194843;2|976|200643|171549|2005519|397864|584861;2|1239|186801|3085636|186803|297314;2|201174;2|976;2|1224;2|544448;2|77133;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|31979|1485|59620;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|2895461;32644,Complete,NA
bsdb:999/6/1,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 6,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5d +  Figure 6 + Figure S6 + Table S7 and S8,19 March 2024,Keamy,"Keamy,Glorious",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Ferrous Sulfate (FS) young Adult rats as determined by DESeq2.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Caldicoprobacteraceae|g__Caldicoprobacter,k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sufflavum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum,s__uncultured organism,k__Bacteria|s__uncultured rumen bacterium,k__Bacteria|s__unidentified rumen bacterium RF32,s__unidentified",2|1239|186801|186802|216572|52784;2|1239|186801|186802|186806|264995;2|1239|91061|1385|186817|1386;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019|1696;2|1239|186801|186802|715221|715222;2|95818|2093818|2093825|2171986|1331051;2|1239|186801|186802|1470353;2|1117;2|200930|68337;2|201174|1760|85007|85029|37914;2|1239|91061|186826|81852|1350;2|1239|186801|186802|186806|1730|290054;2|1239|91061|186826|186827|66831;2|1239|526524|526525|128827|1729679;2|1239|186801|3085636|186803|2005359|290055;2|1224|1236|135625|712|724;2|1239|186801|186802|216572|596767;2|1239|186801|3085636|186803|1410626;2|1239|186801|3085636|186803|437755;2|1239|186801|186802|216572|100175;2;2|1239|186801|186802|216572|1508657|396504;2|1239|186801|186802|216572|3068309;2|1239|186801|186802|216572|1263|438033;2|1239|186801|3085636|186803|1769710;2|1239|91061|1385|90964|1279;2|74201;2|201174|1760|85006|1268|225447;2|1239|186801|186802|543314|35518;155900;2|136703;2|60675;32644,Complete,NA
bsdb:999/6/2,Study 999,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C , Lönnerdal B",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 6,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5d +  Figure 6 + Figure S6 + Table S7 andS8,20 March 2024,Keamy,"Keamy,Glorious",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Ferrous Sulfate (FS) young Adult rats as determined by DESeq2.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium enrichment culture clone 06-1235251-67,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacteria|p__Bacillota|s__uncultured Firmicutes bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,k__Bacteria|s__uncultured bacterium,k__Bacteria|s__uncultured rumen bacterium,s__unidentified,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",2|1239|186801|3085636|186803|1427378;2|1239|186801|3085636|186803|31980;2|201174;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|976;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|1141839;2|1239|186801|3085636|186803|189330;2|201174|84998|1643822|1643826|580024;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803|1506553;2|1239|186801|186802|216572|2895461;2|544448;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|186801|3085636|186803|841;2|976|200643|171549|194843;2|976|200643|171549|2005519|397864|584861;2|1239|344338;2|1239|186801|3085636|186803|297314;2|544448|31969|220137;2|77133;2|136703;32644;2|1239|186801|186802|31979|1485|59620,Complete,NA
bsdb:1000/1/1,Study 1000,case-control,33293403,10.1128/mSystems.00797-20,NA,"Nishiwaki H, Hamaguchi T, Ito M, Ishida T, Maeda T, Kashihara K, Tsuboi Y, Ueyama J, Shimamura T, Mori H, Kurokawa K, Katsuno M, Hirayama M , Ohno K",Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson's Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder,mSystems,2020,"Parkinson’s disease, gut microbiota, meta-analysis, rapid-eye-movement behavior disorder, topic model",Experiment 1,"Germany,Japan",Homo sapiens,Intestine,UBERON:0000160,Parkinson's disease,MONDO:0005180,Controls,Rapid-eye-movement sleep behavior disorder (iRBD) patients,Patients with idiopathic rapid-eye-movement sleep behavior disorder (iRBD) diagnosed according to the International Classification of Sleep Disorders Criteria-Third Edition,137,26,1 month,16S,34,Illumina,"ANCOM,PERMANOVA,T-Test",0.05,TRUE,NA,NA,"age,body mass index,constipation,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 March 2024,Aishat,Aishat,"Read counts of genera Akkermansia, Faecalibacterium, Roseburia, and Lachnospiraceae ND3007 group normalized for 1 × 104 reads in controls, iRBD, and Hoehn and Yahr scales 1 to 5.",increased,NA,NA,Complete,NA
bsdb:1000/1/2,Study 1000,case-control,33293403,10.1128/mSystems.00797-20,NA,"Nishiwaki H, Hamaguchi T, Ito M, Ishida T, Maeda T, Kashihara K, Tsuboi Y, Ueyama J, Shimamura T, Mori H, Kurokawa K, Katsuno M, Hirayama M , Ohno K",Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson's Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder,mSystems,2020,"Parkinson’s disease, gut microbiota, meta-analysis, rapid-eye-movement behavior disorder, topic model",Experiment 1,"Germany,Japan",Homo sapiens,Intestine,UBERON:0000160,Parkinson's disease,MONDO:0005180,Controls,Rapid-eye-movement sleep behavior disorder (iRBD) patients,Patients with idiopathic rapid-eye-movement sleep behavior disorder (iRBD) diagnosed according to the International Classification of Sleep Disorders Criteria-Third Edition,137,26,1 month,16S,34,Illumina,"ANCOM,PERMANOVA,T-Test",0.05,TRUE,NA,NA,"age,body mass index,constipation,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,17 March 2024,Aishat,Aishat,"Read counts of genera Akkermansia, Faecalibacterium, Roseburia, and Lachnospiraceae ND3007 group normalized for 1 × 104 reads in controls, iRBD, and Hoehn and Yahr scales 1 to 5.",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1001/1/1,Study 1001,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S, Melis M, Palmas V, Pisanu S, Serra A, Perra D, Santoru ML, Oppo V, Cusano R, Uva P, Atzori L, Morelli M, Cossu G , Manzin A",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant  - TD,Parkinson's disease patients with Akinetic Rigid - AR,A phenotype category based on motor signs,19,23,3 months prior to enrollment,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure  3a,18 March 2024,Junie,"Junie,Peace Sandy","Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the
significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (a) Positive LDA score (green) highlights the enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows the enriched taxa in PD patients with Akinetic Rigid (AR);",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|g__Sedimentibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|1737404|190972;2|1224|1236|91347|1903411|613;2|1224|1236|91347|543|561;2|1224|1236|91347|543,Complete,Peace Sandy
bsdb:1001/1/2,Study 1001,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S, Melis M, Palmas V, Pisanu S, Serra A, Perra D, Santoru ML, Oppo V, Cusano R, Uva P, Atzori L, Morelli M, Cossu G , Manzin A",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant  - TD,Parkinson's disease patients with Akinetic Rigid - AR,A phenotype category based on motor signs,19,23,3 months prior to enrollment,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3a,18 March 2024,Junie,"Junie,Peace Sandy","Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (a) Positive LDA score (green) highlights the enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows the enriched taxa in PD patients with Akinetic Rigid (AR);",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tindalliaceae|g__Tindallia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",2|1239;2|1239|186801|3085636|186803;2|1239|186801|186802|31979;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|28050;2|1239|186801|3082720|3118658|69894;2|1239|91061|1385|539738;2|1239|91061|1385|539738|1378;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696,Complete,Peace Sandy
bsdb:1001/2/1,Study 1001,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S, Melis M, Palmas V, Pisanu S, Serra A, Perra D, Santoru ML, Oppo V, Cusano R, Uva P, Atzori L, Morelli M, Cossu G , Manzin A",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant - TD,Parkinson's disease patients with Diskinetic - D,A phenotype category based on motor signs,19,14,3 months prior to enrollment,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3B,19 March 2024,Peace Sandy,Peace Sandy,"Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the
significantly different taxa among PD patients with distinct motor phenotypes, based on effect size(Linear discriminant analysis (LDA) score (log 10) > 2). (b) Positive LDA score (green) highlights enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows enriched taxa in PD with Dyskinetic (D)",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|1903411|613;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1224|1236|91347|543|561;2|1224|1236|91347|543,Complete,Peace Sandy
bsdb:1001/2/2,Study 1001,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S, Melis M, Palmas V, Pisanu S, Serra A, Perra D, Santoru ML, Oppo V, Cusano R, Uva P, Atzori L, Morelli M, Cossu G , Manzin A",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant - TD,Parkinson's disease patients with Diskinetic - D,A phenotype category based on motor signs,19,14,3 months prior to enrollment,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3B,19 March 2024,Peace Sandy,Peace Sandy,"Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the
significantly different taxa among PD patients with distinct motor phenotypes, based on effect size(Linear discriminant analysis (LDA) score (log 10) > 2). (b) Positive LDA score (green) highlights enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows enriched taxa in PD with Dyskinetic (D)",decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|g__Sedimentibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tindalliaceae|g__Tindallia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",2|1239;2|1239|186801|186802|216572;2|1239|186801|186802|31979;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|186807;2|1239|1737404|190972;2|1239|186801|3082720|3118658|69894;2|1239|186801|186802|186806;2|1239|186801|186802|216572|258514;2|201174|1760|85006|85019|1696;2|201174|1760|85006|85019;2|1239|91061|1385|539738;2|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:1001/3/1,Study 1001,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S, Melis M, Palmas V, Pisanu S, Serra A, Perra D, Santoru ML, Oppo V, Cusano R, Uva P, Atzori L, Morelli M, Cossu G , Manzin A",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Diskinetic - D,Parkinson's disease patients with Akinetic Rigid - AR,A phenotype category based on motor signs,14,23,3 months prior to enrollment,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3C,19 March 2024,Peace Sandy,Peace Sandy,"Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the
significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (c) Positive LDA score (green) highlights enriched taxa in PD patients with Dyskinetic",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958,Complete,Peace Sandy
bsdb:1002/1/1,Study 1002,"laboratory experiment,meta-analysis",26170900,10.1186/s13073-015-0177-8,NA,"Burns MB, Lynch J, Starr TK, Knights D , Blekhman R",Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment,Genome medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Patient-Matched Normal Colon Tissue Samples,Colorectal Tumor Samples,This group consists of primary tumor tissue samples obtained from patients diagnosed with colorectal cancer. They were collected from the site of tumor microenvironment.,44,44,NA,16S,56,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,NA,Signature 1,Figure 2 and 3A,17 March 2024,Aananditaa,"Aananditaa,Peace Sandy",Differentially abundant taxa between matched normal and colorectal cancer microbiomes.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia",2|32066|203490|203491|203492|848;2|1224|1236|91347|1903414|586,Complete,Peace Sandy
bsdb:1002/1/2,Study 1002,"laboratory experiment,meta-analysis",26170900,10.1186/s13073-015-0177-8,NA,"Burns MB, Lynch J, Starr TK, Knights D , Blekhman R",Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment,Genome medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Patient-Matched Normal Colon Tissue Samples,Colorectal Tumor Samples,This group consists of primary tumor tissue samples obtained from patients diagnosed with colorectal cancer. They were collected from the site of tumor microenvironment.,44,44,NA,16S,56,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,NA,Signature 2,Figure 2 and 3A,18 March 2024,Aananditaa,Aananditaa,Differentially abundant taxa between matched normal and colorectal cancer microbiomes.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16",2|976|200643|171549|815|816|820;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803;2|976|200643|171549|171550;2|1239|186801|186802|216572|552398,Complete,Peace Sandy
bsdb:1003/1/1,Study 1003,randomized controlled trial,35019769,10.1128/spectrum.01757-21,https://pubmed.ncbi.nlm.nih.gov/35019769/,"Plummer EL, Maddaford K, Murray GL, Fairley CK, Pasricha S, Mu A, Bradshaw CS, Williamson DA , Chow EPF",The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial,Microbiology spectrum,2022,"Neisseria gonorrhoeae, men who have sex with men, mouthwash, oral microbiome, oropharyngeal gonorrhea",Experiment 1,Australia,Homo sapiens,Tonsillar fossa,UBERON:0035228,Gonorrhea,DOID:7551,men who have sex with men using Listerine,men who have sex with men using Biotène,men who have sex with men using Biotène for 12 weeks affect the microbial composition of the oropharynx.,78,75,NA,16S,4,Illumina,"ANOVA,ANCOM",0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,discussion,18 March 2024,Uhabiba14,Uhabiba14,observed a small but significant decrease in the abundance following 12 weeks of Biotène using ALDEx2,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",2|32066|203490|203491|1129771|32067;2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|34104,Complete,NA
bsdb:1003/2/1,Study 1003,randomized controlled trial,35019769,10.1128/spectrum.01757-21,https://pubmed.ncbi.nlm.nih.gov/35019769/,"Plummer EL, Maddaford K, Murray GL, Fairley CK, Pasricha S, Mu A, Bradshaw CS, Williamson DA , Chow EPF",The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial,Microbiology spectrum,2022,"Neisseria gonorrhoeae, men who have sex with men, mouthwash, oral microbiome, oropharyngeal gonorrhea",Experiment 2,Australia,Homo sapiens,Tonsillar fossa,UBERON:0035228,Gonorrhea,DOID:7551,did not have gonorrhea detected,gonorrhea detected by NAAT at baseline,the oropharyngeal microbial communities at week-0 in men with and without oropharyngeal N. gonorrhoeae detected by NAAT,99,54,NA,16S,4,Illumina,"ANOVA,PERMANOVA",0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,supplementary figure 4b,18 March 2024,Uhabiba14,Uhabiba14,"The oropharyngeal microbiota of men with oropharyngeal N. gonorrhoeae at baseline compared to men without oropharyngeal N. gonorrhoeae Using ALDEx2, with a detected at week-0 by NAAT.",decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Candidatus Absconditabacteria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|976|117743|200644|2762318|59735;2|221235;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1239|186801|3082720|186804|1257,Complete,NA
bsdb:1003/3/1,Study 1003,randomized controlled trial,35019769,10.1128/spectrum.01757-21,https://pubmed.ncbi.nlm.nih.gov/35019769/,"Plummer EL, Maddaford K, Murray GL, Fairley CK, Pasricha S, Mu A, Bradshaw CS, Williamson DA , Chow EPF",The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial,Microbiology spectrum,2022,"Neisseria gonorrhoeae, men who have sex with men, mouthwash, oral microbiome, oropharyngeal gonorrhea",Experiment 3,Australia,Homo sapiens,Tonsillar fossa,UBERON:0035228,Gonorrhea,DOID:7551,men sex with men who are non-smokers,men sex with men who are smokers,The oropharyngeal microbiota of smokers at week-0,123,22,NA,16S,4,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,supplementary figure 6b,19 March 2024,Uhabiba14,Uhabiba14,PERMANOVA revealed a small but significant difference in the global oropharyngeal microbiota composition between smokers and nonsmokers,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium",2|203691|203692|136|2845253|157;2|508458|649775|649776|3029087|1434006,Complete,NA
bsdb:1003/3/2,Study 1003,randomized controlled trial,35019769,10.1128/spectrum.01757-21,https://pubmed.ncbi.nlm.nih.gov/35019769/,"Plummer EL, Maddaford K, Murray GL, Fairley CK, Pasricha S, Mu A, Bradshaw CS, Williamson DA , Chow EPF",The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial,Microbiology spectrum,2022,"Neisseria gonorrhoeae, men who have sex with men, mouthwash, oral microbiome, oropharyngeal gonorrhea",Experiment 3,Australia,Homo sapiens,Tonsillar fossa,UBERON:0035228,Gonorrhea,DOID:7551,men sex with men who are non-smokers,men sex with men who are smokers,The oropharyngeal microbiota of smokers at week-0,123,22,NA,16S,4,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,supplementary figure 6b,19 March 2024,Uhabiba14,Uhabiba14,PERMANOVA revealed a small but significant difference in the global oropharyngeal microbiota composition between smokers and nonsmokers,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,2|1224|28216|80840|119060|47670,Complete,NA
bsdb:1003/4/1,Study 1003,randomized controlled trial,35019769,10.1128/spectrum.01757-21,https://pubmed.ncbi.nlm.nih.gov/35019769/,"Plummer EL, Maddaford K, Murray GL, Fairley CK, Pasricha S, Mu A, Bradshaw CS, Williamson DA , Chow EPF",The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial,Microbiology spectrum,2022,"Neisseria gonorrhoeae, men who have sex with men, mouthwash, oral microbiome, oropharyngeal gonorrhea",Experiment 4,Australia,Homo sapiens,Tonsillar fossa,UBERON:0035228,Gonorrhea,DOID:7551,men who have sex with men using Biotène,men who have sex with men using listerine,men who have sex with men using Listerine for 12 weeks affect the microbial composition of the oropharynx.,153,153,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,discussion,21 March 2024,Uhabiba14,Uhabiba14,the abundance of Neisseria was nonsignificantly decreased in specimens collected after 12 weeks of Listerine use compared to that in specimens collected at week 0,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,2|1224|28216|206351|481|482,Complete,NA
bsdb:1004/1/1,Study 1004,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,https://journals.asm.org/doi/10.1128/spectrum.03190-23,"Iwase SC, Osawe S, Happel A-U, Gray CM, Holmes SP, Blackburn JM, Abimiku A , Jaspan HB",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants who are HIV unexposed and uninfected (iHUU) at week 1,Infants who are HIV exposed but uninfected (iHEU) at week 1,Infants at 1 week of age born to mothers from South Africa who have HIV but are not themselves infected with HIV,21,61,None,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,18 March 2024,Aishat,"Aishat,Scholastica",Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 1 week of age in South Africa,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",2|1224|1236|91347|543|570|244366;2|1224|28216|80840|995019|40544;2|1239|526524|526525|128827|1573535;2|976|200643|171549|2005525|375288|46503;2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803|572511|40520;2|201174|84998|84999|84107|1473205;2|201174|1760|85004|31953|1678|1685;2|1224|1236|91347|543|570|1463165;2|201174|84998|84999|1643824|2082587;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|2316020|33039;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|216572|292632;2|976|200643|171549|815|909656|821;2|1224|1236|91347|543|570|573;2|1239|909932|909929|1843491|158846;2|1239|186801|3082720|186804|1501226|1115758;2|1239|186801|186802|216572|216851;2|32066|203490|203491|203492|848|850;2|1239|91061|186826|81852|1350|1352;2|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:1004/1/2,Study 1004,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,https://journals.asm.org/doi/10.1128/spectrum.03190-23,"Iwase SC, Osawe S, Happel A-U, Gray CM, Holmes SP, Blackburn JM, Abimiku A , Jaspan HB",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants who are HIV unexposed and uninfected (iHUU) at week 1,Infants who are HIV exposed but uninfected (iHEU) at week 1,Infants at 1 week of age born to mothers from South Africa who have HIV but are not themselves infected with HIV,21,61,None,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,18 March 2024,Aishat,"Aishat,Scholastica",Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 1 week of age in South Africa,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",2|201174|1760|2037|2049|1654;2|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:1004/2/1,Study 1004,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,https://journals.asm.org/doi/10.1128/spectrum.03190-23,"Iwase SC, Osawe S, Happel A-U, Gray CM, Holmes SP, Blackburn JM, Abimiku A , Jaspan HB",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV adjusted by mode of feeding,21,61,None,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,24 June 2024,Scholastica,Scholastica,Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus raffinosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85004|31953|1678|1680;2|201174|84998|84999|84107|102106|74426;2|1239|186801|3085636|186803|189330|39486;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|81852|1350|160453;2|1239|91061|186826|81852|1350|71452;2|1239|186801|186802|216572|216851|853;2|1224|1236|91347|543|570|1463165;2|1239|91061|186826|1300|1357|1358;2|1239|91061|186826|1300|1301|315405;2|1239|909932|1843489|31977|29465|39777;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186828|117563;2|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:1004/2/2,Study 1004,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,https://journals.asm.org/doi/10.1128/spectrum.03190-23,"Iwase SC, Osawe S, Happel A-U, Gray CM, Holmes SP, Blackburn JM, Abimiku A , Jaspan HB",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV adjusted by mode of feeding,21,61,None,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,24 June 2024,Scholastica,Scholastica,Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816|47678;2|1224|1236|91347|543|570|1134687;2|1239|91061|186826|33958|2759736|47715;2|1239|91061|186826|33958|1578|1596;2|1239|909932|1843489|31977|906|907;2|976|200643|171549|171552|2974251|165179;2|1239|186801|3085636|186803|2316020|33039;2|201174|84998|84999|1643824|133925;2|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:1004/3/1,Study 1004,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,https://journals.asm.org/doi/10.1128/spectrum.03190-23,"Iwase SC, Osawe S, Happel A-U, Gray CM, Holmes SP, Blackburn JM, Abimiku A , Jaspan HB",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV when adjusted for reported antibiotic (co-trimoxazole) prophylaxis history adjusted by mode of feeding and reported antibiotics history,21,61,None,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S2,24 June 2024,Scholastica,Scholastica,Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding and reported antibiotics history,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus raffinosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris",2|201174|84998|84999|84107|102106|74426;2|1224|1236|91347|543|570|1463165;2|201174|1760|85004|31953|1678|1680;2|1239|91061|186826|1300|1301|315405;2|1239|91061|186826|81852|1350|160453;2|1239|91061|186826|1300|1357|1358;2|1239|91061|186826|81852|1350|71452;2|1239|186801|3085636|186803|189330|39486;2|201174|1760|85007|1653|1716|43769;2|1239|186801|186802|216572|216851|853;2|1239|91061|186826|33958|1243|1246;2|1239|91061|186826|186828|117563;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|68891,Complete,Svetlana up
bsdb:1004/3/2,Study 1004,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,https://journals.asm.org/doi/10.1128/spectrum.03190-23,"Iwase SC, Osawe S, Happel A-U, Gray CM, Holmes SP, Blackburn JM, Abimiku A , Jaspan HB",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV when adjusted for reported antibiotic (co-trimoxazole) prophylaxis history adjusted by mode of feeding and reported antibiotics history,21,61,None,16S,34,Illumina,ANCOM,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S2,24 June 2024,Scholastica,Scholastica,Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding and reported antibiotics history,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|91061|186826|33958|2742598|1633;2|1239|91061|186826|33958|2742598|1613;2|976|200643|171549|2005525|375288|823;2|1239|91061|186826|33958|2759736|47715;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|81852|1350|160453;2|1239|909932|1843489|31977|906|907;2|201174|84998|84999|1643824|133925;2|201174|84998|84999|84107|1473205;2|1224|1236|91347|543|570|1134687;2|976|200643|171549|815|816|47678;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:1005/1/1,Study 1005,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T, Dodoková A, Kreisinger J, Stopka P , Stopková R","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 1,Czechia,Mus musculus,"Vagina,Saliva","UBERON:0000996,UBERON:0001836",Microbiome measurement,EFO:0007882,Oral (saliva),Vagina,Vaginal samples of lived-trapped females of Mus musculus musculus mice,18,18,None,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 3B,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Bacterial taxa identified by ANCOM exhibiting significant abundance in oral compared to vaginal samples,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1239|91061|186826|81852|1350;2|976|200643|171549|2005473,Complete,Svetlana up
bsdb:1005/1/2,Study 1005,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T, Dodoková A, Kreisinger J, Stopka P , Stopková R","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 1,Czechia,Mus musculus,"Vagina,Saliva","UBERON:0000996,UBERON:0001836",Microbiome measurement,EFO:0007882,Oral (saliva),Vagina,Vaginal samples of lived-trapped females of Mus musculus musculus mice,18,18,None,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3B,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Bacterial taxa identified by ANCOM exhibiting significant abundance in oral compared to vaginal samples,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Muribacter",2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1301;2|201174|1760|85007|1653|1716;2|1239|91061|186826|33958|1578;2|1224|28211|356|119045|407;2|1224|28211|356|41294|374;2|1224|1236|135625|712|1857532,Complete,Svetlana up
bsdb:1005/2/1,Study 1005,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T, Dodoková A, Kreisinger J, Stopka P , Stopková R","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 2,Czechia,Mus musculus,Vagina,UBERON:0000996,Vaginal microbiome measurement,EFO:0011013,Vaginal estrus samples,Vaginal metestrus samples,Vaginal samples collected during the metestrus phase,18,18,None,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 5D,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Bacterial taxa identified by ANCOM exhibiting significant abundance in estrus compared to metestrus phase,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1224|28216|80840|75682|149698;2|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:1005/2/2,Study 1005,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T, Dodoková A, Kreisinger J, Stopka P , Stopková R","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 2,Czechia,Mus musculus,Vagina,UBERON:0000996,Vaginal microbiome measurement,EFO:0011013,Vaginal estrus samples,Vaginal metestrus samples,Vaginal samples collected during the metestrus phase,18,18,None,16S,34,Illumina,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 5D,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Bacterial taxa identified by ANCOM exhibiting significant abundance in estrus compared to metestrus phase,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Muribacter,2|1224|1236|135625|712|1857532,Complete,Svetlana up
bsdb:1006/1/1,Study 1006,"cross-sectional observational, not case-control",34954497,10.1016/j.parkreldis.2021.12.012,https://doi.org/10.1016/j.parkreldis.2021.12.012,"Takahashi K, Nishiwaki H, Ito M, Iwaoka K, Takahashi K, Suzuki Y, Taguchi K, Yamahara K, Tsuboi Y, Kashihara K, Hirayama M, Ohno K , Maeda T",Altered gut microbiota in Parkinson's disease patients with motor complications,Parkinsonism & related disorders,2022,"Dyskinesia, Gut microbiota, Motor complications, Parkinson's disease, Wearing-off",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients with dyskinesia,PD patients with  wearing-off,Parkinson's disease patients with wearing-off,106,49,Within a month before the start of this study,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,18 March 2024,PraiseAgbetuyi,"PraiseAgbetuyi,Peace Sandy","Relationships between Lachnospiraceae Blautia or Lactobacillaceae Lactobacillus and motor complications  In patients with wearing-off, the relative abundance of Lachnospiraceae Blautia (A) and Lactobacillaceae Lactobacillus (C) significantly decreased and increased, respectively. Patients with dyskinesia (B and D) showed no change in relative abundance.",increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:1006/1/2,Study 1006,"cross-sectional observational, not case-control",34954497,10.1016/j.parkreldis.2021.12.012,https://doi.org/10.1016/j.parkreldis.2021.12.012,"Takahashi K, Nishiwaki H, Ito M, Iwaoka K, Takahashi K, Suzuki Y, Taguchi K, Yamahara K, Tsuboi Y, Kashihara K, Hirayama M, Ohno K , Maeda T",Altered gut microbiota in Parkinson's disease patients with motor complications,Parkinsonism & related disorders,2022,"Dyskinesia, Gut microbiota, Motor complications, Parkinson's disease, Wearing-off",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients with dyskinesia,PD patients with  wearing-off,Parkinson's disease patients with wearing-off,106,49,Within a month before the start of this study,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,18 March 2024,PraiseAgbetuyi,"PraiseAgbetuyi,Peace Sandy",". Relationships between Lachnospiraceae Blautia or Lactobacillaceae Lactobacillus and motor complications In patients with wearing-off, the relative abundance of Lachnospiraceae Blautia (A) and Lactobacillaceae Lactobacillus (C) significantly decreased and increased, respectively. Patients with dyskinesia (B and D) showed no change in relative abundance.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,2|1239|186801|3085636|186803|572511,Complete,Peace Sandy
bsdb:1007/1/1,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 1,Malta,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,97,66,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 5,24 March 2024,Samreen-19,Samreen-19,Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|216572|946234|292800;2|1239|909932|1843488|909930|904;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|186801|186802|216572|459786,Complete,NA
bsdb:1007/1/2,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 1,Malta,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,97,66,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 5,24 March 2024,Samreen-19,Samreen-19,Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|33042;2|1224|28216|80840|75682|846;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|459786;2|1239|186801|186802;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724|729;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:1007/2/1,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 2,Malta,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Crohn’s disease (CD),Patients with Crohn’s disease (CD) in a state of remission,97,32,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,unchanged,NA,decreased,Signature 1,Appendix Table 5,24 March 2024,Samreen-19,Samreen-19,Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|216572|946234|292800;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572;2|1239|186801|186802|216572|292632;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|459786;2|976|200643|171549|815|816;2|1239|909932|1843488|909930|904,Complete,NA
bsdb:1007/2/2,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 2,Malta,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Crohn’s disease (CD),Patients with Crohn’s disease (CD) in a state of remission,97,32,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,unchanged,NA,decreased,Signature 2,Appendix Table 5,24 March 2024,Samreen-19,Samreen-19,Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|33042;2|1224|28216|80840|75682|846;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816;2|1239|186801|3085636|186803;2|1239|186801|186802|216572|459786;2|1239|186801|186802;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724|729;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:1007/3/1,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 3,Malta,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Crohn's disease (CD),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,32,66,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 5,24 March 2024,Samreen-19,Samreen-19,Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|1224|28216|80840|995019|577310,Complete,NA
bsdb:1007/3/2,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 3,Malta,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Crohn's disease (CD),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,32,66,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 5,24 March 2024,Samreen-19,Samreen-19,Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1239|186801|3085636|186803|189330;2|1239|186801|186802|216572|292632;2|1224|1236|91347|543|561,Complete,NA
bsdb:1007/4/1,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 4,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,No,Yes,Patients with Inflammatory Bowel Disease (IBD) who are smokers,63,10,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 9,24 March 2024,Samreen-19,Samreen-19,Differential abundance analysis for smoking behaviour,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801|3085636|186803;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:1007/4/2,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 4,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,No,Yes,Patients with Inflammatory Bowel Disease (IBD) who are smokers,63,10,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 9,24 March 2024,Samreen-19,Samreen-19,Differential abundance analysis for smoking behaviour,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|357276;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|200940|3031449|213115|194924|35832;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572;2|1224|28216|80840|995019|577310;2|1224|1236|91347|543|544,Complete,NA
bsdb:1007/5/1,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 5,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,No,Ex,"Patients with Inflammatory Bowel Disease (IBD) who were ex-smokers (had
stopped smoking for at least 6 months).",63,15,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 9,24 March 2024,Samreen-19,Samreen-19,Differential abundance analysis for smoking behaviour,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|815|909656|357276;2|1239|186801|3085636|186803;2|976|200643|171549|815|816;2|1224|28216|80840|995019|577310;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1007/5/2,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 5,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,No,Ex,"Patients with Inflammatory Bowel Disease (IBD) who were ex-smokers (had
stopped smoking for at least 6 months).",63,15,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 9,24 March 2024,Samreen-19,Samreen-19,Differential abundance analysis for smoking behaviour,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|976|200643|171549|815|816|28116;2|1239|186801|3085636|186803|207244;2|200940|3031449|213115|194924|35832;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572;2|1224|28216|80840|995019|40544;2|1224|1236|91347|543|544,Complete,NA
bsdb:1007/6/1,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 6,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Ex,Yes,Patients with Inflammatory Bowel Disease (IBD) who are smokers,25,10,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 9,25 March 2024,Samreen-19,Samreen-19,Differential abundance analysis for smoking behaviour,increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|200940|3031449|213115|194924|35832;2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:1007/6/2,Study 1007,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A , Ellul P",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 6,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Ex,Yes,Patients with Inflammatory Bowel Disease (IBD) who are smokers,25,10,3 months,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 9,25 March 2024,Samreen-19,Samreen-19,Differential abundance analysis for smoking behavior,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|357276;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1224|28216|80840|995019|577310;2|1224|1236|91347|543|544,Complete,NA
bsdb:1008/1/1,Study 1008,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee CC, Liang F, Lee IC, Lu TH, Shan YY, Jeng CF, Zou YF, Yu HT , Chen Alen SK",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 1,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - Control group,Dim light at night (dLAN) - Control group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the control group,NA,NA,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4B,20 March 2024,Aleru Divine,Aleru Divine,Figure 4B represents a cladogram that shows the difference in the relative abundance of microbes from control mice housed under conditions of LD and dLAN.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",2|976|200643|171549|2005473;2|976|200643|171549|171552|577309;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:1008/1/2,Study 1008,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee CC, Liang F, Lee IC, Lu TH, Shan YY, Jeng CF, Zou YF, Yu HT , Chen Alen SK",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 1,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - Control group,Dim light at night (dLAN) - Control group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the control group,NA,NA,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4B,20 March 2024,Aleru Divine,Aleru Divine,Figure 4B represents a cladogram that shows the difference in the relative abundance of microbes from control mice housed under conditions of LD and dLAN.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|976|200643|171549|171550|28138;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231,Complete,Svetlana up
bsdb:1008/2/NA,Study 1008,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee CC, Liang F, Lee IC, Lu TH, Shan YY, Jeng CF, Zou YF, Yu HT , Chen Alen SK",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 2,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - MKO group,Dim light at night (dLAN) - MKO group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the group with knockout of the photopigment melanopsin (MKO).,NA,NA,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1008/3/1,Study 1008,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee CC, Liang F, Lee IC, Lu TH, Shan YY, Jeng CF, Zou YF, Yu HT , Chen Alen SK",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 3,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - DTA group,Dim light at night (dLAN) - DTA group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the group that underwent the genetic elimination of ipRGCs using the Opn4‐DTA or Opn4‐Cre (DTA).,NA,NA,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4D,20 March 2024,Aleru Divine,Aleru Divine,The cladogram shows the difference in relative abundance of microbes from Opn4DTA/DTA mice under LD and dLAN conditions.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",2|1239|186801|186802|31979;2|1239|526524|526525|128827|174708;2|1239|526524|526525|128827;2|1239|526524|526525;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|203557;2|74201|203494|48461,Complete,Svetlana up
bsdb:1008/3/2,Study 1008,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee CC, Liang F, Lee IC, Lu TH, Shan YY, Jeng CF, Zou YF, Yu HT , Chen Alen SK",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 3,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - DTA group,Dim light at night (dLAN) - DTA group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the group that underwent the genetic elimination of ipRGCs using the Opn4‐DTA or Opn4‐Cre (DTA).,NA,NA,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4D,20 March 2024,Aleru Divine,Aleru Divine,The cladogram shows the difference in relative abundance of microbes from Opn4DTA/DTA mice under LD and dLAN conditions.,decreased,"k__Bacteria|s__rumen bacterium YS2,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|s__bacterium AF12,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacteria|s__bacterium F16,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral clone CW040",2|209265;2|976|200643|171549|171550;2|1729795;2|1239|91061|186826|81852|423410;2|1932694;2|95818|163601,Complete,Svetlana up
bsdb:1009/1/1,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),68,168,within 3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,FIG 1 (F),19 March 2024,Rahila,"Rahila,Scholastica",LEfSe analysis identified the differentially abundant taxa between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 3.0),increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1224|1236;2|1224|1236|91347|543|570;2|1224;2|1239|909932|1843489|31977|29465;2|74201|203494|48461;2|74201|203494;2|74201,Complete,Svetlana up
bsdb:1009/1/2,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),68,168,within 3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,FIG 1 (F),25 June 2024,Scholastica,Scholastica,LEfSe analysis identified the differentially abundant taxa between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 3.0),decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239;2|1224|28216|80840|119060;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|186804|1505657;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491|52225;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:1009/2/1,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),57,106,within 3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,FIG 2 (D),19 March 2024,Rahila,Rahila,LEfSe analysis identified the differences in abundance between I-PJS and NI-PJS patients (LDA > 3.0).,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1224|28216|80840|119060;2|1239|186801|186802|216572|216851;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:1009/2/2,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),57,106,within 3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,FIG 2 (D),19 March 2024,Rahila,Rahila,LEfSe analysis identified the differences in abundance between I-PJS and NI-PJS patients (LDA > 3.0).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota",2|1239|186801|3085636|186803|572511;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1224|1236;2|1224|1236|91347|543|570;2|1224,Complete,Svetlana up
bsdb:1009/3/1,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),27,61,within 3 months,WMS,NA,Illumina,"Mann-Whitney (Wilcoxon),LEfSe",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (D),19 March 2024,Rahila,"Rahila,Scholastica",LEfSe analysis identified the differential species between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 2.0),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas|s__Plesiomonas shigelloides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota",2|1224|1236|2887326|468|469|470;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|1463165;2|1224|1236|91347|543|570|244366;2|976|200643|171549|171552|2974265|363265;2|976|200643|171549|171552|2974265|363265;2|1224|1236|91347|543|702|703;2|1224|1236|91347|543|590|28901;2|1224|1236|91347|543|620|621;2|1224|1236|91347|543|620|622;2|1224|1236|91347|543|620|623;2|1224|1236|91347|543|620|624;2;2|1224|1236|91347|543|547;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236;2|1224|1236|91347|543|570;2|1224,Complete,Svetlana up
bsdb:1009/3/2,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),27,61,within 3 months,WMS,NA,Illumina,"Mann-Whitney (Wilcoxon),LEfSe",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (D),25 June 2024,Scholastica,Scholastica,LEfSe analysis identified the differential species between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 2.0),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. 51_20,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__uncultured Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM33-3,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacteria|p__Bacillota|s__Firmicutes bacterium CAG:227,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SS2/1,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:248,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia",2|1239|186801|186802|216572|216851|853;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802;2|1239|186801|3085636|186803|207244|649756;2|1224|28211|204441|2829815|191|1896972;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3082720|186804|1505657|261299;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|2316020|46228;2|1239|526524|526525|128827;2|1239|91061|186826|1300|1301|1304;2|1239|186801|3085636|186803|189330|39486;2|1239|186801|186802|216572|216851|259315;2|1239|186801|186802|31979|1485|84024;2|1239|186801|186802|31979|1485|2292206;2|1239|186801|186802|31979|1485|2292304;2|1239|186801|3085636|186803|189330;2|201174|1760|2037|2049|1654|936548;2|1239|1263010;2|1239|186801|186802|31979|1485|411484;2|1239|186801|186802|186806|1730|1262885;2|1224|28216|80840|80864|80865,Complete,Svetlana up
bsdb:1009/4/1,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),26,35,within 3 months,WMS,NA,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D),19 March 2024,Rahila,Rahila,LEfSe analysis showed the differential species between I-PJS and NI-PJS patients (LDA > 2.0).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas veronii,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. AF08-23,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrogenes,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|s__bacterium 1xD8-27",2|1224|1236|135624|84642|642|654;2|201174|84998|84999|84107|102106|2292211;2|1239|909932|1843489|31977|39948|218538;2|32066|203490|203491|203492|848|858;2|32066|203490|203491|203492|848|68766;2|1224|1236|135624|84642|642;2|2320108,Complete,Svetlana up
bsdb:1009/4/2,Study 1009,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B , Chen Y",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),26,35,within 3 months,WMS,NA,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 4 (D),19 March 2024,Rahila,Rahila,LEfSe analysis showed the differential species between I-PJS and NI-PJS patients (LDA > 2.0).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74_58_120,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. AM42-24,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF10-46,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|216572|216851|1897005;2|976|200643|171549|171552|838|2293125;2|976|200643|171549|171550|239759|1288121;2|976|117743|200644|49546;2|976|200643|171549|2005519|1348911|1099853;2|1239|186801|186802|216572|216851|2302955;2|1224|1236|135625|712|724|729,Complete,Svetlana up
bsdb:1010/1/1,Study 1010,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E, Nearing J, Fischer JA, Ma Y, Wang S, Krouen H, Goldfarb DM , Karakochuk CD","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Placebo group,Ferrous bisglycinate group,"Healthy, non pregnant women of reproductive age who received oral supplementation of ferrous bisglycinate capsule containing 18 mg of elemental iron.",47,46,Women who were taking antibiotics in the previous 12 weeks were excluded.,16S,678,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 4, Figure 5",29 March 2024,Manisha28,Manisha28,Differentially abundant bacterial Taxa in the Ferrous bisglycinate group compared to the Placebo group.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1239|91061|186826|33958|46255,Complete,NA
bsdb:1010/1/2,Study 1010,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E, Nearing J, Fischer JA, Ma Y, Wang S, Krouen H, Goldfarb DM , Karakochuk CD","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Placebo group,Ferrous bisglycinate group,"Healthy, non pregnant women of reproductive age who received oral supplementation of ferrous bisglycinate capsule containing 18 mg of elemental iron.",47,46,Women who were taking antibiotics in the previous 12 weeks were excluded.,16S,678,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,29 March 2024,Manisha28,Manisha28,Differentially abundant bacterial Taxa in the Ferrous bisglycinate group compared to the Placebo group.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,NA
bsdb:1010/2/1,Study 1010,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E, Nearing J, Fischer JA, Ma Y, Wang S, Krouen H, Goldfarb DM , Karakochuk CD","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Placebo Group,Ferrous sulfate group,"Healthy, non pregnant women of reproductive age who received oral supplementation of ferrous sulfate capsule containing 60 mg of elemental iron.",47,40,Women who were taking antibiotics in the previous 12 weeks were excluded.,16S,678,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,29 March 2024,Manisha28,Manisha28,Differentially abundant bacterial Taxa in the Ferrous sulfate group compared to the Placebo group.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|46255,Complete,NA
bsdb:1010/2/2,Study 1010,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E, Nearing J, Fischer JA, Ma Y, Wang S, Krouen H, Goldfarb DM , Karakochuk CD","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Placebo Group,Ferrous sulfate group,"Healthy, non pregnant women of reproductive age who received oral supplementation of ferrous sulfate capsule containing 60 mg of elemental iron.",47,40,Women who were taking antibiotics in the previous 12 weeks were excluded.,16S,678,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,29 March 2024,Manisha28,Manisha28,Differentially abundant bacterial Taxa in the Ferrous sulfate group compared to the Placebo group.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1224|1236|91347|543;2|1224|1236|91347|543|1940338,Complete,NA
bsdb:1011/1/1,Study 1011,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M, Fan Q, Shang F, Zhang T, Ogino S , Liu H",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 1,China,Homo sapiens,Colorectum,UBERON:0012652,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the supplementary discovery cohort (cohort 1),10,8,Within 3 months prior to specimen collection.,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 1,"Figure 4a, 4b and Figure 5c",20 April 2024,Aleru Divine,Aleru Divine,"Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 1.",increased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Deinococcota|c__Deinococci,k__Bacteria|p__Deinococcota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Nitrospirota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Synergistota,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Bacteroidota",2|57723;2|201174;2|67819;2|1239;2|1224|28216;2|1224|28216|80840;2|95818;2|200795|32061;2|1224|28216|80840|119060|106589;2|1117;2|1297|188787;2|1297;2|32066;2|142182|219685;2|544448;2|40117;2|1224|28216|80840|75682;2|203682;2|203691|203692|136;2|508458;2|1297|188787|68933|188786;2|1297|188787|68933;2|1297|188787|68933|188786|270;2|74201;2|976,Complete,Svetlana up
bsdb:1011/1/2,Study 1011,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M, Fan Q, Shang F, Zhang T, Ogino S , Liu H",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 1,China,Homo sapiens,Colorectum,UBERON:0012652,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the supplementary discovery cohort (cohort 1),10,8,Within 3 months prior to specimen collection.,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 2,"Figure 4a, 4b and Figure 5c",20 April 2024,Aleru Divine,Aleru Divine,"Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 1.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|1236|2887326|468|469;2|1224|28211;2|74152|641853;2|1224|1236;2|1224|1236|2887326|468;2;2|1224|1236|72274;2|1224;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:1011/2/1,Study 1011,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M, Fan Q, Shang F, Zhang T, Ogino S , Liu H",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the discovery cohort (cohort 2),36,18,Within 3 months prior to specimen collection.,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4c, 4d and Figure 5d",20 April 2024,Aleru Divine,Aleru Divine,"Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 2.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Lentisphaerota,k__Bacteria,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Verrucomicrobiota",2|976|200643|171549|171550|239759;2|1239;2|976|200643;2|95818;2|1090;2|200795|32061;2|1117;2|32066;2|142182|219685;2|256845;2;2|203682;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|200643|171549|171550;2|203691;2|508458;2|1239|909932|1843489|31977;2|74201,Complete,Svetlana up
bsdb:1011/2/2,Study 1011,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M, Fan Q, Shang F, Zhang T, Ogino S , Liu H",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the discovery cohort (cohort 2),36,18,Within 3 months prior to specimen collection.,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4c, 4d and Figure 5d",20 April 2024,Aleru Divine,Aleru Divine,"Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 2.",decreased,"k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Deinococcota,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Nitrospirota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota",2|57723;2|201174;2|1297;2|544448;2|40117;2|976|200643|171549|171551|836;2|1224,Complete,Svetlana up
bsdb:1011/3/1,Study 1011,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M, Fan Q, Shang F, Zhang T, Ogino S , Liu H",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the validation cohort (cohort 3),41,13,Within 3 months prior to specimen collection.,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4e, 4f and Figure 5e",21 April 2024,Aleru Divine,Aleru Divine,"Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Bacteria|p__Elusimicrobiota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Planctomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Promicromonospora,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Rhodomicrobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota",2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1239;2|1239|526524|526525|128827|118747;2|1090;2|200795;2|1239|186801|3082768|990719;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|33042;2|1224|1236|118969|118968;2|1117|3028117;2|28221;2|200940|3031449|213115|194924|872;2|508458|649775|649776|3029088;2|1224|28211|356|2831106|46913;2|1239|186801|3085636|186803|189330;2|74152|641853;2|74152|641853|641854|641876;2|74152|641853|641854;2|74152;2|976|117743|200644|1853230|332102;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738;2|142182|219685;2|1239|186801|186802|204475;2|1224|28216|80840|80864|47420;2|203682|203683|2691356|1763524;2|1239|186801|3085636|186803|140625;2|256845;2|1224|28216|32003|32011;2|976|200643|171549|2005473;2|1224|28216|32003;2|1239|186801|186802|216572|119852;2|976|200643|171549|171552|577309;2;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|1239|909932|1843488|909930|33024;2|203682;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|201174|1760|85006|85017|43676;2|1224|1236|135614|32033|83618;2|508458|649775|649776|3029088|638847;2|1224|28211|356|45401|1068;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|203691;2|1239|186801|186802|216572|292632;2|1117|3028117|1890424|1890426;2|1117|3028117|1890424;2|1117|3028117|1890424|1890426|1129;2|508458|649775|649776;2|508458|649775;2|508458;2|1224|1236|72273;2|1239|1737404|1737405|1737406;2|1239|909932|1843489|31977;2|976,Complete,Svetlana up
bsdb:1011/3/2,Study 1011,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M, Fan Q, Shang F, Zhang T, Ogino S , Liu H",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the validation cohort (cohort 3),41,13,Within 3 months prior to specimen collection.,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4e, 4f and Figure 5e",21 April 2024,Aleru Divine,Aleru Divine,"Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Nitrospirota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Deinococcota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Acidobacteriota",2|976|200643|171549|1853231;2|976|200643|171549|171551|836;2|74201;2|95818;2|544448;2|40117;2|201174;2|1297;2|1224;2|1117;2|57723,Complete,Svetlana up
bsdb:1013/1/1,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 1,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Microbiome measurement,EFO:0007882,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Use of antibiotics,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,FIG. 3B,21 April 2024,Rahila,"Rahila,Scholastica",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",2|1239|91061|186826|186827|46123|46125;2|976|117743|200644|49546|1016|1019;2|201174|1760|85007|1653|1716|61592;2|201174|1760|85007|1653|1716|43768;2|1224|28216|206351|481|32257|504;2|1224|28216|206351|481|32257|505;2|1224|28216|80840|119060|47670|47671;2|201174|1760|85006|1268|32207|172042;2|201174|1760|85006|1268|32207|2047;2|976|200643|171549|171552|2974251|439703;2|976|200643|171549|171552|2974251|28135;2|1239|909932|909929|1843491|970|671224;2|1239|909932|909929|1843491|970|69823;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|1300|1301|1304,Complete,Svetlana up
bsdb:1013/1/2,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 1,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Microbiome measurement,EFO:0007882,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Use of antibiotics,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,FIG. 3B,21 April 2024,Rahila,"Rahila,Scholastica",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis",2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|2974257|425941;2|1224|28216|206351|481|71|72;2|32066|203490|203491|1129771|168808|187101,Complete,Svetlana up
bsdb:1013/2/1,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 2,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Microbiome measurement,EFO:0007882,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,FIG. 3C,21 April 2024,Rahila,"Rahila,Scholastica",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius",2|1239|91061|186826|186827|46123|46125;2|201174|1760|2037|2049|1654|52769;2|1224|1236|135625|712|416916|732;2|29547|3031852|213849|72294|194|824;2|29547|3031852|213849|72294|194|203;2|976|117743|200644|49546|1016|1017;2|976|117743|200644|49546|1016|45242;2|976|117743|200644|49546|1016|327575;2|976|117743|200644|49546|1016|1019;2|1224|1236|135615|868|2717|2718;2|201174|1760|85007|1653|1716|61592;2|201174|1760|85007|1653|1716|43768;2|1224|28216|206351|481|538|539;2|1224|28216|206351|481|32257|505;2|1224|28216|80840|119060|47670|47671;2|32066|203490|203491|1129771|32067|554406;2|201174|1760|85006|1268|32207|172042;2|201174|1760|85006|1268|32207|2047;2|1239|909932|909929|1843491|970|671224;2|1239|909932|909929|1843491|970|69823;2|1239|91061|186826|1300|1301|1338,Complete,Svetlana up
bsdb:1013/2/2,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 2,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Microbiome measurement,EFO:0007882,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,FIG. 3C,21 April 2024,Rahila,"Rahila,Scholastica",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis",2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|724|729;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207|43675;2|32066|203490|203491|1129771|168808|187101,Complete,Svetlana up
bsdb:1013/3/1,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 3,Canada,Homo sapiens,"Supragingival dental plaque,Saliva","UBERON:0016485,UBERON:0001836",Microbiome measurement,EFO:0007882,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,5 June 2024,Scholastica,Scholastica,Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Thelephorales|f__Thelephoraceae,k__Eukaryota|k__Fungi|p__Zoopagomycota|o__Ramicandelaberales|f__Ramicandelaberaceae|g__Ramicandelaber|s__Ramicandelaber taiwanensis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium sp.,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae|g__Stereum|s__Stereum rugosum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia tropicalis",2759|4751|4890|3239874|2916678|766764|5475|42374;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|5204|155619|56487|56488;2759|4751|1913638|2219773|2219775|304330|858342;2759|4751|4890|147550|5125|110618|5506|29916;2759|4751|5204|155619|452342|103376|5644|55358;2759|4751|5204|431957|431958|431959|148959|1708540,Complete,Svetlana up
bsdb:1013/3/2,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 3,Canada,Homo sapiens,"Supragingival dental plaque,Saliva","UBERON:0016485,UBERON:0001836",Microbiome measurement,EFO:0007882,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 2,5 June 2024,Scholastica,Scholastica,Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon|s__Trichosporon asahii,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",2759|4751|5204|155619;2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|5204|155616|1851469|1759442|5552|82508;2759|4751|5204|1538075|162474|742845|55193|76773,Complete,Svetlana up
bsdb:1013/4/1,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 4,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Microbiome measurement,EFO:0007882,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,5 June 2024,Scholastica,Scholastica,Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the caries-free group,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria|s__Blumeria sp.,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon|s__Trichosporon asahii,k__Eukaryota|k__Fungi|p__Zoopagomycota|o__Ramicandelaberales|f__Ramicandelaberaceae|g__Ramicandelaber|s__Ramicandelaber taiwanensis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium sp.,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Meyerozyma|s__Meyerozyma guilliermondii,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Eukaryota|k__Fungi|p__Cryptomycota,k__Eukaryota|k__Fungi|p__Chytridiomycota,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia tropicalis",2759|4751|4890|147548|5120|34371|34372|2874738;2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|5204|155616|1851469|1759442|5552|82508;2759|4751|1913638|2219773|2219775|304330|858342;2759|4751|4890|147550|5125|110618|5506|29916;2759|4751|4890|3239874|2916678|766764|766728|4929;2759|4751|5204|1538075|162474;2759|4751|1031332;2759|4751|4761;2759|4751|5204|431957|431958|431959|148959|1708540,Complete,Svetlana up
bsdb:1013/4/2,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 4,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Microbiome measurement,EFO:0007882,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,5 June 2024,Scholastica,Scholastica,Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the caries-free group,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Eukaryota|k__Fungi|p__Ascomycota",2759|4751|5204|155619;2759|4751|4890,Complete,Svetlana up
bsdb:1013/5/1,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 5,Canada,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Oral swab from caries-free,Oral swab from severe early childhood caries (S-ECC),"Oral swap samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,5 June 2024,Scholastica,Scholastica,Differential abundance analysis of fungal taxa in oral swab samples within the caries-free group versus oral swab samples within the  S-ECC (severe early childhood caries) group,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis",2759|4751|4890|3239874|2916678|766764|5475|42374;2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|4890|3239874|2916678|766764|5475|5482,Complete,Svetlana up
bsdb:1013/5/2,Study 1013,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ , Chelikani P",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 5,Canada,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Oral swab from caries-free,Oral swab from severe early childhood caries (S-ECC),"Oral swap samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,5 June 2024,Scholastica,Scholastica,Differential abundance analysis of fungal taxa in oral swab samples within the caries-free group versus oral swab samples within the  S-ECC (severe early childhood caries) group,decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Thelephorales|f__Thelephoraceae,2759|4751|5204|155619|56487|56488,Complete,Svetlana up
bsdb:1014/1/1,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 5 Abx,Prophylactic oats Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with oats as a preventive measure during amoxicillin treatment,10,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,20 March 2024,Barrakat,Barrakat,Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata",2|976|200643|171549|815|816|871325;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|371601;2|1239|91061|1385|90964|1279|1288;2|1239|526524|526525|2810280|3025755|69824,Complete,NA
bsdb:1014/1/2,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 5 Abx,Prophylactic oats Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with oats as a preventive measure during amoxicillin treatment,10,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,20 March 2024,Barrakat,Barrakat,Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides congonensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus asini",2|976|200643|171549|171550|239759|328813;2|976|200643|171549|815|816|1871006;2|976|200643|171549|815|816|871325;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|371601;2|1239|91061|186826|81852|1350|57732,Complete,NA
bsdb:1014/2/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 0 Abx,Always Dextrose Day 5 Abx,Always Dextrose plus amoxicillin fecal pellets that were collected on day 5,9,10,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/3/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 0 Abx,Always Dextrose Day 9 Post Abx,Always Dextrose without amoxicillin fecal pellets that were collected on day 9,9,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/4/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 0 Abx,Always Dextrose Day 14 Post Abx,Always Dextrose without amoxicillin fecal pellets that were collected on day 14,9,7,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/5/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 5 Abx,Always Dextrose Day 9 Post A Pbx,Always Dextrose without amoxicillin fecal pellets that were collected on day 9,10,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/6/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 5 Abx,Always Dextrose Day 14 Post Abx,Always Dextrose without amoxicillin fecal pellets that were collected on day 14,10,7,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/7/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 9 Post Abx,Always Dextrose Day 14 Post Abx,Always Dextrose without amoxicillin fecal pellets that were collected on day 14,3,7,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/8/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Oats Day 0 Abx,Always oats Day 5 Abx,Always Oats with amoxicillin fecal pellets that were collected on day 5,12,6,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/9/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 9,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Oats Day 0 Abx,Always oats Day 11 Post Abx,Always oats without amoxicillin fecal pellets that were collected on day 11,12,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/10/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 10,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Oats Day 0 Abx,Always oats Day 14 Post Abx,Always oats without amoxicillin fecal pellets that were collected on day 14,12,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/11/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 11,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Oats Day 5 Abx,Always Oats Day 11 Post Abx,Always oats without amoxicillin fecal pellets that were collected on day 11,6,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/12/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 12,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always oats Day 5 Abx,Always oats Day 14 Post Abx,Always oats without amoxicillin fecal pellets that were collected on day 14,6,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/13/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 13,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always oats Day 11 Post Abx,Always oats Day 14 Post Abx,Always oats without amoxicillin fecal pellets that were collected on day 14,3,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/14/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 14,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Prophylactic oats Day 0 Abx,Prophylactic oats Day 6 Post Abx,Prophylactic oats without amoxicillin fecal pellets that were collected on day 6,9,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/15/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 15,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Prophylactic oats Day 0 Abx,Prophylactic oats Day 14 Post Abx,Prophylactic oats without amoxicillin fecal pellets that were collected on day 14,9,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/16/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 16,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Prophylactic oats Day 6 Post Abx,Prophylactic oats Day 14 Post Abx,Prophylactic oats without amoxicillin fecal pellets that were collected on day 14,3,3,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/17/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 17,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Recovery oats Day 0 Abx,Recovery oats Day 5 Abx,Recovery oats with amoxicillin fecal pellets that were collected on day 5,6,10,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/18/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 18,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Recovery oats Day 0 Abx,Recovery oats Day 7 Post Abx,Recovery oats without amoxicillin fecal pellets that were collected on day 7,6,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/19/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 19,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Recovery oats Day 0 Abx,Recovery oats Day 14 Post Abx,Recovery oats without amoxicillin fecal pellets that were collected on day 14,6,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/20/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 20,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Recovery oats Day 5 Abx,Recovery oats Day 7 Post Abx,Recovery oats without amoxicillin fecal pellets that were collected on day 7,10,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/21/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 21,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Recovery oats Day 5 Abx,Recovery oats Day 14 Post Abx,Recovery oats without amoxicillin fecal pellets that were collected on day 14,10,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1014/22/NA,Study 1014,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S , Belenky P",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 22,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Recovery oats Day 7 Post Abx,Recovery oats Day 14 Post Abx,Recovery oats without amoxicillin fecal pellets that were collected on day 14,4,4,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1015/1/1,Study 1015,case-control,37800955,10.1128/spectrum.00234-23,NA,"Ji X, Li P, Guo Q, Guan L, Gao P, Wu B, Cheng H, Xiao J , Ye L",Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing,Microbiology spectrum,2023,"clinical phenotype, diagnostics, pituitary adenomas, saliva microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Pituitary Gland Adenoma,EFO:1000478,Healthy controls,Patients with pituitary adenomas (PA),"Patients with pituitary adenomas (PA) which included four clinical phenotypes: adrenocorticotropic hormone-secreting PA (n = 6), growth hormone-secreting PA (n = 9), prolactin-secreting PA (n = 18), and nonfunctioning PA (n = 9)",20,42,6 months,16S,NA,PacBio RS,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig 2D,19 March 2024,Scholastica,Scholastica,Differential abundance of microbes in patients with pituitary adenomas (PA) versus healthy individual,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|201174|1760|2037|2049|1654;2|201174|1760|85009|31957|2801844;2|1239|186801|3085636|186803|830;2|1224|1236|135615|868|2717;2|201174|1760|85007|1653|1716;2|201174|84998|84999|1643824|2767353;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2759|33090|35493|3398|72025|3803|3814|508215;2|201174|1760|2037|2049|2529408;2|1239|186801|3085636|186803|177971;2|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:1015/1/2,Study 1015,case-control,37800955,10.1128/spectrum.00234-23,NA,"Ji X, Li P, Guo Q, Guan L, Gao P, Wu B, Cheng H, Xiao J , Ye L",Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing,Microbiology spectrum,2023,"clinical phenotype, diagnostics, pituitary adenomas, saliva microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Pituitary Gland Adenoma,EFO:1000478,Healthy controls,Patients with pituitary adenomas (PA),"Patients with pituitary adenomas (PA) which included four clinical phenotypes: adrenocorticotropic hormone-secreting PA (n = 6), growth hormone-secreting PA (n = 9), prolactin-secreting PA (n = 18), and nonfunctioning PA (n = 9)",20,42,6 months,16S,NA,PacBio RS,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig 2D,19 March 2024,Scholastica,Scholastica,Differential abundance of microbes in patients with pituitary adenomas (PA) versus healthy individual,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Casaltella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816;2|976|117743|200644|2762318|59735;2|29547|3031852|213849|72294|194;2|1239|186801|186802|543314|1715793;2|1239|909932|909929|1843491|82202;2|1239|909932|1843489|31977|39948;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|976|200643|171549|171552|1926672;2|1224|1236|91347|543|620;2|1224|28216|206351|481|71;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1016/1/3,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Treatment,EFO:0000727,Pre-treatment (baseline),Post-treatment (6 months later),Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months after treatment,106,72,None,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,decreased,decreased,Signature 3,Supplementary Fig. 1B,23 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",Differentially abundant taxa at pre-treatment (0 month) compared to post-treatment (6 months later) by Linear discriminant analysis Effect Size (LEfSe) analysis,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207;2|1224|1236|72274|135621|286;2|201174|1760|85004|31953|196081;2|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:1016/1/4,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Treatment,EFO:0000727,Pre-treatment (baseline),Post-treatment (6 months later),Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months after treatment,106,72,None,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,decreased,decreased,Signature 4,Supplementary Fig. 1B,23 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",Differentially abundant taxa at pre-treatment (0 month) compared to post-treatment (6 months later) by Linear discriminant analysis Effect Size (LEfSe) analysis,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|201174|1760|85007|1653|1716;2|32066|203490|203491|1129771|32067;2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838;2|201174|1760|2037|2049|1654;2|976|200643|171549;2|1239|909932|1843489|31977|906;2|1239|91061|186826;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1224|1236|135625|712,Complete,Svetlana up
bsdb:1016/2/1,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to surgery,EFO:0009951,Pre-surgery,Post-surgery,Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months after treatment with surgery alone,15,15,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,unchanged,decreased,Signature 1,Figure 3E,24 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",Most differentially abundant OTUs between pre‑ and post‑surgery salivary microbiomes based on LEfSe analysis,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:1016/2/2,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to surgery,EFO:0009951,Pre-surgery,Post-surgery,Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months after treatment with surgery alone,15,15,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,unchanged,decreased,Signature 2,Figure 3E,24 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",Most differentially abundant OTUs between pre‑ and post‑surgery salivary microbiomes based on LEfSe analysis,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|29465;2|976|117743|200644|49546;2|1239|91061|186826|33958,Complete,Svetlana up
bsdb:1016/3/3,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Pre-chemoradiotherapy,Post-chemoradiotherapy,Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months who had undergone chemoradiotherapy,33,33,None,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,unchanged,decreased,Signature 3,Supplementary Fig. 2,23 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",Differentially abundant taxa before and after chemoradiotherapy (6 months later) by Linear discriminant analysis Effect Size (LEfSe) analysis,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|196081;2|1224|1236|72274|135621|286;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:1016/3/4,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Pre-chemoradiotherapy,Post-chemoradiotherapy,Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months who had undergone chemoradiotherapy,33,33,None,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,unchanged,decreased,Signature 4,Supplementary Fig. 2,23 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",Differentially abundant taxa before and after chemoradiotherapy (6 months later) by Linear discriminant analysis Effect Size (LEfSe) analysis,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|1239|186801|3085636|186803|1213720;2|976|117743|200644|49546|1016;2|1239|186801|3085636|186803|1164882;2|29547|3031852|213849|72294|194;2|1239|186801|3085636|186803|265975;2|201174|84998|84999|1643824|1380;2|976|200643|171549;2|32066|203490|203491|1129771|32067;2|201174|1760|2037|2049|1654;2|976|200643|171549|171551|836;2|1239|91061|186826;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|1224|1236|135625|712,Complete,Svetlana up
bsdb:1016/4/1,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to combination chemotherapy,EFO:0007965,Responders at baseline,Non-Responders at baseline,Patients with oral squamous cell carcinoma (SCC) at baseline deemed non-responders if any recurrence (local or metastatic) occurred within the follow-up period,39,11,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Figure 4F,23 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",LEfSe analysis showing the most differentially abundant OTUs in responders versus non‑responders before chemoradiotherapy,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|909932|1843489|31977|156454;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:1016/4/2,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to combination chemotherapy,EFO:0007965,Responders at baseline,Non-Responders at baseline,Patients with oral squamous cell carcinoma (SCC) at baseline deemed non-responders if any recurrence (local or metastatic) occurred within the follow-up period,39,11,None,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 2,Figure 4F,24 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",LEfSe analysis showing the most differentially abundant OTUs in responders versus non‑responders before chemoradiotherapy,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|1239|91061|186826|186827|46123;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712,Complete,Svetlana up
bsdb:1016/5/1,Study 1016,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros MC, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY , D'Silva NJ",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to combination chemotherapy,EFO:0007965,Responders at 6 months,Non-Responders at 6 months,Patients with oral squamous cell carcinoma (SCC) at 6 months deemed non-responders if any recurrence (local or metastatic) occurred within the follow-up period,25,8,None,16S,4,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Figure 5F,24 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica",LEfSe analysis identifying the most differentially abundant OTUs in responders versus non‑responders after chemoradiotherapy.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1018/1/1,Study 1018,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw CG, Pavloudi C, Crow RS, Saw JH , Smith LC","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 1,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Strongylocentrotus purpuratus,NCBITAXON:7668,Healthy sea urchins,Diseased sea urchins,Sea urchins with spotting disease,4,4,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table S3,20 March 2024,Ndruscilla,"Ndruscilla,Scholastica",Significantly differentially abundant taxa as identified by LEfSe for diseased versus healthy global surface microbiome samples,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudoteredinibacter,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae",2|976|117743|200644|49546|358023;2|1224|1236|1706369|1706371|1122284;2|976|768503|768507|563798,Complete,Svetlana up
bsdb:1018/1/2,Study 1018,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw CG, Pavloudi C, Crow RS, Saw JH , Smith LC","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 1,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Strongylocentrotus purpuratus,NCBITAXON:7668,Healthy sea urchins,Diseased sea urchins,Sea urchins with spotting disease,4,4,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table S3,20 March 2024,Ndruscilla,"Ndruscilla,Scholastica",Significantly differentially abundant taxa as identified by LEfSe for diseased versus healthy global surface microbiome samples,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",2|1224|1236|91347;2|1798710|1906119,Complete,Svetlana up
bsdb:1018/2/1,Study 1018,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw CG, Pavloudi C, Crow RS, Saw JH , Smith LC","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 2,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Microbiome measurement,EFO:0007882,Lesion surface samples (LS),Lesion body wall samples (LBW),Lesion body wall samples from sea urchins with spotting disease,5,7,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table S6,1 August 2024,Scholastica,Scholastica,Significantly differentially abundant taxa as identified by LEFSe for the lesion surface (LS) versus lesion body wall (LBW) microbiome samples,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Candidatus Photodesmus,2|1224|1236|135623|641|1076727,Complete,Svetlana up
bsdb:1018/2/2,Study 1018,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw CG, Pavloudi C, Crow RS, Saw JH , Smith LC","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 2,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Microbiome measurement,EFO:0007882,Lesion surface samples (LS),Lesion body wall samples (LBW),Lesion body wall samples from sea urchins with spotting disease,5,7,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table S6,1 August 2024,Scholastica,Scholastica,Significantly differentially abundant taxa as identified by LEFSe for the lesion surface (LS) versus lesion body wall (LBW) microbiome samples,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudophaeobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Roseobacter",2|1224|1236|1706369|1706371;2|1224|28211|204455|31989|1541822;2|1224|1236;2|1224|28211|204455|2854170|2433,Complete,Svetlana up
bsdb:1018/3/1,Study 1018,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw CG, Pavloudi C, Crow RS, Saw JH , Smith LC","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 3,United States of America,Strongylocentrotus purpuratus,"Coelomic fluid,Body wall","UBERON:0036217,UBERON:0000309",Microbiome measurement,EFO:0007882,Healthy coelomic fluid (HCF),Diseased coelomic fluid (DCF) and lesion body wall (LBW),Diseased coelomic fluid (DCF) and lesion body wall (LBW) samples from sea urchins with spotting disease,3,10,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S9,1 August 2024,Scholastica,Scholastica,Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",2|201174|1760|85006|85023|33882;2|976|200643;2|201174|1760|85006|85019|1696,Complete,Svetlana up
bsdb:1018/4/1,Study 1018,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw CG, Pavloudi C, Crow RS, Saw JH , Smith LC","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 4,United States of America,Strongylocentrotus purpuratus,"Coelomic fluid,Body wall","UBERON:0036217,UBERON:0000309",Microbiome measurement,EFO:0007882,Healthy coelomic fluid (HCF) and diseased coelomic fluid (DCF),Lesion body wall (LBW),Lesion body wall (LBW) samples from sea urchins with spotting disease,6,7,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S9,1 August 2024,Scholastica,Scholastica,Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples,increased,"k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Candidatus Photodesmus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudoteredinibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter",2|976|768503|768507|563798;2|1224|1236|135623|641|1076727;2|976|117743|200644|246874;2|1224|1236|135623|641|662;2|1224|1236|1706369|1706371|1122284;2|976|117743|200644|49546|358023,Complete,Svetlana up
bsdb:1018/5/1,Study 1018,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw CG, Pavloudi C, Crow RS, Saw JH , Smith LC","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 5,United States of America,Strongylocentrotus purpuratus,"Coelomic fluid,Body wall","UBERON:0036217,UBERON:0000309",Microbiome measurement,EFO:0007882,Healthy coelomic fluid (HCF) and lesion body wall (LBW),Diseased coelomic fluid (DCF),Diseased coelomic fluid (DCF) samples from sea urchins with spotting disease,10,3,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S9,1 August 2024,Scholastica,Scholastica,Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudophaeobacter",2|1224|1236|135622|267888|53246;2|1224|28211|204455|31989|1541822,Complete,Svetlana up
bsdb:1019/1/1,Study 1019,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S, Imad S, Hussain S, Xiao S, Yu X , Cao H","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 1,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Sex design,EFO:0001752,male,female,female black spotted frog,8,8,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3a,20 March 2024,Idiaru angela,"Idiaru angela,Scholastica",differential abundance of bacteria genera in frog guts between female and male frog samples.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:1019/1/2,Study 1019,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S, Imad S, Hussain S, Xiao S, Yu X , Cao H","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 1,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Sex design,EFO:0001752,male,female,female black spotted frog,8,8,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3a,20 March 2024,Idiaru angela,"Idiaru angela,Scholastica",Differential abundance of bacterial genera in frog guts between male and female frog samples.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Aquaspirillaceae|g__Laribacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus",2|1224|28216|206351|2897176|168470;2|1239|91061|1385|186823|432330,Complete,Svetlana up
bsdb:1019/2/1,Study 1019,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S, Imad S, Hussain S, Xiao S, Yu X , Cao H","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 2,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Infectious meningitis,EFO:0000584,H: uninfected individuals,NH: infected individuals,frogs found to be infected with Meningitis-like infectious diseases.,8,8,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3b,20 March 2024,Idiaru angela,Idiaru angela,comparison of gut bacterial communities in frogs between healthy and unhealthy frog samples,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:1019/2/2,Study 1019,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S, Imad S, Hussain S, Xiao S, Yu X , Cao H","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 2,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Infectious meningitis,EFO:0000584,H: uninfected individuals,NH: infected individuals,frogs found to be infected with Meningitis-like infectious diseases.,8,8,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3b,20 March 2024,Idiaru angela,Idiaru angela,comparison of gut bacterial communities in frogs between healthy and unhealthy frog samples,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|74201|203494|48461|1647988|239934;2|976|200643|171549|1853231|283168,Complete,Svetlana up
bsdb:1020/1/1,Study 1020,case-control,38491387,10.1186/s12866-024-03233-4,NA,"Chen H, Jiang X, Zhu F, Yang R, Yu X, Zhou X , Tang N",Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma,BMC microbiology,2024,"Amplicon sequencing analysis, Early esophageal cancer, Gastric microbiome, Intramucosal esophageal squamous carcinoma, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,NC_oral - No carcinoma.,EIESC_oral - Early-stage intramucosal esophageal squamous carcinoma.,Patients diagnosed with Early-stage Intramucosal Esophageal Squamous Carcinoma (EIESC) who provided Oral samples (saliva).,21,31,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig. 5A,20 March 2024,Victoria,Victoria,"LEfSe analysis. Plot of LDA Effect Size. The length of the bar column represents the LDA score.
The figure shows the oral microbial taxa with significant differences between the EIESC (orange) and Control (green) (LDA score>2)",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter",2|32066|203490|203491;2|32066|203490;2|32066;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|508458|649775|649776|3029088|638847,Complete,Svetlana up
bsdb:1020/1/2,Study 1020,case-control,38491387,10.1186/s12866-024-03233-4,NA,"Chen H, Jiang X, Zhu F, Yang R, Yu X, Zhou X , Tang N",Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma,BMC microbiology,2024,"Amplicon sequencing analysis, Early esophageal cancer, Gastric microbiome, Intramucosal esophageal squamous carcinoma, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,NC_oral - No carcinoma.,EIESC_oral - Early-stage intramucosal esophageal squamous carcinoma.,Patients diagnosed with Early-stage Intramucosal Esophageal Squamous Carcinoma (EIESC) who provided Oral samples (saliva).,21,31,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig. 5A,20 March 2024,Victoria,Victoria,"LEfSe analysis. Plot of LDA Effect Size. The length of the bar column represents the LDA score.
The figure shows the oral microbial taxa with significant differences between the EIESC (orange) and Control (green) (LDA score > 2).",decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Bacteria|p__Thermomicrobiota|c__Thermomicrobia",2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|1239|186801|186802|31979|1485;2|29547|3031852;2|142182|219685|219686;2|1224|1236|135614|32033|68;2|201174|1760|85006|85017;2|3027942|189775,Complete,Svetlana up
bsdb:1020/2/NA,Study 1020,case-control,38491387,10.1186/s12866-024-03233-4,NA,"Chen H, Jiang X, Zhu F, Yang R, Yu X, Zhou X , Tang N",Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma,BMC microbiology,2024,"Amplicon sequencing analysis, Early esophageal cancer, Gastric microbiome, Intramucosal esophageal squamous carcinoma, Oral microbiome",Experiment 2,China,Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Esophageal squamous cell carcinoma,EFO:0005922,No Carcinoma (NC)_gastric,Early-stage Intramucosal Esophageal Squamous Carcinoma  (EIESC)_gastric,Patients diagnosed with Early-stage Intramucosal Esophageal Squamous Carcinoma (EIESC) who provided Gastric biopsy samples.,21,31,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1021/1/1,Study 1021,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y, Tun HM, Ng SC, Wai HK, Zhang X, Parks J, Field CJ, Mandhane P, Moraes TJ, Simons E, Turvey SE, Subbarao P, Brook JR, Takaro TK, Scott JA, Chan FK , Kozyrskyj AL",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Early infants (3 months) with maternal history of  'NO' 'smoking,Early infants (3 months) with maternal history of  'YES' 'smoking,"Infants (3 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 2B, Supplementary Table S8",21 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed early infants (3 months old),increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239;2|1224|28216|80840;2|1239|186801;2|1239|186801|3082720|186804|1870884;2|1239|186801|186802;2|1239|186801|186802|216572|946234;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|186801|3085636;2|1239|186801|3085636|186803|2316020|33038;2|1239|909932|1843489|31977|906;2|1239|909932;2|1239|186801|186802|216572;2|1239|186801|186802|216572;2|1239|186801|3082720|186804;2|1239|186801|3082720;2|1239|909932|909929;2|1224|28216|80840|995019|40544;2|1224|28216|80840|995019;2|1239|1737404|1737405;2|1239|909932|1843489|31977;2|1239|909932|1843489;2|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:1021/1/2,Study 1021,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y, Tun HM, Ng SC, Wai HK, Zhang X, Parks J, Field CJ, Mandhane P, Moraes TJ, Simons E, Turvey SE, Subbarao P, Brook JR, Takaro TK, Scott JA, Chan FK , Kozyrskyj AL",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Early infants (3 months) with maternal history of  'NO' 'smoking,Early infants (3 months) with maternal history of  'YES' 'smoking,"Infants (3 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 2B, Supplementary Table S8",21 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed early infants (3 months old),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|186801|3085636|186803|572511;2|1224|1236|135625|712|724;2|201174|1760|85006|1268;2|201174|1760|85006;2|1239|186801|186802|216572;2|1224|1236|135625|712;2|1224|1236|135625;2|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:1021/2/1,Study 1021,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y, Tun HM, Ng SC, Wai HK, Zhang X, Parks J, Field CJ, Mandhane P, Moraes TJ, Simons E, Turvey SE, Subbarao P, Brook JR, Takaro TK, Scott JA, Chan FK , Kozyrskyj AL",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Late infants (12months) with maternal history of  'NO' 'smoking,Late infants (12months) with maternal history of  'YES' 'smoking,"Infants (12 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 2B, Supplementary Table S8",22 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed late infants (12 months old),increased,"k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2|200940|3031449|213115|194924|35832;2|1239|186801|186802|3085642;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|1980681;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|200940|3031449;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572;2|1239|186801|186802|216572;2|1224|28216|80840|995019|40544;2|200940;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:1021/2/2,Study 1021,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y, Tun HM, Ng SC, Wai HK, Zhang X, Parks J, Field CJ, Mandhane P, Moraes TJ, Simons E, Turvey SE, Subbarao P, Brook JR, Takaro TK, Scott JA, Chan FK , Kozyrskyj AL",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Late infants (12months) with maternal history of  'NO' 'smoking,Late infants (12months) with maternal history of  'YES' 'smoking,"Infants (12 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 2B, Supplementary Table S8",22 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed late infants (12 months old),decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|28050;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:1022/1/1,Study 1022,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD , Foster JT",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 1,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Pseudogymnoascus Destructans (PD) Negative,Pseudogymnoascus Destructans (PD) positive,Myotis lucifugus Bats species infected with Pseudogymnoascus destructans (Pd).,29,81,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Results Text and Fig 4,21 March 2024,MyleeeA,MyleeeA,Taxonomic differential abundance analyses in Pseudogymnoascus destructans (Pd)-positive and Pseudogymnoascus destructans (Pd)-negative M.  lucifugus.,increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,2|201174|1760|85010|2070,Complete,Svetlana up
bsdb:1022/1/2,Study 1022,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD , Foster JT",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 1,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Pseudogymnoascus Destructans (PD) Negative,Pseudogymnoascus Destructans (PD) positive,Myotis lucifugus Bats species infected with Pseudogymnoascus destructans (Pd).,29,81,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Results Text and Fig 4,21 March 2024,MyleeeA,MyleeeA,Taxonomic differential abundance analyses in Pseudogymnoascus destructans (Pd)-positive and Pseudogymnoascus destructans (Pd)-negative M. lucifugus.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae",2|1224|28211|356|118882;2|1224|1236|135613;2|976|768503|768507|89373;2|1224|28211|356|82115,Complete,Svetlana up
bsdb:1022/2/NA,Study 1022,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD , Foster JT",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 2,United States of America,Perimyotis subflavus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Pseudogymnoascus Destructans (PD) Negative,Pseudogymnoascus Destructans (PD) positive,Perimyotis subflavus Bats species infected with Pseudogymnoascus destructans (Pd).,43,95,NA,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1022/3/1,Study 1022,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD , Foster JT",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 3,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Batsskin swaps,Substrate (Environmental swaps),Substrate swab samples simultaneously collected from the ceiling or walls of each hibernaculum at least 10 cm from the bat species.,154,70,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure S8,21 March 2024,MyleeeA,MyleeeA,Bacterial differential abundance between bat and substrate samples.,increased,"k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylocystaceae,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae|s__bacterium Ellin6075",2|201174|1497346|1154584|1154585;2|1224|28211|356|45401;2|40117|203693|189778|189779;2|201174|1760|85010|2070;2|1224|28211|204441|41295;2|1224|28211|204457|41297;2|200940|3024408|213462|213465;2|1224|1236|1775403|568386;2|203682|203683|2691355|1914233;2|1224|28211|356|31993;2|203682|203683|2691354|2691357;2|57723|204432|204433|204434|234266,Complete,Svetlana up
bsdb:1022/3/2,Study 1022,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD , Foster JT",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 3,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Batsskin swaps,Substrate (Environmental swaps),Substrate swab samples simultaneously collected from the ceiling or walls of each hibernaculum at least 10 cm from the bat species.,154,70,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure S8,21 March 2024,MyleeeA,MyleeeA,Bacterial differential abundance between bat and substrate samples.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1224|1236|72274|135621;2|1224|1236|91347|543;2|201174|1760|85006|1268;2|1239|91061|1385|90964;2|1239|91061|1385|186818;2|1239|91061|186826|186828;2|1239|91061|186826|1300,Complete,Svetlana up
bsdb:1023/1/1,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,123,Illumina,LEfSe,0.05,TRUE,2,date,NA,unchanged,decreased,NA,NA,NA,decreased,Signature 1,Table S1D + Figure S1M,8 April 2024,Joan Chuks,"Joan Chuks,Adeitan",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|3118652|2039240;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816|818;2|976|200643;2|976;2|1239|186801|3085636|186803|572511;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|186801|3085636|186803;2|976|200643|171549|815|909656;2|1239|186801|3085636|186803|2719313,Complete,NA
bsdb:1023/1/2,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,123,Illumina,LEfSe,0.05,TRUE,2,date,NA,unchanged,decreased,NA,NA,NA,decreased,Signature 2,Table S1D + Figure S1M,8 April 2024,Joan Chuks,Joan Chuks,Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Beduinibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Ihubacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",2|201174|1760;2|1239|186801|186802|3082771|1918385;2|976|200643|171549|2005519;2|1239|186801|3082768|990719|1987009;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802|3085642|580596;2|1239|186801|3082768|990719|990721;2|1239|186801|186802|1980681;2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|33042;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924|872|876;2|1239|186801|186802|543314;2|1239|186801|3085636|186803|2005359;2|1224|1236|135625|712|724;2|1239|186801|186802|543314|1926667;2|1224|28211|204441|597359;2|1239|186801|3085636|186803|2163168;2|1239|186801|3085636|186803|1763508;2|200940|3031449|213115|194924|1981028;2|1239|186801|3082720|3030910|86331;2|1239|186801|3085656|3085657|2039302;2|201174|1760|85007;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1224|28216|80840|75682|846;2|1224|28216|80840|75682;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|837;2|1224|28211|204441;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775;2|508458;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281|191303|154288,Complete,NA
bsdb:1023/2/1,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,4,Illumina,LEfSe,0.05,TRUE,2,date,NA,increased,increased,NA,NA,NA,increased,Signature 1,Table S1D + Figure S1M,12 April 2024,Joan Chuks,Joan Chuks,Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Iamiaceae|g__Aquihabitans|s__Aquihabitans daechungensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia languida,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium lindanitolerans,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Intrasporangium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Micropruina,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Ohtaekwangia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus siganidrum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia koreensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",2|1224|1236|135625|712|416916|739;2|1224|1236|135622|72275|111142;2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|1283313|76122;2|1239|1737404|1737405|1570339|165779|54007;2|1239|1737404|1737405|1570339|165779|938293;2|1239|1737404|1737405|1570339|165779|33037;2|201174|84992|84993|633392|1648491|1052257;2|201174|84998|84999|1643824|1380;2|976|200643|171549;2|976|200643;2|976;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294|194|204;2|29547|3031852|213849|72294|194|827;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|29547;2|95818;2|976|117743|200644|49546|1016|1019;2|1239|186801;2|201174|84998;2|200940|3031449|213115|194924;2|1239|909932|1843489|31977|39948|309120;2|201174|1760|85007|85029|37914;2|201174|1760|85007|85029;2|976|117743|200644|2762318|59734;2|29547|3031852;2|1239|186801|186802|216572|253238;2|1239|186801|186802|186806;2|1239|186801|186802;2|1239|186801|186802|543314;2|1239|186801|186802|186806|1730;2|1239|91061|186826|186827|66831|82347;2|976|117743|200644;2|976|117743;2|976|117743|200644|49546|237|428988;2|976|768503|768507|2762286;2|201174|1760|85004|31953|2701;2|203682|203683|2691355|1914233;2|201174|1760|85006|85021;2|201174|1760|85006|85021|53357;2|1224|28216|206351|481|32257;2|1224|28216|206351|481|32257|505;2|201174|1760|85007|2805586|1847725;2|201174|1760|85007|2805586;2|1224|1236|135614|32033|68;2|1239|909932|1843489|31977|906;2|1224|28216|32003|32011|16;2|201174|1760|85009|85015|116071;2|1239|186801|3082720|3030910|86331;2|1239|909932|1843489|31977|909928;2|1239|909932;2|976|768503|768507|2762286|1210119;2|1224|28211|204455|31989|265|1276757;2|1239|1737404|1737405|1570339;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836|501496;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|28133;2|976|200643|171549|171552;2|1224|1236|118969|118968|59195;2|201174|1760|85006|1268|32207|592378;2|976|200643|171549|171552|2974251|228604;2|1224|28216|80840|114248;2|1239|91061|1385|186824;2|1239|909932|1843489|31977;2|1239|909932|1843489;2|976|117743|200644|2762318,Complete,NA
bsdb:1023/2/2,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,4,Illumina,LEfSe,0.05,TRUE,2,date,NA,increased,increased,NA,NA,NA,increased,Signature 2,Table S1D + Figure S1M,12 April 2024,Joan Chuks,"Joan Chuks,Adeitan",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus yeei,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas ginsengisoli (ex Hoang et al. 2012),k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Patulibacteraceae|g__Patulibacter|s__Patulibacter minatonensis,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Roseisolibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales",2|201174;2|201174|1760|2037|2049|1653174;2|976|200643|171549|2005519|397864;2|976|200643|171549|2005519;2|1224|28211|356|45404;2|201174|1760|85009|31957|1912216;2|1239|909932|1843489|31977|39948;2|976|1853228|1853229|563835|398041;2|1239|186801|3085636|186803|140625;2|201174|1760|85006;2|1224|28211|204455|31989;2|1224|28211|204455|31989|265;2|201174|1760|85009;2|1224|28216|80840|119060|48736;2|1239|186801|3085636|186803|841;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279|1283;2|1224|1236|135614|32033|338;2|1224|28211|356|255475;2|1224|28211|204455|31989|265|147645;2|1224|28211|204457|41297|13687|1706000;2|201174|1497346|588673|361606|361607|298163;2|142182|219685|219686|219687|2093335;2|1224|28211|204455,Complete,NA
bsdb:1023/3/1,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 3,United States of America,Homo sapiens,Anterior naris,UBERON:2001427,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,123,Illumina,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S1D,12 April 2024,Joan Chuks,"Joan Chuks,Adeitan",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Salinimicrobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus senegalensis",2|201174|1760|85006|85019|1696;2|1224|28211|204458|76892;2|976|768503|768507|89373;2|201174|1760|85006|1268|1269|1270;2|1239|91061|1385|90964|1279|29388;2|976|117743|200644|49546|561367;2|976|200643|171549|171551|836|28124;2|1239|1737404|1737405|1570339|165779|1288120,Complete,NA
bsdb:1023/3/2,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 3,United States of America,Homo sapiens,Anterior naris,UBERON:2001427,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,123,Illumina,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S1D,12 April 2024,Joan Chuks,Joan Chuks,Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga canimorsus,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Ihubacter,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Actinomycetota|c__Nitriliruptoria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Sanguibacteraceae|g__Sanguibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila palaticanis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Allorhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium oleivorans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium testaceum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Bacteria|p__Mycoplasmatota",2|1239|91061|186826|186827|1375;2|1239|186801|3085636|186803|2569097;2|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|371601;2|201174|1760|1643682|85030|38501;2|976|200643|171549|1853231|574697;2|976|117743|200644|49546|1016|28188;2|200795|32061;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|2719313;2|1224|1236;2|201174|1760|1643682|85030;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|29547|3031852|213849|72293;2|1239|186801|186802|543314|1926667;2|544448|31969;2|1239|186801|3085656|3085657|2039302;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1224|28216|206351|481|482|484;2|201174|908620;2|1224|1236|135619;2|976|200643|171549|1853231;2|976|200643|171549|2005523|346096;2|1224|28216|206389;2|1224|28211|204441|41295;2|201174|1760|85006|145360|60919;2|976|200643|171549|171552|2974251|228604;2|1239|186801|186802|216572|292632;2|1224|1236|135614|32033|338;2|201174|1760|1643682;2|1239|186801|186802|31979|1485;2|1224|28216|206389|2008795;2|1239|91061|1385|539738|3076174|81950;2|1224|28211|356|82115|78526;2|1224|28211|204457|2820280;2|201174|1760|85006|85023|33882|273677;2|1224|28216|32003|32011|404;2|201174|1760|85006|85023|33882|2033;2|976|200643|171549|2005523;2|544448,Complete,NA
bsdb:1023/4/1,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 4,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,4,Illumina,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S1D,12 April 2024,Joan Chuks,Joan Chuks,Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales,k__Bacteria|p__Bacteroidota|c__Cytophagia",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|46125;2|1239|91061|186826|186827;2|1224|28211|204457|335929;2|1239|186801|3085636|186803|1164882|617123;2|201174|84998|84999|1643824|133925;2|976|200643|171549|171552|838|189723;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|976|768503|768507;2|976|768503,Complete,NA
bsdb:1023/4/2,Study 1023,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM , Snyder MP",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 4,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,No,16S,4,Illumina,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S1D,12 April 2024,Joan Chuks,"Joan Chuks,Adeitan",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii",2|1239|186801|3085636|186803|43996;2|1239|186801;2|1117;2|1239|186801|3082720|3118655|44259;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|3118655|44259|143361;2|1239|186801|186802;2|1239|186801|3085636|186803|265975|237576;2|32066|203490|203491|1129771|2755140|157692,Complete,NA
bsdb:1024/1/1,Study 1024,case-control,29758946,http://dx.doi. 438 org/10.3233/JAD-180176,NA,"Zhuang ZQ, Shen LL, Li WW, Fu X, Zeng F, Gui L, Lü Y, Cai M, Zhu C, Tan YL, Zheng P, Li HY, Zhu J, Zhou HD, Bu XL , Wang YJ",Gut Microbiota is Altered in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2018,"16S ribosomal RNA sequencing, Alzheimer’s disease, amyloid-β peptide, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's disease,Patients with active Alzheimer's disease,43,43,6 Months,16S,34,Illumina,LEfSe,0.01,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4 B,26 March 2024,Temitayo,"Temitayo,Peace Sandy","Differences of bacterial taxa between AD and control group b) Histogram of the LDA scores for different abundant genera. Positive LDA scores indicate the enrichment of taxa
in AD group (red) relative to control group (green), and negative LDA scores indicate the depletion of taxa in AD group relative to control group. Box shows statistically significant different bacteria",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella coagulans,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.",2|201174;2|1239|186801|186802|216572|244127;2|1239|186801|3082768|424536;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|33043;2|1239|1737404|1582879|46507;2|201174|84998|1643822|1643826|644652|471189;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|186802|216572;2|976|200643|171549|171551|836|501496;2|976|200643|171549|171552|838;2|1224|28211|204441|41295;2|1224|28211|204441;2|1239|186801|186802|31979|1266;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|292632;2|976|200643|171549|815|816|162156,Complete,Peace Sandy
bsdb:1024/1/2,Study 1024,case-control,29758946,http://dx.doi. 438 org/10.3233/JAD-180176,NA,"Zhuang ZQ, Shen LL, Li WW, Fu X, Zeng F, Gui L, Lü Y, Cai M, Zhu C, Tan YL, Zheng P, Li HY, Zhu J, Zhou HD, Bu XL , Wang YJ",Gut Microbiota is Altered in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2018,"16S ribosomal RNA sequencing, Alzheimer’s disease, amyloid-β peptide, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's disease,Patients with active Alzheimer's disease,43,43,6 Months,16S,34,Illumina,LEfSe,0.01,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4 B,26 March 2024,Temitayo,"Temitayo,Peace Sandy","Differences of bacterial taxa between AD and control group b) Histogram of the LDA scores for different abundant genera. Positive LDA scores indicate the enrichment of taxa in AD group (red) relative to control group (green), and negative LDA scores indicate the depletion of taxa in AD group relative to control group. Box shows statistically significant different bacteria",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus grandis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella secunda",2|1239|186801|3085636|186803|207244|105841;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|815|816|85831;2|1239|186801|3085636|186803|572511;2|1297|188787|118964;2|1297|188787|118964|183710|1298;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|946234|292800;2|32066|203490|203491|203492|848|856;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1898203;2|1239|186801|3085636|186803|1235800;2|1239|909932;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|909656|310297;2|1239|909932|909929;2|201174|84998|1643822|1643826|84108;2|1239|186801|3085636|186803|1213720;2|1239|526524|526525|2810280|3025755|1547;2|1224|1236|135623|641|662;2|1224|1236|135623|641;2|1224|1236|135623;2|1239|186801|186802|216572|1263;2|77133;2|1297|188787|118964|183710|1298|57498;2|1224|28216|80840|995019|577310|626947,Complete,Peace Sandy
bsdb:1025/1/1,Study 1025,"cross-sectional observational, not case-control",38387693,10.1016/j.alcohol.2024.02.003,NA,"Qiao NN, Fang Q, Zhang XH, Ke SS, Wang ZW, Tang G, Leng RX , Fan YG",Effects of alcohol on the composition and metabolism of the intestinal microbiota among people with HIV: a cross-sectional study,"Alcohol (Fayetteville, N.Y.)",2024,"Alcohol, Cross-sectional study, HIV/AIDS, Intestinal microbiota, Metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Non Drinking,Low to Moderate drinking,HIV infected persons who consume alcohol ≥1 time/month or ≥12 times/year in the last year. Individuals in the low to moderate drinking group consumed <210 g of alcohol per week.,72,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4C,21 April 2024,MyleeeA,MyleeeA,Differentially enriched bacterial taxa between low to moderate drinking and non-drinking groups in HIV-infected patients.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|526524|526525|2810280|100883;2|1239|186801|3085636|186803|46205;2|32066|203490|203491|203492|180162;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|3082720|186804|1501226;2|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:1025/1/2,Study 1025,"cross-sectional observational, not case-control",38387693,10.1016/j.alcohol.2024.02.003,NA,"Qiao NN, Fang Q, Zhang XH, Ke SS, Wang ZW, Tang G, Leng RX , Fan YG",Effects of alcohol on the composition and metabolism of the intestinal microbiota among people with HIV: a cross-sectional study,"Alcohol (Fayetteville, N.Y.)",2024,"Alcohol, Cross-sectional study, HIV/AIDS, Intestinal microbiota, Metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Non Drinking,Low to Moderate drinking,HIV infected persons who consume alcohol ≥1 time/month or ≥12 times/year in the last year. Individuals in the low to moderate drinking group consumed <210 g of alcohol per week.,72,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4C,21 April 2024,MyleeeA,MyleeeA,Differentially enriched bacterial taxa between low to moderate drinking and non-drinking groups in HIV-infected patients.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus",2|1224|1236|135614|32033;2|1224|1236|135614|32033|40323;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|1236|135614;2|1224|1236|135625|712|724;2|201174|1760|85009|31957|72763,Complete,Svetlana up
bsdb:1026/1/1,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (< 8 days),SARS-CoV-2-infected PLWH (< 8 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (< 8 days),10,10,None,16S,34,Illumina,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2C,21 March 2024,Ardeybisi,"Ardeybisi,Adenike Oladimeji-Kasumu",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH within 7 days of COVID-19 onset.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|216572|1263|41978;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|815,Complete,Svetlana up
bsdb:1026/1/2,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (< 8 days),SARS-CoV-2-infected PLWH (< 8 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (< 8 days),10,10,None,16S,34,Illumina,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2C,21 March 2024,Ardeybisi,"Ardeybisi,Adenike Oladimeji-Kasumu",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH within 7 days of COVID-19 onset.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|186801|3085636|186803|1766253;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|42322;2|1239|186801|3085636|186803|1407607;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|186804|1904861;2|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:1026/2/1,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (8–14 days),SARS-CoV-2-infected PLWH (8–14 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) 8 − 14 days after COVID-19 onset,9,9,None,16S,34,Illumina,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,8 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH  8−14 days after COVID-19 onset.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|1239|186801|3085636|186803|1164882;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|3030910|86331;2|1239|526524|526525|128827|1472649;2|201174|84998|1643822|1643826;2|201174|1760|85007|1653|1716;2|976|200643|171549|815|816;2|976|200643|171549|815,Complete,Svetlana up
bsdb:1026/2/2,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (8–14 days),SARS-CoV-2-infected PLWH (8–14 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) 8 − 14 days after COVID-19 onset,9,9,None,16S,34,Illumina,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2D,8 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH  8−14 days after COVID-19 onset.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|1239|909932|1843489|31977|906;2|1239|909932|1843488|909930|904;2|1239|909932|1843489|31977;2|1239|909932|909929;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:1026/3/1,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (>1 M),SARS-CoV-2-infected PLWH (>1 M),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) over 1 month after COVID-19 onset,7,7,None,16S,34,Illumina,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2E,8 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH over 1 month after COVID-19 onset.,increased,"k__Bacteria|p__Candidatus Saccharibacteria|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|95818|2093818|2093825|2171986|1331051;2|1224|1236|91347|1903410|204037;2|1224|1236|91347|543;2|1224|1236|91347|543|1849603;2|1224|1236;2|1224|28211|356|82115;2|1224|1236|91347;2|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:1026/3/2,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (>1 M),SARS-CoV-2-infected PLWH (>1 M),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) over 1 month after COVID-19 onset,7,7,None,16S,34,Illumina,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2E,8 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH over 1 month after COVID-19 onset.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1239|186801|3085636|186803|1766253;2|1239|186801;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|841;2|1239|186801|186802,Complete,Svetlana up
bsdb:1026/4/1,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Illness severity status,EFO:0007863,Mildly ill SARS-CoV-2-infected PLWH (8–14 days),Moderately/severely ill SARS-CoV-2-infected PLWH (8–14 days),Moderately (n = 4) and severely (n = 1) ill hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (8–14 days),6,5,None,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,body mass index,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3F,20 June 2024,Scholastica,Scholastica,"Changes in the gut microbiota in PLWH-CoV (8-14 days) analyzed by linear discriminant analysis (LDA) effect size, compared by disease severity (mild, n = 6 vs. moderate/severe, n = 5)",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,2|1239|186801|186802|216572|244127,Complete,Svetlana up
bsdb:1026/4/2,Study 1026,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Illness severity status,EFO:0007863,Mildly ill SARS-CoV-2-infected PLWH (8–14 days),Moderately/severely ill SARS-CoV-2-infected PLWH (8–14 days),Moderately (n = 4) and severely (n = 1) ill hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (8–14 days),6,5,None,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,body mass index,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3F,20 June 2024,Scholastica,Scholastica,"Changes in the gut microbiota in PLWH-CoV (8-14 days) analyzed by linear discriminant analysis (LDA) effect size, compared by disease severity (mild, n = 6 vs. moderate/severe, n = 5)",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552|1283313;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330;2|1239|186801;2|1239|186801|186802;2|1224|1236|135625|712,Complete,Svetlana up
bsdb:1027/1/1,Study 1027,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N, Jian C, Jingjing W, Zhanbo Q, Yifei S, Jing Z , Shuwen H",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Healthy,Colorectal cancer (CRC),Patients who has colorectal cancer (CRC),56,55,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig. 2B,20 March 2024,Ayibatari,"Ayibatari,Scholastica",Gut microbiota with significant differences in colorectal cancer (CRC) patients compared to healthy individuals.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales",2|1224|1236|2887326|468|469;2|201174|1760|2037|2049|1654;2|1224|1236|135624|84642|642;2|1224|1236|135625|712|416916;2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|419014;2|1239|909932|1843489|31977|156454;2|1224|28216|80840|92793;2|201174|1760|85006|1268|1663;2|1224|28211|356|41294|374;2|1224|28211|204458|76892|41275;2|976|200643|171549|1853231|574697;2|1239|186801|3082768|990719|990721;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|538;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|91061|1385|33986;2|508458|649775|649776|3029087|1434006;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|1506553;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|3030910|86331;2|1224|1236|91347|1903414|581;2|201174|84998|84999|1643824|133925;2|976|200643|171549|2005525|375288;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3082720|186804|1257;2|201174|1760|85009|31957|1743;2|1239|186801|186802|186806|113286;2|1224|28216|80840|119060|48736;2|1224|1236|91347|543|160674;2|201174|1760|85007|85025|1827;2|201174|1760|85004|31953|196081;2|1239|909932|909929|1843491|970;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827|123375;2|1224|28211|204457|41297|13687;2|1239|91061|186826|1300|1301;2|1224|28216|80840|80864;2|201174|84998|84999;2|1224|1236|91347|543;2|1239|91061|186826,Complete,Svetlana up
bsdb:1027/1/2,Study 1027,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N, Jian C, Jingjing W, Zhanbo Q, Yifei S, Jing Z , Shuwen H",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Healthy,Colorectal cancer (CRC),Patients who has colorectal cancer (CRC),56,55,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig. 2B,19 June 2024,Scholastica,Scholastica,Gut microbiota with significant differences in colorectal cancer (CRC) patients compared to healthy individuals.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis",2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1766253;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|1263;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|2316020|33039;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|189330;2|1239|186801|186802|186806|1730|290054;2|1239|526524|526525|128827|331630;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730|39496;2|976|200643|171549|171550|239759;2|1239|186801|3085656|3085657|2039302;2|1224|28216|80840|995019|577310;2|1239|186801|186802|216572;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|877420;2|32066|203490|203491|1129771|168808;2|1239|1980693;2|1239|186801|3085636|186803|1506577;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|28050;2|1239|186801|186802|216572|459786;2|200940|3031449|213115|194924|35832;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572;2|1239|186801|3082768|424536;2|1239|186801|186802|1980681;2|1239|526524|526525|128827|1573534;2|1239|186801|186802|216572|3028852,Complete,Svetlana up
bsdb:1027/2/1,Study 1027,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N, Jian C, Jingjing W, Zhanbo Q, Yifei S, Jing Z , Shuwen H",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Leukopenia,EFO:0004233,Normal leukocytes,Hypoleukocytes,Colorectal cancer patients with lower-than-normal levels of leukocytes (below 3.5 × 10^9/L) after chemotherapy,42,13,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig. 6B,20 March 2024,Ayibatari,"Ayibatari,Scholastica",Gut microbiota with significant differences in colorectal cancer (CRC) patients with hypoleukocytes compared to normal leukocytes.,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Candidatus Saccharibacteria",2|32066|203490|203491|203492|180162;2|1239|526524|526525|2810280|1279384;2|1239|91061|186826|186828|117563;2|95818,Complete,Svetlana up
bsdb:1027/2/2,Study 1027,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N, Jian C, Jingjing W, Zhanbo Q, Yifei S, Jing Z , Shuwen H",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Leukopenia,EFO:0004233,Normal leukocytes,Hypoleukocytes,Colorectal cancer patients with lower-than-normal levels of leukocytes (below 3.5 × 10^9/L) after chemotherapy,42,13,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig. 6B,20 March 2024,Ayibatari,"Ayibatari,Scholastica",Gut microbiota with significant differences in colorectal cancer (CRC) patients with hypoleukocytes compared to normal leukocytes.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Eukaryota|p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|1239|186801|3082768|990719|990721;2|1239|526524|526525|2810280|100883;2|201174|84998|84999|84107|1472762;2|1224|1236|91347|543|1940338;2|1239|186801|186802|186806|1730|42322;2|1239|1737404|1582879;2|32066|203490|203491|203492|848;2|1224|1236|91347|543|570;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|216572|459786;2759|2763|2806|31370|31371|2729669;2|1239|186801|3082720|186804|1849822;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|1506577;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|216572;2|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:1028/1/1,Study 1028,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González RA, Peña-Rodríguez M, Pereira-Suárez AL, Rubio-Sánchez AX, García-Chagollán M, Valenzuela-Orozco DN, Lizarazo-Taborda MDR, Mora-Mora J , Vega-Magaña N",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 1,Mexico,Homo sapiens,Saliva,UBERON:0001836,Menopause,EFO:0003922,Premenopausal women group,Postmenopausal women group,Postmenopausal women with COVID-19,20,18,30 days,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3c,20 March 2024,EniolaAde,"EniolaAde,Scholastica",DeSeq2 deferentially abundant taxa in premenopausal women compared to postmenopausal women group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",2|976|200643|171549|171552|1283313;2|1224|1236|135625|712|724;2|976|200643|171549|171552|2974257|425941;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838|28132,Complete,Svetlana up
bsdb:1028/1/2,Study 1028,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González RA, Peña-Rodríguez M, Pereira-Suárez AL, Rubio-Sánchez AX, García-Chagollán M, Valenzuela-Orozco DN, Lizarazo-Taborda MDR, Mora-Mora J , Vega-Magaña N",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 1,Mexico,Homo sapiens,Saliva,UBERON:0001836,Menopause,EFO:0003922,Premenopausal women group,Postmenopausal women group,Postmenopausal women with COVID-19,20,18,30 days,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3c,26 March 2024,EniolaAde,"EniolaAde,Scholastica",DeSeq2 deferentially abundant taxa in premenopausal women compared to postmenopausal women group,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,2|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:1028/2/1,Study 1028,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González RA, Peña-Rodríguez M, Pereira-Suárez AL, Rubio-Sánchez AX, García-Chagollán M, Valenzuela-Orozco DN, Lizarazo-Taborda MDR, Mora-Mora J , Vega-Magaña N",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 2,Mexico,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Adequate oral health group,Poor oral health group,"COVID-19 patients with poor oral health status. Patients were classified as having poor oral health when there were more than two caries, hygiene index higher than 2.5, gingival inflammation between 2–3 and bleeding when toothbrushing.",NA,NA,30 days,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3f,22 March 2024,EniolaAde,"EniolaAde,Scholastica",DESeq2 differentially abundant taxa in poor oral health group compared to adequate oral health group,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1224|28216|206351|481|482|33053;2|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:1028/2/2,Study 1028,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González RA, Peña-Rodríguez M, Pereira-Suárez AL, Rubio-Sánchez AX, García-Chagollán M, Valenzuela-Orozco DN, Lizarazo-Taborda MDR, Mora-Mora J , Vega-Magaña N",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 2,Mexico,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Adequate oral health group,Poor oral health group,"COVID-19 patients with poor oral health status. Patients were classified as having poor oral health when there were more than two caries, hygiene index higher than 2.5, gingival inflammation between 2–3 and bleeding when toothbrushing.",NA,NA,30 days,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3f,22 March 2024,EniolaAde,"EniolaAde,Scholastica",DESeq2 differentially abundant taxa in poor oral health group compared to adequate oral health group,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|s__uncultured Bacteroidetes bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171552|1283313;2|976;2|1239|186801|186802|1898207;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|1283313;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|976|152509;2|1224|1236|135625|712|724;2|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:1028/3/1,Study 1028,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González RA, Peña-Rodríguez M, Pereira-Suárez AL, Rubio-Sánchez AX, García-Chagollán M, Valenzuela-Orozco DN, Lizarazo-Taborda MDR, Mora-Mora J , Vega-Magaña N",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 3,Mexico,Homo sapiens,Saliva,UBERON:0001836,Viral load,EFO:0010125,Moderate SARS-CoV-2 viral load group,High SARS-CoV-2 viral load group,COVID-19 patients with high SARS-CoV-2 viral load,11,41,30 days,16S,34,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3i,22 March 2024,EniolaAde,"EniolaAde,Scholastica",DESeq2 differentially abundant taxa in moderate compared to high SARS-CoV-2 viral load group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|s__uncultured Bacteroidetes bacterium",2|976|200643|171549|171552|1283313;2|1224|1236|135625|712|724;2|976|200643|171549|171552|2974257|425941;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|838|28132;2|976|152509,Complete,Svetlana up
bsdb:1029/1/1,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 1,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women & High‑risk human papillomavirus(HR-HPV) Infected Women (HPV),Bacterial Vaginosis (BV) Infected Women,"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with Bacterial Vaginosis (BV) Infection.",136,52,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,22 April 2024,Joan Chuks,Joan Chuks,Bacterial Taxa differentially abundant in the vaginal microbiome of Bacterial Vaginosis (BV) Infected women compared to Normal healthy women & High‑risk human papillomavirus(HR-HPV) Infected Women as determined by LEfSe Analysis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549;2|976|200643;2|976;2|976|200643|171549|171552|2974257|386414;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Svetlana up
bsdb:1029/2/1,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 2,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women & Bacterial Vaginosis (BV) Infected Women,High‑risk human papillomavirus(HR-HPV) Infected Women (HPV),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with High‑risk human papillomavirus (HR-HPV) infection.",117,71,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,22 April 2024,Joan Chuks,Joan Chuks,Bacterial Taxa differentially abundant in the vaginal microbiome of High‑risk human papillomavirus(HR-HPV) Infected Women compared to Normal healthy women & Bacterial Vaginosis (BV) Infected Women as determined by LEfSe Analysis.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,2|1239|91061|186826|33958|1578|147802,Complete,Svetlana up
bsdb:1029/3/1,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 3,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women,Bacterial vaginosis (BV) infected women & High‑risk human papillomavirus (HR-HPV) (HPV) infected Women,"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with Bacterial vaginosis (BV) infection and those diagnosed with High‑risk human papillomavirus (HR-HPV) infection.",65,123,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,22 April 2024,Joan Chuks,Joan Chuks,Bacterial Taxa differentially abundant in the vaginal microbiome of  Bacterial Vaginosis (BV) infected women and High‑risk human papillomavirus (HR-HPV) infected women compared to Normal healthy women as determined by LEfSe Analysis.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061;2|1239;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:1029/4/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 4,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women,High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",65,48,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,unchanged,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/5/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 5,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women,Bacteial Vaginosis (BV) & High‑risk human papillomavirus(HR-HPV) with Cervical Intraepithelial Neoplasia(CIN) co-infected women (BHC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with co-infection of Bacteial Vaginosis (BV) & High‑risk human papillomavirus (HR-HPV) in combination with Cervical Intraepithelial Neoplasia (CIN).",65,46,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/6/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 6,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Bacterial Vaginosis (BV) Infected Women,High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",52,48,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,decreased,decreased,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/7/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 7,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,High‑risk human papillomavirus (HR-HPV) Infected Women (HPV),High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",71,48,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,decreased,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/8/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 8,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Bacterial vaginosis (BV) and High‑risk human papillomavirus (HR-HPV) (HPV) co-infected Women (BH),High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",60,48,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/9/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 9,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,High‑risk human papillomavirus(HR-HPV) Infected Women (HPV),Bacteial Vaginosis (BV) & High‑risk human papillomavirus(HR-HPV) with Cervical Intraepithelial Neoplasia(CIN) co-infected women (BHC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with with co-infection of Bacteial Vaginosis (BV) & High‑risk human papillomavirus (HR-HPV) in combination with Cervical Intraepithelial Neoplasia (CIN).",71,46,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/10/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 10,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),Bacteial Vaginosis (BV) & High‑risk human papillomavirus(HR-HPV) with Cervical Intraepithelial Neoplasia(CIN) co-infected women (BHC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with with co-infection of Bacteial Vaginosis (BV) & High‑risk human papillomavirus (HR-HPV) in combination with Cervical Intraepithelial Neoplasia (CIN).",48,46,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/11/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 11,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women,Bacterial Vaginosis (BV) Infected Women,"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with Bacterial Vaginosis (BV) Infection.",65,52,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/12/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 12,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women,High‑risk human papillomavirus(HR-HPV) Infected Women (HPV),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with High‑risk human papillomavirus (HR-HPV) infection.",65,71,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1029/13/NA,Study 1029,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X, Zhang Y, Yu L, Shi X, Min M, Xiong L, Pan J, Liu P, Wu G , Gao G","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 13,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Vaginal microbiome measurement,EFO:0011013,Normal Healthy Women,Bacterial vaginosis (BV) and High‑risk human papillomavirus (HR-HPV) (HPV) co-infected Women (BH),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with co-infection of Bacterial vaginosis (BV) and High‑risk human papillomavirus (HR-HPV).",65,71,30 days,16S,34,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1031/1/1,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,Controls,Covid-19,Patients who tested positive for SARS-CoV-2 based on nasopharyngeal swabs and who did not require intensive care at admission.,54,46,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Results text (Page 3),4 May 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa between COVID-19 positive patients versus controls,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,2|976|200643|171549|171552|838|60133,Complete,Svetlana up
bsdb:1031/1/2,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,Controls,Covid-19,Patients who tested positive for SARS-CoV-2 based on nasopharyngeal swabs and who did not require intensive care at admission.,54,46,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Results text (Page 3),4 May 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa between COVID-19 positive patients versus controls,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1306,Complete,Svetlana up
bsdb:1031/2/1,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Saliva Negative,SARS Cov-2 Saliva Positive,COVID-19 patients with positive SARS-CoV-2 viral load in saliva,15,28,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3,22 April 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive (pink) versus -negative (blue) saliva,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum sp.",2|976|200643|171549|171552|838|60133;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|1305;2|203691|203692|136|2845253|157|166;2|976|200643|171549|171552|1283313|712469;2|201174|1760|2037|2049|1654|712118;2|201174|1760|2037|2049|1654|651609;2|1239|186801|3085636|186803|1213720|1984869,Complete,Svetlana up
bsdb:1031/2/2,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Saliva Negative,SARS Cov-2 Saliva Positive,COVID-19 patients with positive SARS-CoV-2 viral load in saliva,15,28,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3,22 April 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive (pink) versus -negative (blue) saliva,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 356",2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|2974251|28135;2|1239|91061|186826|1300|1301|68891;2|1239|91061|186826|1300|1301|1306;2|95818|713057,Complete,Svetlana up
bsdb:1031/3/1,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Negative,SARS Cov-2 Low Viral Load,Patients who tested positive to SARS Cov-2 with low viral load (CT>30) in saliva,15,14,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with low viral load (pink) versus negative (blue) saliva,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 074,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum sp.",2|32066|203490|203491|203492|848|860;2|976|200643|171549|171552|838|60133;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|1305;2|201174|1760|2037|2049|1654|651609;2|201174|1760|2037|2049|1654|712118;2|976|200643|171549|171552|1283313|712469;2|1239|91061|186826|1300|1301|712631;2|1239|186801|3085636|186803|1213720|1984869,Complete,Svetlana up
bsdb:1031/3/2,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Negative,SARS Cov-2 Low Viral Load,Patients who tested positive to SARS Cov-2 with low viral load (CT>30) in saliva,15,14,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with low viral load (pink) versus negative (blue) saliva,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 351,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 356",2|201174|1760|2037|2049|1654|114702;2|32066|203490|203491|203492|848|155615;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|2974251|28135;2|976|200643|171549|171552|2974251|228604;2|976|200643|171549|171552|838|712461;2|1239|91061|186826|1300|1301|1306;2|95818|713053;2|95818|713057,Complete,Svetlana up
bsdb:1031/4/1,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2 Negative,SARS-CoV-2 High Viral load,Patients who tested positive to SARS-CoV-2 with high (CT<30) viral load in saliva,15,14,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with high viral load (pink) versus negative (blue) saliva,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 074,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.",2|976|200643|171549|171552|838|60133;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|1305;2|976|200643|171549|171552|1283313|712469;2|1239|91061|186826|1300|1301|712631;2|1239|186801|3085636|186803|1213720|1984869;2|201174|1760|2037|2049|1654|712118;2|201174|1760|2037|2049|1654|29317,Complete,Svetlana up
bsdb:1031/4/2,Study 1031,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC , Abrams JA",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2 Negative,SARS-CoV-2 High Viral load,Patients who tested positive to SARS-CoV-2 with high (CT<30) viral load in saliva,15,14,None,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with high viral load (pink) versus negative (blue) saliva,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 356,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 304,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 066",2|32066|203490|203491|203492|848|155615;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|2974251|28135;2|976|200643|171549|171552|2974251|228604;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|68891;2|1239|91061|186826|1300|1301|1306;2|95818|713057;2|976|200643|171549|171552|838|712459;2|1239|91061|186826|1300|1301|712626,Complete,Svetlana up
bsdb:1032/1/1,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Healthy controls,Patients with Hepatocellular carcinoma (HCC),"patients with viral related hepatocellular carcinoma or non-hepatitis B-, non-hepatitis C-related hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",16,51,within 2 weeks of fecal sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,25 April 2024,Idiaru angela,Idiaru angela,The significant taxa from the top 50 relative abundance genus level compared between healthy controls and Hepatocellular carcinoma patients.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|976|200643|171549|815|816;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33038;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:1032/1/2,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Healthy controls,Patients with Hepatocellular carcinoma (HCC),"patients with viral related hepatocellular carcinoma or non-hepatitis B-, non-hepatitis C-related hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",16,51,within 2 weeks of fecal sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,25 April 2024,Idiaru angela,Idiaru angela,The significant taxa from the top 50 relative abundance genus level compared between healthy controls and Hepatocellular carcinoma patients.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3082720|186804|1501226;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:1032/2/1,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,within 2 weeks of fecal sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Table 3,26 April 2024,Idiaru angela,Idiaru angela,The significant taxa from the top 50 relative abundance genus level compared between Viral- and NBNC-HCC,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|976|200643|171549|815|816;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|2005525|375288;2|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:1032/2/2,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,within 2 weeks of fecal sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Table 3,26 April 2024,Idiaru angela,Idiaru angela,The significant taxa from the top 50 relative abundance genus level compared between Viral- and NBNC-HCC,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|216572|292632;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:1032/3/1,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,within 2 weeks of fecal sample collection,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 4B,26 April 2024,Idiaru angela,Idiaru angela,LEfSe identifies the microbiota that differed the most between NBNC-HCC and Viral-HCC,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",2|1239|186801|186802|31979;2|1239|186801|186802;2|1239|186801|186802|216572;2|1239|91061|186826;2|1239|91061|186826|186828;2|1239|91061|186826|186828|117563;2|1239;2|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:1032/3/2,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,within 2 weeks of fecal sample collection,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 4B,26 April 2024,Idiaru angela,Idiaru angela,LEfSe identifies the microbiota that differed the most between NBNC-HCC and Viral-HCC,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|186801|3085636;2|1239|186801|3085636|186803;2|976;2|976|200643;2|976|200643|171549;2|976|200643|171549|171552,Complete,Svetlana up
bsdb:1032/4/NA,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 4,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Healthy controls,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",16,18,within 2 weeks of fecal sample collection,16S,34,Illumina,NA,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1032/5/NA,Study 1032,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N , Tangkijvanich P",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 5,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,Hepatitis-B virus related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",17,18,within 2 weeks of fecal sample collection,16S,34,Illumina,NA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1033/1/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 1,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,PTC patients with mild lesions (T1_2),PTC patients with advanced lesions (T3_4),Papillary thyroid cancer (PTC) patients with advanced lesions.,64,16,NA,16S,34,Illumina,LEfSe,0.05,TRUE,3.2,NA,NA,NA,increased,NA,decreased,NA,unchanged,Signature 1,Figure 2g and 2h,24 April 2024,Aleru Divine,Aleru Divine,"Taxonomic cladogram from LEfSe, depicting taxonomic associations between microbiome communities from patients with T1_2 and T3_4 PTC and LDA score computed from differentially abundant features between T1_2 and T3_4.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|28211|356;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|201174|84998|84999;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724,Complete,NA
bsdb:1033/1/2,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 1,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,PTC patients with mild lesions (T1_2),PTC patients with advanced lesions (T3_4),Papillary thyroid cancer (PTC) patients with advanced lesions.,64,16,NA,16S,34,Illumina,LEfSe,0.05,TRUE,3.2,NA,NA,NA,increased,NA,decreased,NA,unchanged,Signature 2,Figure 2g and 2h,24 April 2024,Aleru Divine,Aleru Divine,"Taxonomic cladogram from LEfSe, depicting taxonomic associations between microbiome communities from patients with T1_2 and T3_4 PTC and LDA score computed from differentially abundant features between T1_2 and T3_4.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|1236|72274|135621;2|1224|1236|72274|135621|286;2|1224|1236|72274;2|201174|1760|85007;2|201174|1760|85007|85025;2|201174|1760|85007|85025|1827;2|1224|28211|204457;2|1224|28211|204457|41297;2|1224|28211|204457|41297|13687,Complete,NA
bsdb:1033/2/NA,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 2,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T2,Patients with Papillary thyroid cancer (PTC) at clinical stage T2.,35,29,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1033/3/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 3,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,35,10,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,Aleru Divine,"Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|1236|72274|135621|286;2|201174|1760|85007|85025|1827;2|1224|28211|204457|41297|13687,Complete,NA
bsdb:1033/4/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 4,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,35,6,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,Aleru Divine,"Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,NA
bsdb:1033/5/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 5,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,29,10,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,Aleru Divine,"Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|1236|72274|135621|286;2|1224|28211|204457|41297|13687,Complete,NA
bsdb:1033/6/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 6,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,29,6,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,Aleru Divine,"Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,2|1224|1236|72274|135621|286,Complete,NA
bsdb:1033/7/NA,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 7,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T3,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,10,6,NA,16S,34,Illumina,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1033/8/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 8,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Male Patients with PTC (G1),Female Patients with PTC (G2),Female Patients with Papillary thyroid cancer (PTC),19,61,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,decreased,NA,unchanged,Signature 1,Figure 4c,24 April 2024,Aleru Divine,Aleru Divine,Microbiome alterations at the genus level in patients of different sexes with PTC. Differences between groups were analyzed using the Wilcoxon rank-sum test,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Caballeronia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia",2|201174|1760|85007|85025|1827;2|1224|28216|80840|119060|48736;2|976|117743|200644|2762318|59732;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060|1827195;2|1224|28216|80840|119060|1822464,Complete,NA
bsdb:1033/9/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 9,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Thyroid-Stimulating Hormone (TSH),The association between Thyroid-Stimulating Hormone (TSH) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|91061|186826|186828|2747;2|976|200643|171549|171552|838,Complete,NA
bsdb:1033/10/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 10,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Triiodothyronine (T3),The association between Triiodothyronine (T3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,2|1239|91061|186826|186828|117563,Complete,NA
bsdb:1033/11/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 11,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Thyroxine (T4),The association between Thyroxine (T4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|1224|1236|91347|543|1940338;2|1224|1236|91347|543|570,Complete,NA
bsdb:1033/12/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 12,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Free Triiodothyronine (FT3),The association between Free Triiodothyronine (FT3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,increased,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,2|203691|203692|136|2845253|157,Complete,NA
bsdb:1033/13/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 13,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Free Thyroxine (FT4),The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,2|1224|28216|206351|481|482,Complete,NA
bsdb:1033/13/2,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 13,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Free Thyroxine (FT4),The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,2|1224|1236|91347|543|570,Complete,NA
bsdb:1033/14/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 14,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,NA,Anti-thyroid-stimulating receptors (Anti-TSHR),The association between Anti-thyroid-stimulating receptors (Anti-TSHR) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Caballeronia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia",2|1224|1236|91347|543|570;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060|1827195;2|1224|28216|80840|119060|1822464,Complete,NA
bsdb:1033/15/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 15,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,NA,Anti-thyroid peroxidase (Anti-TPO),The association between Anti-thyroid peroxidase (Anti-TPO) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,25 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|1760|85004|31953|1678;2|1239|909932|909929|1843491|970;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|543311;2|74201|203494|48461|1647988|239934;2|976|200643|171549|815|816;2|1224|1236|135625|712|724,Complete,NA
bsdb:1033/16/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 16,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,NA,Anti-thyroglobulin (Anti-TG),The association between Anti-thyroglobulin (Anti-TG) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,26 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas",2|1224|28211|204457|41297|13687;2|201174|1760|85007|85025|1827;2|1224|28216|80840|119060|48736;2|1224|28211|204458|76892|41275,Complete,NA
bsdb:1033/16/2,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 16,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,NA,Anti-thyroglobulin (Anti-TG),The association between Anti-thyroglobulin (Anti-TG) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,26 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|1239|1737404|1737405|1570339|165779;2|74201|203494|48461|1647988|239934,Complete,NA
bsdb:1033/17/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 17,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Triiodothyronine (T3),The association between Triiodothyronine (T3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5c,26 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,2|1239|91061|186826|186828|117563,Complete,NA
bsdb:1033/18/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 18,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Free Triiodothyronine (FT3),The association between Free Triiodothyronine (FT3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5c,26 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,2|1239|91061|186826|186828|117563,Complete,NA
bsdb:1033/19/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 19,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,NA,Free Thyroxine (FT4),The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5c,26 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.,increased,NA,NA,Complete,NA
bsdb:1033/20/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 20,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,NA,Anti-thyroid-stimulating receptors (Anti-TSHR),The association between Anti-thyroid-stimulating receptors (Anti-TSHR) and microbial abundance in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5d,26 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies in the validation set.,increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,2|32066|203490|203491|1129771|32067,Complete,NA
bsdb:1033/21/1,Study 1033,prospective cohort,36002642,10.1038/s42003-022-03814-x,https://www.nature.com/articles/s42003-022-03814-x,"Yuan L, Yang P, Wei G, Hu X, Chen S, Lu J, Yang L, He X , Bao G",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 21,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,NA,Anti-thyroid peroxidase (Anti-TPO),The association between Anti-thyroid peroxidase (Anti-TPO) and microbial abundance in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5d,26 April 2024,Aleru Divine,Aleru Divine,Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies in the validation set.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|1760|85004|31953|1678;2|1224|1236|135625|712|724,Complete,NA
bsdb:1034/1/1,Study 1034,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S, Chen M, Kundu S, Wang X, Zhou Z, Zheng Z, Qing W, Sheng H, Wang Y, He Y, Bennett PR, MacIntyre DA , Zhou H",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Low vaginal sialidase activity,High vaginal sialidase activity,"Women with high vaginal sialidase activity, which is often associated with bacterial vaginosis (BV)",783,36,Within 30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,FIG 2 (C),23 April 2024,Rahila,"Rahila,Scholastica",LDA analysis in vaginal microbiota of women with low (green) versus high (red) vaginal sialidase activity,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174;2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|1239|91061|186826|186827|1375|1872398;2|201174|84998|84999|1643824|1380;2|976|200643|171549;2|976|200643;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1506;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|1955814;2|1239|186801|186802;2|201174|84998|84999|1643824|2767327|82135;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|2701|2049026;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539738|1378|1966354;2|1239|91061|1385|539738;2|1239|91061|186826|33958|2742598|1613;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906|2023260;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|543311|1944660;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552;2|1239|1737404|1737405|1737406;2|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:1034/1/2,Study 1034,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S, Chen M, Kundu S, Wang X, Zhou Z, Zheng Z, Qing W, Sheng H, Wang Y, He Y, Bennett PR, MacIntyre DA , Zhou H",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Low vaginal sialidase activity,High vaginal sialidase activity,"Women with high vaginal sialidase activity, which is often associated with bacterial vaginosis (BV)",783,36,Within 30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,FIG 2 (C),23 April 2024,Rahila,"Rahila,Scholastica",LDA analysis in vaginal microbiota of women with low (green) versus high (red) vaginal sialidase activity,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Saprospira,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium|s__Sediminibacterium sp.",2|1224|28211;2|1239|91061;2|1239;2|1224|28216;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060|32008|36773;2|1224|28216|80840|119060;2|1224|28216|80840;2|976|1853228|1853229|563835;2|1224|28216|80840|80864;2|1224|28216|80840|80864|80865;2|1224|28216|80840|80864|80865|1886637;2|1224|28216|80840|75682|963;2|1224|28216|80840|75682|963|1890675;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|109790;2|1224;2|976|1937959|1936988|89374|1007;2|976|1937959|1936988;2|976|1853228|1853229|563835|504481;2|976|1853228|1853229|563835|504481|1917865,Complete,Svetlana up
bsdb:1034/2/1,Study 1034,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S, Chen M, Kundu S, Wang X, Zhou Z, Zheng Z, Qing W, Sheng H, Wang Y, He Y, Bennett PR, MacIntyre DA , Zhou H",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Leukocyte low (grades I-II),Leukocyte high (grades III-IV),Vaginal microbiota of women  with Leukocyte high (grades III-IV),783,36,Within 30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (C),23 April 2024,Rahila,"Rahila,Scholastica","LDA analysis in vaginal microbiota of women with leukocyte low (grades I-II, green) versus leukocyte high (grades III-IV, red)",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.",2|1239|91061;2|1239;2|1224|28216;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060|32008|36773;2|1224|28216|80840|119060;2|1224|28216|80840;2|1224|28216|80840|80864|80865;2|1224|28216|80840|80864|80865|1886637;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|147802;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|162289|1971214,Complete,Svetlana up
bsdb:1034/2/2,Study 1034,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S, Chen M, Kundu S, Wang X, Zhou Z, Zheng Z, Qing W, Sheng H, Wang Y, He Y, Bennett PR, MacIntyre DA , Zhou H",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Leukocyte low (grades I-II),Leukocyte high (grades III-IV),Vaginal microbiota of women  with Leukocyte high (grades III-IV),783,36,Within 30 days,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (C),23 April 2024,Rahila,"Rahila,Scholastica","LDA analysis in vaginal microbiota of women with leukocyte low (grades I-II, green) versus leukocyte high (grades III-IV, red)",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",2|1224|28216|80840|506;2|1224|28211;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|1872515;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|186801;2|1224|28216|80840|80864;2|1239|186801|186802;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|150055;2|1224|28216|80840|995019|40544;2|1224|28216|80840|995019|40544|1981025;2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1737406,Complete,Svetlana up
bsdb:1035/1/1,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 1,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Infection-Only,Urine samples infected with urogenital schistosomiasis,13,25,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 6B,25 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Differentially abundant microbiome between urogenital schistosomiasis (infection-only) and healthy controls,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1224|1236|2887326|468|469;2|1239|91061|186826|186827|1375;2|976|117743|200644|2762318|59732;2|1239|91061|186826|186827|66831;2|1224|1236|91347|543|570;2|1224|1236|72274|135621|286;2|1224|1236|135622|267890|22;2|1239|91061|1385|90964|1279;2|1239|91061|186826|186828;2|1239|91061|1385|186818;2|1224|1236|72274|135621,Complete,Svetlana up
bsdb:1035/1/2,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 1,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Infection-Only,Urine samples infected with urogenital schistosomiasis,13,25,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 6B,25 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Differentially abundant microbiome between urogenital schistosomiasis (infection-only) and healthy controls,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|1236|2887326|468|469;2|1224|1236|91347|1903412|635;2|1224|1236|91347|543|547;2|1224|1236|91347|1903409|551;2|201174|1760|85004|31953|2701;2|1224|1236|91347|1903412|568;2|1224|28216|80840|119060|131079;2|1224|28211|356|82115|13159;2|1224|1236|91347|1903414|29487;2|1224|1236|2887326|468|497;2|1239|91061|186826|33958|46255;2|1224|1236|135624;2|201174|1760|85004|31953;2|1224|1236|91347|543;2|1224|1236|2887326|468;2|1224|1236|72274|135621;2|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:1035/2/1,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 2,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Advanced,Urine samples infected with urogenital schistosomiasis induced bladder pathology.,13,22,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 6A,29 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Differentially abundant microbiome between urogenital schistosomiasis induced bladder pathology (advanced) and healthy controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales",2|976|200643|171549|815|816;2|1239|91061|1385|90964|227979;2|976|200643|171549|171552|838;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|186827|1375;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186827|66831;2|201174|1760|85006|85019|1696;2|1239|1737404|1737405|1570339|162289;2|1224|28211|204458|76892|75;2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1224|1236|2887326|468|469;2|1224|1236|135615,Complete,Svetlana up
bsdb:1035/2/2,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 2,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Advanced,Urine samples infected with urogenital schistosomiasis induced bladder pathology.,13,22,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 6A,29 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Differentially abundant microbiome between urogenital schistosomiasis induced bladder pathology (advanced) and healthy controls.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1239|91061|186826|81852;2|201174|1760|85004|31953;2|1224|1236|135622|267888;2|1224|1236|91347|543;2|1224|1236|2887326|468;2|1224|1236|135624;2|1224|1236|91347|543|547;2|1224|1236|91347|1903412|635;2|1239|91061|186826|33958|46255;2|1224|1236|91347|1903409|551;2|1224|1236|91347|1903414|29487;2|1224|1236|91347|1903412|568;2|1224|1236|72274|135621|286;2|1239|91061|1385|90964|1279;2|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:1035/3/1,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 3,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Infected with urogenital schistosomiasis,24,46,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Figure 5A, 5B",30 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Differentially abundant microbiome genera in urogenital schistosomiasis (infected) and controls (non-infected).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae",2|1224|1236|2887326|468|469;2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|976|200643|171549|815;2|976|200643|171549|815|816;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696;2|1239|91061|186826|186828;2|976|117743|200644|2762318|59732;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|186827|66831;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1239|91061|1385|90964|227979;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|81852|33969;2|1224|1236|2887326|468;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300;2|1239|1737404|1737405|1737406;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|976|117743|200644|2762318;2|1224|1236|135615;2|1239|91061|186826|186828,Complete,Svetlana up
bsdb:1035/3/2,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 3,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Infected with urogenital schistosomiasis,24,46,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Figure 5A, 5B",30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Differentially abundant microbiome genera in urogenital schistosomiasis (infected) and controls (non-infected).,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|2887326|468|469;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|201174|1760|85004|31953;2|1224|28211|204458|76892;2|976|117743|200644|2762318|59732;2|1224|1236|91347|1903412|635;2|1224|28211|356|212791;2|1224|1236|91347|543|547;2|1224|1236|91347|543;2|1224|1236|91347|1903409|551;2|201174|1760|85004|31953|2701;2|1224|1236|91347|1903412|568;2|1224|28216|80840|75682|29580;2|1224|28216|80840|119060|131079;2|1224|1236|2887326|468;2|1224|28211|356|82115|13159;2|1224|28216|80840|75682;2|1224|1236|91347|1903414|29487;2|1224|1236|135622|267888;2|1224|1236|2887326|468|497;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|976|117743|200644|2762318;2|1239|91061|186826|33958|46255;2|1224|1236|135624;2|201174|1760|85004|31953;2|1224|1236|135622|267888;2|1239|91061|186826|33958;2|1224|28216|80840|80864;2|1224|1236|2887326|468;2|1224|1236|91347|543,Complete,Svetlana up
bsdb:1035/4/1,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 4,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology only,Advanced,Urogenital schistosomiasis induced bladder pathology.,10,22,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 5D,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Differentially abundant microbiome genera in non-infected bladder pathology (pathology-only) and urogenital schistosomiasis induced bladder pathology (advanced).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hylemonella",2|1224|1236|2887326|468|469;2|1239|91061|186826|186827|1375;2|976|200643|171549|815|816;2|201174|1760|85006|85019|1696;2|1224|28216|80840|80864|283;2|1239|91061|186826|186827|66831;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1239|91061|1385|90964|227979;2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171552|838;2|976|117747|200666|84566|28453;2|1239|909932|1843489|31977|29465;2|976|117743|200644|2762318|343873;2|976|117743|200644|2762318|1013;2|1224|1236|135615;2|1224|1236|72274|135621;2|1224|28216|80840|80864|232523,Complete,Svetlana up
bsdb:1035/4/2,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 4,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology only,Advanced,Urogenital schistosomiasis induced bladder pathology.,10,22,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 5D,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica",Differentially abundant microbiome genera in non-infected bladder pathology (pathology-only) and urogenital schistosomiasis induced bladder pathology (advanced).,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus",2|1224|1236|2887326|468|469;2|1239|91061|1385|186817|1386;2|976|117743|200644|2762318|59732;2|1224|1236|91347|1903412|635;2|1224|28211|356|212791;2|1224|1236|91347|1903412|568;2|1224|28216|80840|75682|29580;2|1224|1236|72274|135621|286;2|1239|91061|1385|90964|1279;2|1224|1236|135624;2|1224|1236|91347|543;2|1239|91061|1385|186818;2|1224|1236|135622|267888;2|1224|1236|91347|1903409|551;2|1224|1236|91347|1903414|29487,Complete,Svetlana up
bsdb:1035/5/1,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 5,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Infection Only,Advanced,urogenital schistosomiasis induced bladder pathology.,25,22,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 5C,30 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Differential microbiome genera between urogenital schistosomiasis (infection-only) and urogenital schistosomiasis induced bladder pathology (advanced).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|1236|72274|135621;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|227979;2|1224|1236|2887326|468;2|1224|1236|135615;2|1224|1236|2887326|468|497;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186827|66831;2|201174|1760|85006|85019|1696;2|1239|1737404|1737405|1570339|162289;2|201174|1760|85004|31953;2|1224|28211|204458|76892|75;2|201174|1760|85004|31953|2701;2|976|117747|200666|84566|28453;2|976|117743|200644|2762318|343873;2|1224|28216|80840|119060|131079;2|976|117743|200644|2762318|1013;2|1239|91061|186826|33958|1578;2|1224|28211|356|82115|13159;2|1224|1236|2887326|468|469;2|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:1035/5/2,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 5,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Infection Only,Advanced,urogenital schistosomiasis induced bladder pathology.,25,22,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 5C,30 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Differential microbiome genera between urogenital schistosomiasis (infection-only) and urogenital schistosomiasis induced bladder pathology (advanced).,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae",2|1239|91061|186826|81852;2|1239|91061|186826|186828;2|976|117743|200644|2762318|59732;2|1224|1236|2887326|468|469;2|1239|91061|1385|90964|1279;2|1224|1236|72274|135621|286;2|1239|91061|1385|186818,Complete,Svetlana up
bsdb:1035/6/1,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 6,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology Only,Infection Only,Urogenital schistosomiasis infection,10,25,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure S2B,30 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Differential abundance in the urine microbiome of persons with urogenital schistosomiasis infection without bladder pathology (infection-only) and pathology without schistosomiasis infection (pathology-only).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1239|91061|186826|186827|1375;2|1224|1236|72274|135621;2|1224|28216|80840|80864|283;2|1239|91061|186826|81852|1350;2|976|117743|200644|2762318|59732;2|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:1035/6/2,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 6,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology Only,Infection Only,Urogenital schistosomiasis infection,10,25,Recent use of Antibiotics,16S,3,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure S2B,30 April 2024,Adenike Oladimeji-Kasumu,Adenike Oladimeji-Kasumu,Differential abundance in the urine microbiome of persons with urogenital schistosomiasis infection without bladder pathology (infection-only) and pathology without schistosomiasis infection (pathology-only).,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1224|1236|135622|267888;2|1224|1236|91347|543|547;2|1224|1236|91347|1903412|635;2|1224|1236|91347|1903409|551;2|1224|1236|91347|1903414|29487;2|1224|28211|204458|76892|75;2|1224|1236|91347|543;2|1239|91061|1385|90964|1279;2|1224|28211|356|212791;2|976|117743|200644|2762318|59732;2|1239|91061|1385|186817|1386;2|1224|28216|80840|75682|29580;2|1224|1236|2887326|468|497;2|1224|1236|2887326|468;2|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:1035/7/1,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 7,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Not infected with urogenital schistosomiasis.,24,46,Recent use of Antibiotics,16S,3,Ion Torrent,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 7,1 May 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica","Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls
(non-infected).",decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|1737404|1737405|1570339|165779;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|201174|1760|85011|2062;2|1224|1236|91347|543|158851;2|1239|91061|186826|33958|46255;2|1224|1236|91347|1903414|626;2|1224|1236|91347|543;2|1239|91061|186826|33958,Complete,Svetlana up
bsdb:1035/7/2,Study 1035,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI , Shouche YS",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 7,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Not infected with urogenital schistosomiasis.,24,46,Recent use of Antibiotics,16S,3,Ion Torrent,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 7,1 May 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica","Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls
(non-infected).",increased,"k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales",2|976|117747|200666|84566;2|976|117747|200666;2|976|117747;2|976|117747|200666|84566|28453;2|1224|1236|135614|32033|40323;2|1239|91061|1385,Complete,Svetlana up
bsdb:1036/1/1,Study 1036,laboratory experiment,34568329,10.3389/fcell.2021.716760,NA,"Wang Q, Yi S, Su G, Du Z, Pan S, Huang X, Cao Q, Yuan G, Kijlstra A , Yang P",Changes in the Gut Microbiome Contribute to the Development of Behcet's Disease <i>via</i> Adjuvant Effects,Frontiers in cell and developmental biology,2021,"Behcet’s disease, T cells, autoimmune disease, fecal transplantation, gut microbiome, neutrophils",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy controls-recipient mice,Behcet's disease-recipient mice,Mice colonized by fecal microbial transplantation (FMT) from Behcet's disease patients,5,5,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1C,24 April 2024,Scholastica,"Scholastica,Peace Sandy",Differentially abundant taxa in Behcet's disease-recipient mice versus healthy controls-recipient mice,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella",2|1239|91061|186826|1300|1357;2|200940|3031449|213115|194924|35832;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236;2|1239|186801|3085636|186803|33042;2|1224|28216|80840|80864|283;2|976|200643|171549|1853231|283168;2|201174|84998|1643822|1643826|580024;2|201174|84995|84996|84997;2|201174|84995|84996;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930;2|201174|84995|84996|84997|42255;2|1239|186801|3085636|186803|1432051;2|1239|909932|909929;2|1239|909932;2|544448|2790996|2790998|2129;2|1224|28216|80840|75682;2|1224|28216|80840|75682|149698;2|1239|909932|1843489|31977|209879,Complete,Peace Sandy
bsdb:1036/1/2,Study 1036,laboratory experiment,34568329,10.3389/fcell.2021.716760,NA,"Wang Q, Yi S, Su G, Du Z, Pan S, Huang X, Cao Q, Yuan G, Kijlstra A , Yang P",Changes in the Gut Microbiome Contribute to the Development of Behcet's Disease <i>via</i> Adjuvant Effects,Frontiers in cell and developmental biology,2021,"Behcet’s disease, T cells, autoimmune disease, fecal transplantation, gut microbiome, neutrophils",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy controls-recipient mice,Behcet's disease-recipient mice,Mice colonized by fecal microbial transplantation (FMT) from Behcet's disease patients,5,5,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 1C,24 April 2024,Scholastica,"Scholastica,Peace Sandy",Differentially abundant taxa in Behcet's disease-recipient mice versus healthy controls-recipient mice,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|201174|84998|84999;2|201174;2|201174|84998|84999|1643824|133925;2|201174|84998|84999|84107;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|976|200643|171549|171552;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461|1647988|239934;2|74201|203494|48461;2|976|200643|171549|171552|1283313,Complete,Peace Sandy
bsdb:1037/1/1,Study 1037,case-control,33552996,10.3389/fcimb.2020.557515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859112/,"Li H, Chen J, Ren X, Yang C, Liu S, Bai X, Shan S , Dong X",Gut Microbiota Composition Changes in Constipated Women of Reproductive Age,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene sequencing, chronic constipation, gut microbiota, influence factors, women of reproductive age",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy women,Constipated women,Female constipated patients of reproductive age.,30,29,One month preceding sample collection.,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2 and Figure3f,26 April 2024,Aleru Divine,Aleru Divine,Significant Differences in the Microbiota of Constipated Women of Reproductive Age and Healthy Controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|976;2|1239|909932;2|976|200643|171549|815|909656|310298;2|1239|909932|909929;2|1239|186801|3085636|186803|1407607;2|1239|91061|186826|33958;2|976|200643|171549|2005525;2|976|200643|171549|2005525|375288;2|1224|1236|91347|543|544,Complete,Svetlana up
bsdb:1037/1/2,Study 1037,case-control,33552996,10.3389/fcimb.2020.557515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859112/,"Li H, Chen J, Ren X, Yang C, Liu S, Bai X, Shan S , Dong X",Gut Microbiota Composition Changes in Constipated Women of Reproductive Age,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene sequencing, chronic constipation, gut microbiota, influence factors, women of reproductive age",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy women,Constipated women,Female constipated patients of reproductive age.,30,29,One month preceding sample collection.,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 2 and Figure3f,26 April 2024,Aleru Divine,Aleru Divine,Significant Differences in the Microbiota of Constipated Women of Reproductive Age and Healthy Controls.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561|562;2|1224|1236;2|1224|1236|91347|543|570;2|1224|1236|91347|543|570|573;2|1224;2|1224|1236|91347|543;2|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:1038/1/1,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 1,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Premenopausal healthy controls (HPV Negative women),Premenopausal Pre-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,6,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Table 2,27 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239|1737404|1737405|1570339|165779;2|201174|84998|84999|1643824|1380;2|1239|526524|526525|128827|118747;2|29547|3031852|213849|72294|194;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|236752;2|1239|186801|186802|1686313;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|201174|1760|2037|2049|2050;2|1239|186801|3085636|186803|437755;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186807|2740;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|526524|526525|128827|123375;2|1239|186801|3085636|186803|1213720,Complete,NA
bsdb:1038/1/2,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 1,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Premenopausal healthy controls (HPV Negative women),Premenopausal Pre-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,6,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Table 2,27 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|1236|2887326|468|469;2|1224|28211|356|69277|31988;2|201174|1760|85009|31957|1912216;2|1224|1236|91347|543|1940338;2|1239|91061|186826|33958|1578;2|1224|1236|72274|135621|286;2|1224|1236|135613|1046|67575;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1038/2/1,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 2,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Pre-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,10,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Table 2,28 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|201174|1760|2037|2049|28263;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|437755;2|1239|186801|186802|186807|2740;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|1239|186801|3085636|186803|1213720,Complete,NA
bsdb:1038/2/2,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 2,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Pre-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,10,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Table 2,28 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Lentilitoribacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium",2|201174|1760|85004|31953|2701;2|1239|91061|1385|539738|1378;2|1224|28211|356|82115|1649463;2|1224|28211|356|69277|68287,Complete,NA
bsdb:1038/3/1,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 3,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Premenopausal healthy controls (HPV Negative women),Premenopausal Post-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,6,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S2,28 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",increased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales bacterium S5-A14a,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|1737404|1737405|1570339|165779;2|29547|3031852|213849|72294|194;2|1239|186801|186802|543314|1230734;2|201174|1760|85007|1653|1716;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:1038/3/2,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 3,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Premenopausal healthy controls (HPV Negative women),Premenopausal Post-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,6,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S2,28 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Hoeflea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter",2|1224|28211|356|69277|31988;2|201174|1760|85004|31953|1678;2|1224|28211|356|118882|234;2|1239|91061|186826|186828|117563;2|1224|28211|356|82115|274591;2|1224|28216|80840|80864|219181;2|976|200643|171549|2005525|375288;2|1224|1236|91347|543|1330546,Complete,NA
bsdb:1038/4/1,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 4,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Post-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,10,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S2,29 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Renibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|28211|204458|76892|75;2|1224|28216|80840|80864|238749;2|976|200643|171549|171551|836;2|201174|1760|85006|1268|1645;2|1224|28211|204457|41297|13687,Complete,NA
bsdb:1038/4/2,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 4,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Post-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,10,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S2,29 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Lentilitoribacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium",2|201174|1760|85004|31953|2701;2|1224|28211|356|82115|1649463;2|1224|28211|356|69277|68287,Complete,NA
bsdb:1038/5/1,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 5,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Pre-treatment group,Post-treatment group,"Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,15,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,29 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Renibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|2887326|468|469;2|1239|186801|3085636|186803|572511;2|1224|28211|204458|76892|75;2|976|117743|200644|2762318|501783;2|201174|1760|85007|1653|1716;2|1224|28216|80840|119060|106589;2|201174|1760|85009|31957|1912216;2|1224|28216|80840|80864|238749;2|1239|1737404|1737405|1570339|150022;2|1239|91061|186826|1300|1357;2|1224|28216|80840|75682|149698;2|976|200643|171549|2005473|1918540;2|1224|28216|206351|481|482;2|976|117747|200666|84566|84567;2|1224|1236|72274|135621|286;2|1224|28216|80840|119060|48736;2|201174|1760|85006|1268|1645;2|1224|1236|135613|1046|67575;2|1224|28216|80840|2975441|93681;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:1038/5/2,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 5,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Pre-treatment group,Post-treatment group,"Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,15,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,29 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239|526524|526525|128827|118747;2|32066|203490|203491|203492|848;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186807|2740;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|526524|526525|128827|123375;2|1239|186801|3085636|186803|1213720,Complete,NA
bsdb:1038/6/1,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 6,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Pre-treatment group,3-months post treatment group (follow-up samples),"Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), 3 months after the last fraction of brachytherapy (ICBT) was given.",15,9,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,29 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to 3-months after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis",increased,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,2|1239|1737404|1737405|1570339|150022,Complete,NA
bsdb:1038/6/2,Study 1038,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M , Ostrowski J",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 6,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Pre-treatment group,3-months post treatment group (follow-up samples),"Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), 3 months after the last fraction of brachytherapy (ICBT) was given.",15,9,2 months,16S,23456789,Ion Torrent,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,29 April 2024,Joan Chuks,Joan Chuks,"Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT), compared to 3-months after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis",decreased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,2|1239|526524|526525|128827|123375,Complete,NA
bsdb:1039/1/1,Study 1039,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R , O'Keefe SJD",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,People from Urban Xhosa of South Africa transitioning from traditional high-fiber to Western diets,21,20,6 weeks,16S,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 1D,28 April 2024,Scholastica,Scholastica,Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Rural Xhosa versus Urban Xhosa cohorts,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacillota|g__Negativibacillus",2|976|200643|171549|815|816;2|1239|909932|1843488|909930|33024;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|830;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|1506553;2|1239|526524|526525|2810280|3025755;2|976|200643|171549|171550|239759;2|1239|526524|526525|128827|1522;2|200940|3031449|213115|194924|35832;2|1239|186801|186802|216572|946234;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005519|397864;2|1239|186801|186802|216572|459786;2|1239|186801|3085636|186803|1432051;2|1239|1980693,Complete,Svetlana up
bsdb:1039/1/2,Study 1039,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R , O'Keefe SJD",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,People from Urban Xhosa of South Africa transitioning from traditional high-fiber to Western diets,21,20,6 weeks,16S,NA,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 1D,28 April 2024,Scholastica,Scholastica,Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Rural Xhosa versus Urban Xhosa cohorts,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|3085636|186803|265975;2|1239|186801|186802|1470353;2|74152|641853|641854|641876|423604;2|976|200643|171549|171552|370804;2|1239|186801|3085636|186803|877406;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:1039/3/1,Study 1039,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R , O'Keefe SJD",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 3,South Africa,Homo sapiens,Ingested food,UBERON:0012112,Diet,EFO:0002755,Frozen food samples from rural Xhosa households,Frozen food samples from urban Xhosa households,Frozen food samples collected from representative households of urban Xhosa of South Africa,7,6,6 weeks,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4D,30 April 2024,Idiaru angela,Idiaru angela,Significantly different abundance at the genus level. Statistical analysis using a two-sided Wilcoxon test corrected for multiple testing by the Benjamini–Hochberg method using normalized samples,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Rosenbergiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1224|1236|91347|1903409|1356488;2|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:1039/4/1,Study 1039,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R , O'Keefe SJD",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 4,South Africa,Homo sapiens,Manual digit skin,UBERON:0003533,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,Hand skin swabs from urban Xhosa cohort of South Africa,7,6,Oral or I.V antibiotic therapy within the last 6 weeks,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplementary Table 3,28 April 2024,Scholastica,Scholastica,Significantly different abundant bacterial genera or families on hand skin swabs from rural versus urban Xhosa cohorts,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Flaviflexus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",2|1224|1236|2887326|468|469;2|1239|91061|186826|186827|1375;2|1224|1236|2887326|468|222991;2|1224|28216|80840|92793;2|201174|84998|84999|84107|102106;2|1239|91061|186826|186828|82800;2|201174|1760|2037|2049|1522056;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|90964|227979;2|1224|28211|204455|31989|265;2|976|200643|171549|171552|838;2|1239|91061|1385|186818|162291;2|1224|1236|2887326|468|497;2|1239|186801|186802|216572|1263;2|1224|1236|135614|32033|141948;2|1239|91061|186826|186828|82802;2|1224|1236|135624|83763|83770;2|1224|1236|135623|641|662,Complete,Svetlana up
bsdb:1039/4/2,Study 1039,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R , O'Keefe SJD",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 4,South Africa,Homo sapiens,Manual digit skin,UBERON:0003533,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,Hand skin swabs from urban Xhosa cohort of South Africa,7,6,Oral or I.V antibiotic therapy within the last 6 weeks,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplementary Table 3,28 April 2024,Scholastica,Scholastica,Significantly different abundant bacterial genera or families on hand skin swabs from rural versus urban Xhosa cohorts,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Williamsia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|201174|1760|85010|2070|402649;2|1239|91061|1385|186817|1386;2|1239|91061|186826|1300|1357;2|1239|91061|1385|186817|400634;2|201174|1760|85009|85015|86795;2|1224|28211|204457|41297|165696;2|1224|28211|356|118882|528;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3082720|186804;2|1224|1236|91347|1903411|613;2|1224|28211|204457|41297|13687;2|976|117743|200644|2762318;2|201174|1760|85007|85025|85043;2|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:1040/1/1,Study 1040,case-control,37158877,10.1186/s12866-023-02872-3,NA,"Wei N, Zhu G, Zhao T, Wang Y, Lou H, Li H, Yang Z, Zhang Z, Wang Q, Han M, Lin Z , Li S",Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients,BMC microbiology,2023,"COVID-19, Oral bacteria, Oral fungi, Recovered patients, Virus clearance",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,COVID-19,MONDO:0100096,HCs (Healthy Controls),RPs (Recovered Patients),This group consists of patients who have recovered from COVID-19.,29,23,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig. 3A & Fig. 6A,9 August 2024,Victoria,Victoria,"Images showing the differences in taxa between RPs and HCs. (Fig. 3A shows oral bacterial taxa, while Fig. 6A shows oral fungi taxa).",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aquamicrobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Liberibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|29547|3031852|213849|2808963|28196;2|29547|3031852|213849|2808963;2759|4751|4890|147550|5114|767018;2759|4751|4890|147550|5114;2759|4751|4890|147550|5114|767018|36922;2|1239|91061|186826|33958;2|1239|91061|1385|186822|44249;2759|4751|4890|147550;2759|4751|4890|147545|5042|28568|5094;2|1297|188787|68933|188786;2|1297|188787|68933|188786|270;2|1239|91061|186826|33958|46255;2|1239|186801|3085636|186803|43994;2|1239|186801|3085636|186803|265975;2|1239|186801|3085636|186803|1213720;2|1239|186801|3085636|186803;2|1239|526524|526525|128827|118747;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|32066|203490|203491|1129771|168808;2|1224|28211|356|69277|69278;2|1224|28211|356|82115|34019;2|1224|28211|356|118882|528;2|1224|28211|356|82115;2|1224|28216|206351|1499392|57739;2|1224|28216|206351|1499392;2|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:1040/1/2,Study 1040,case-control,37158877,10.1186/s12866-023-02872-3,NA,"Wei N, Zhu G, Zhao T, Wang Y, Lou H, Li H, Yang Z, Zhang Z, Wang Q, Han M, Lin Z , Li S",Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients,BMC microbiology,2023,"COVID-19, Oral bacteria, Oral fungi, Recovered patients, Virus clearance",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,COVID-19,MONDO:0100096,HCs (Healthy Controls),RPs (Recovered Patients),This group consists of patients who have recovered from COVID-19.,29,23,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig. 3A & Fig. 6A,10 August 2024,Victoria,Victoria,"Images showing the differences in taxa between RPs and HCs. (Fig. 3A shows oral bacterial taxa, while Fig. 6A shows oral fungi taxa).",decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|g__Candidatus Profftella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae",2759|4751|4890|3239874|2916678|766764|5475;2|201174|1760|85009|31957|2801844;2|201174|1760|85009|31957;2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|838;2|976|117743|200644|2762318|308865;2|976|117743|200644|2762318|59734;2|1239|91061|186826|81852|2737;2|1224|28211|204458|76892;2|1224|28211|356|119045|407;2|1224|28211|356|69277|68287;2|1224|28211|356|41294|374;2|1224|28211|356|335928;2|1224|28211|766|942|953;2|1224|28211|766|942;2|1224|28216|1381133;2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060|48736;2|1224|28216|80840|119060;2|1224|1236|135625|712|416916;2|1224|1236|135623|641|662;2|1224|1236|135623|641,Complete,Svetlana up
bsdb:1041/1/1,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 1,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Tumor tissue (TT) samples,Tumor tissue (TT) specimens were obtained from the inner part of the tumor,20,NA,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Figure 3A,28 April 2024,MyleeeA,MyleeeA,Differential abundance of core bacterial genera among adjacent tumor tissue and tumor tissues.,increased,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,2|1224|28211|204458|76892|41275,Complete,Svetlana up
bsdb:1041/1/2,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 1,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Tumor tissue (TT) samples,Tumor tissue (TT) specimens were obtained from the inner part of the tumor,20,NA,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Supplementary Figure 2B, 3A and 3c",28 April 2024,MyleeeA,MyleeeA,"Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and tumor tissues.",decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota",2|1224|28211|204458|76892|41275|293;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|488;2|1224|28216|206351|481|482|28449;2|1224|28211|356|118882|528;2759|33090|35493|3398|72025|3803|3814|508215;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465;2|1224,Complete,Svetlana up
bsdb:1041/2/1,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 2,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Precancer,"Precancerous lesion samples were collected from patients with leukoplakia, fibrosis, and
erythroplakia.",20,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Figure 2C, 3B and 3D",28 April 2024,MyleeeA,MyleeeA,"Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and Precancer Samples.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",2|201174|1760|2037|2049|1654;2|976|200643|171549|815|816;2|976|200643;2|95818;2|976|117743|200644|49546|1016;2|976|117743|200644|49546|1016|45242;2|976|117743|200644|49546|1016|327575;2|976|117743|200644|49546|1016|1018;2|976|117743|200644|49546|1016|1019;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924;2|1239|186801|3085636|186803;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|1239|186801|186802|216572|119852;2|976|117747|200666|84566|84567;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|203691|203692|136;2|203691|203692|136|2845253|157;2|203691|203692|136|2845253|157|158;2|203691|203692|136|2845253|157|58231,Complete,Svetlana up
bsdb:1041/2/2,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 2,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Precancer,"Precancerous lesion samples were collected from patients with leukoplakia, fibrosis, and
erythroplakia.",20,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3D,28 April 2024,MyleeeA,MyleeeA,Differential abundances of core bacterial Species among adjacent tumor tissue and Precancer lesions.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,2|1239|91061|186826|1300|1301|2490633,Complete,Svetlana up
bsdb:1041/3/1,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 3,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Early Stage Cancer,Cancer Samples subdivided into T1 and T2,20,30,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,28 April 2024,MyleeeA,MyleeeA,Differential abundances of core bacterial species between the precancer group with early (T1 and T2),increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola",2|976|117743|200644|49546|1016|1018;2|976|117743|200644|49546|1016|45242;2|976|117743|200644|49546|1016|327575;2|32066|203490|203491|203492|848|851;2|32066|203490|203491|203492|848|285729;2|203691|203692|136|2845253|157|158,Complete,Svetlana up
bsdb:1041/3/2,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 3,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Early Stage Cancer,Cancer Samples subdivided into T1 and T2,20,30,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,28 April 2024,MyleeeA,MyleeeA,Differential abundances of core bacterial species between the precancer group and early (T1 and T2),decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae",2|1239|91061|186826|1300|1301|2490633;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1334,Complete,Svetlana up
bsdb:1041/4/1,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 4,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,20,30,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,28 April 2024,MyleeeA,MyleeeA,Differential abundances of core bacterial species between the precancer group and late cancer (T3 and T4) groups,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri",2|976|117743|200644|49546|1016|1018;2|976|117743|200644|49546|1016|45242;2|976|117743|200644|49546|1016|1019;2|976|117743|200644|49546|1016|327575,Complete,Svetlana up
bsdb:1041/4/2,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 4,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,20,30,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,28 April 2024,MyleeeA,MyleeeA,Differential abundances of core bacterial species between the precancer group and late cancer (T3 and T4) groups,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa",2|1239|91061|186826|1300|1301|1334;2|1239|91061|186826|1300|1301|2490633;2|201174|1760|85006|1268|32207|43675;2|201174|1760|85006|1268|32207|2047,Complete,Svetlana up
bsdb:1041/5/1,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 5,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Cancer,Participants at different stages of disease pathogenesis (T1 to T4).,15,60,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2B, 2C, 3A and Supplementary Fig 2D",29 April 2024,MyleeeA,MyleeeA,"Differential abundances of core bacterial Phyla, Family, Genera and Species between Precancer and Cancer Samples.",increased,"k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa",2|363464;2|74201;2|95818;2|976|200643;2|203691|203692|136;2|976|200643|171549|171551;2|976|200643|171549|171552;2|1239|1737404|1737405|1737406;2|1224|1236|72274|135621;2|200940|3031449|213115|194924;2|1239|186801|3082720|186804;2|1239|186801|3085636|186803;2|203691|203692|136|137;2|976|117743|200644|49546;2|1224|28216|80840|80864;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|203691|203692|136|2845253|157;2|32066|203490|203491|1129771|32067;2|976|117743|200644|49546|1016;2|1239|186801|186802|216572|119852;2|203691|203692|136|2845253|157|158;2|976|117743|200644|49546|1016|327575;2|976|117743|200644|49546|1016|1018;2|976|117743|200644|49546|1016|1019;2|976|117743|200644|49546|1016|45242,Complete,Svetlana up
bsdb:1041/5/2,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 5,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Cancer,Participants at different stages of disease pathogenesis (T1 to T4).,15,60,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, 2C, 3A and Supplementary Fig 2D",29 April 2024,MyleeeA,MyleeeA,"Differential abundances of core bacterial Phyla, Family, Genera and Species between Precancer and Cancer Samples.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|201174;2|201174|1760|2037|2049|28263;2|1239;2|1239|186801|186802;2|1239|1737404|1737405|1570339|543311;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301|1334;2|1239|91061|186826|1300|1301|2490633;2759|33090|35493|3398|72025|3803|3814|508215,Complete,Svetlana up
bsdb:1041/6/1,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 6,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Early Stage Cancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,30,30,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D and Supplementary Figure 2A,29 April 2024,MyleeeA,MyleeeA,Differential abundances of core bacterial species between the Early stage cancer groups (T1 and T2) and Late Stage cancer (T3 and T4) groups,increased,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,2|976|117747|200666|84566|84567,Complete,Svetlana up
bsdb:1041/6/2,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 6,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Early Stage Cancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,30,30,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2D and Supplementary Figure 2A,29 April 2024,MyleeeA,MyleeeA,Differential abundances of core bacterial species between the Early stage cancer groups (T1 and T2) and Late Stage cancer (T3 and T4) groups,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|32066|203490;2|32066|203490|203491|1129771|32067;2|200940|3031449|213115|194924;2|1239|186801|186802,Complete,Svetlana up
bsdb:1041/7/NA,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 7,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T1,Early Stage Cancer Patients grouped as T1,15,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1041/8/NA,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 8,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T2,Early Stage Cancer Patients grouped as T2,15,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1041/9/NA,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 9,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T3,Late Stage Cancer Patients grouped as T3,15,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1041/10/NA,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 10,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T4,Late Stage Cancer Patients grouped as T4,15,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1041/11/NA,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 11,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,T1,T3,Late Stage Cancer Patients grouped as T3,15,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1041/12/NA,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 12,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,T2,T4,Late Stage Cancer Patients grouped as T4,15,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1041/13/NA,Study 1041,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S , Kumar R",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 13,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,T3,T4,Late Stage Cancer Patients grouped as T4,15,15,N/A,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1042/1/1,Study 1042,laboratory experiment,33557825,10.1186/s12936-021-03606-4,NA,"Omoke D, Kipsum M, Otieno S, Esalimba E, Sheth M, Lenhart A, Njeru EM, Ochomo E , Dada N",Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota,Malaria journal,2021,"16S rRNA gene amplicon sequencing, Anopheles gambiae s.s., Insecticide resistance, Metabarcoding, Mosquito microbiome, Mosquito microbiota, pyrethroid resistance",Experiment 1,Kenya,Anopheles gambiae,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,permethrin susceptible mosquito,permethrin resistant mosquito,Mosquitoes that were alive after the bioassay with permethrin insecticide were categorized as resistant,36,39,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5,29 April 2024,Idiaru angela,Idiaru angela,Differentially abundant bacterial genera between permethrin resistant and susceptible mosquitoes determined by Lefse analysis,increased,"k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria,k__Bacteria|p__Actinomycetota",2|976|117747|200666|84566|28453;2|1239|91061|1385|186817|400634;2|1239|91061|186826|1300|1301;2|1224|28211|204441;2|77133;2|1224|28211|204441;2|1224|28211;2|201174|84995|84996|84997;2|201174|84995|84996;2|201174|84995|84996|84997|42255;2|201174|84995;2|201174,Complete,Svetlana up
bsdb:1042/1/2,Study 1042,laboratory experiment,33557825,10.1186/s12936-021-03606-4,NA,"Omoke D, Kipsum M, Otieno S, Esalimba E, Sheth M, Lenhart A, Njeru EM, Ochomo E , Dada N",Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota,Malaria journal,2021,"16S rRNA gene amplicon sequencing, Anopheles gambiae s.s., Insecticide resistance, Metabarcoding, Mosquito microbiome, Mosquito microbiota, pyrethroid resistance",Experiment 1,Kenya,Anopheles gambiae,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,permethrin susceptible mosquito,permethrin resistant mosquito,Mosquitoes that were alive after the bioassay with permethrin insecticide were categorized as resistant,36,39,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5,29 April 2024,Idiaru angela,Idiaru angela,Differentially abundant bacterial genera between permethrin resistant and susceptible mosquitoes determined by Lefse analysis,decreased,"k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Myxococcaceae|g__Myxococcus,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Myxococcaceae",2|2818505|32015|29;2|28221;2|2818505|32015|29|31|32;2|2818505|32015|29|31,Complete,Svetlana up
bsdb:1043/1/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants at baseline (A0),Men who have sex with men (MSM) with acute HIV infection at baseline (A0).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2a,30 April 2024,Aleru Divine,Aleru Divine,Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552;2|976|200643|171549|171552|838,Complete,NA
bsdb:1043/1/2,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants at baseline (A0),Men who have sex with men (MSM) with acute HIV infection at baseline (A0).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2a,30 April 2024,Aleru Divine,Aleru Divine,Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella",2|32066|203490|203491|1129771|32067;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|32207;2|1224|28216|80840|119060|47670;2|976|200643|171549|2005525|195950;2|203691|203692|136|137;2|1239|186801|186802|216572;2|201174|1760|85007|1653|1716;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801|186802;2|1239|186801|3082720|186804|1501226;2|976|200643|171549|815|816;2|32066|203490|203491|1129771;2|1239|909932|909929|1843491|82202;2|1239|186801|186802|216572|459786;2|1224|1236|2887326|468|475;2|1239|186801|3085636|186803|43996,Complete,NA
bsdb:1043/2/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants at baseline (B0),Men who have sex with men (MSM) with Chronic HIV infection at baseline (B0).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2b,30 April 2024,Aleru Divine,Aleru Divine,Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|91061|186826|1300|1301;2|976|200643|171549|171552,Complete,NA
bsdb:1043/2/2,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants at baseline (B0),Men who have sex with men (MSM) with Chronic HIV infection at baseline (B0).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2b,30 April 2024,Aleru Divine,Aleru Divine,Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",2|201174|1760|2037|2049|1654;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|32207;2|1224|28216|80840|119060|47670;2|976|200643|171549|2005525|195950;2|203691|203692|136|137;2|1239|186801|186802|216572;2|201174|1760|85007|1653|1716;2|1239|526524|526525|2810281|191303;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|841;2|1239|186801|186802;2|1239|186801|3082720|186804|1501226;2|976|200643|171549|815|816;2|1239|909932|909929|1843491|82202;2|1239|186801|186802|216572|459786;2|1224|1236|2887326|468|475;2|1239|186801|3085636|186803|1213720;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|265975,Complete,NA
bsdb:1043/3/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3a,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants (A12) and control (D) groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1224|28211|356|41294|374|29448;2|1224|28211|356|41294|374;2|1224|28211|356|335928;2|1224|28211|356;2|1224|28211;2|1224|1236|135625|712|724,Complete,NA
bsdb:1043/3/2,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3a,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants (A12) and control (D) groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",2|1239|186801;2|1239|186801|186802;2|201174;2|201174;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|186801|186802|216572;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|1760|2037|2049|1654;2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268,Complete,NA
bsdb:1043/4/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 4,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants (B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3c,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Ihuprevotella|s__Ihuprevotella massiliensis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria",2|976|200643|171549|171552|3151711|1852368;2|1224|28211|356|41294|374|29448;2|1224|28211|356|41294|374;2|1224|28211|356|335928;2|1224|28211|356;2|1224|28211,Complete,NA
bsdb:1043/4/2,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 4,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants (B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3c,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",2|1239|186801;2|1239|186801|186802;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|201174;2|201174;2|1239|186801|186802|216572;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|724|735;2|1224|1236|135625|712|713,Complete,NA
bsdb:1043/5/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 5,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants at baseline (A0),Acute HIV-infected participants on Antiretroviral Therapy (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4a,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants on Antiretroviral Therapy(A12) and Acute HIV-infected participants (A0).,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae",2|1224|28211;2|1224|28211|356|41294|374;2|1224|28211|356|41294|374|29448;2|1224|28211|356;2|1224|28211|356|335928,Complete,NA
bsdb:1043/5/2,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 5,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants at baseline (A0),Acute HIV-infected participants on Antiretroviral Therapy (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4a,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants on Antiretroviral Therapy(A12) and Acute HIV-infected participants (A0).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|28132;2|976|200643;2|976;2|976|200643|171549|171552;2|976|200643|171549;2|976|200643|171549|171552,Complete,NA
bsdb:1043/6/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 6,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Chronic HIV-infected participants at baseline (B0),Chronic HIV-infected participants on Antiretroviral Therapy(B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 4c,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants on Antiretroviral Therapy(B12) and Chronic HIV-infected participants (B0).,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii",2|1224|28211;2|1224|28211|356;2|1224|28211|356|335928;2|1224|28211|356|41294|374;2|1224|28211|356|41294|374|29448,Complete,NA
bsdb:1043/6/2,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 6,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Chronic HIV-infected participants at baseline (B0),Chronic HIV-infected participants on Antiretroviral Therapy(B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 4c,30 April 2024,Aleru Divine,Aleru Divine,Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants on Antiretroviral Therapy(B12) and Chronic HIV-infected participants (B0).,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|909932;2|976|200643|171549|171552|838|470565;2|1239|909932|909929;2|1239|909932|1843489|31977;2|976|200643|171549|171552;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1043/7/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 7,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants at baseline (A0),Chronic HIV-infected participants at baseline (B0),Men who have sex with men (MSM) with Chronic HIV infection.,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 4e,30 April 2024,Aleru Divine,Aleru Divine,Comparisons of the relative abundance in oral microbiota at the genus level between people living with acute HIV infection at baseline (A0) and people living with chronic HIV infection at baseline (B0).,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,2|1239|186801|3085636|186803|265975,Complete,NA
bsdb:1043/8/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 8,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants on Antiretroviral Therapy(A12),Chronic HIV-infected participants on Antiretroviral Therapy(B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4f,30 April 2024,Aleru Divine,Aleru Divine,Comparisons of the relative abundance in oral microbiota at the genus level between people living with acute HIV infection after 12 weeks of ART (A12) and people living with chronic HIV infection after 12 weeks of ART (B12).,increased,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,2|29547|3031852|213849|72294|194,Complete,NA
bsdb:1043/9/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 9,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Uninfected Controls,CD4+ T cells < 200 cells/mm3,Subjects whose CD4+ T cells were defined as < 200 cells/mm3.,15,NA,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,1 May 2024,Aleru Divine,Aleru Divine,The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|1236|135625|712|724;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572,Complete,NA
bsdb:1043/10/2,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 10,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Uninfected Controls,CD4+ T cells > 200 cells/mm3,Subjects whose CD4+ T cells were defined as > 200 cells/mm3.,15,NA,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,1 May 2024,Aleru Divine,Aleru Divine,The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|201174|1760|2037|2049|1654;2|1239|186801|186802|216572;2|201174|1760|85006|1268|32207,Complete,NA
bsdb:1043/11/1,Study 1043,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q , Zhang T",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 11,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,CD4+ T cells < 200 cells/mm3,CD4+ T cells > 200 cells/mm3,Subjects whose CD4+ T cells were defined as > 200 cells/mm3.,NA,NA,Participants who had used antibiotics within the previous 4 weeks were excluded,16S,45,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,1 May 2024,Aleru Divine,Aleru Divine,The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1224|1236|135625|712|724;2|201174|1760|2037|2049|1654;2|1239|186801|186802|216572;2|201174|1760|85006|1268|32207,Complete,NA
bsdb:1044/1/NA,Study 1044,"cross-sectional observational, not case-control",35416686,https://doi.org/10.1128/spectrum.00344-21,NA,"Su J, Li CX, Liu HY, Lian QY, Chen A, You ZX, Li K, Cai YH, Lin YX, Pan JB, Zhang GX, Ju CR, You CX , He JX",The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients,Microbiology spectrum,2022,"16S rRNA, airway microbiota, infection, lung transplant, rejection",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Lung transplantation,EFO:0010721,Clinically stable (or event-free) recipients,Recipients with infection,Lung transplant recipients (LTRs) with infection,47,103,None,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1044/2/1,Study 1044,"cross-sectional observational, not case-control",35416686,https://doi.org/10.1128/spectrum.00344-21,NA,"Su J, Li CX, Liu HY, Lian QY, Chen A, You ZX, Li K, Cai YH, Lin YX, Pan JB, Zhang GX, Ju CR, You CX , He JX",The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients,Microbiology spectrum,2022,"16S rRNA, airway microbiota, infection, lung transplant, rejection",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,Lung transplantation,EFO:0010721,Clinically stable (or event-free) recipients,Recipients with rejection,Lung transplant recipients (LTRs) with rejection,47,31,None,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 4C,26 March 2024,Scholastica,Scholastica,LEfSe analysis identifying the airway microbiota that were differentially altered among the transplant groups. Only those taxa with LDA scores 4.0 were ultimately considered.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|201174;2|201174|1760|85006|1268;2|201174|1760|85006;2|201174|1760|85006|1268|32207;2|1239|91061|186826|186827;2|1239|91061|186826|186827|46123;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|201174|1760|2037|2049|1654;2|201174|1760|2037;2|201174|1760|2037|2049;2|32066|203490|203491;2|32066|203490|203491|1129771|32067;2|32066|203490;2|32066|203490|203491|1129771,Complete,Peace Sandy
bsdb:1044/3/1,Study 1044,"cross-sectional observational, not case-control",35416686,https://doi.org/10.1128/spectrum.00344-21,NA,"Su J, Li CX, Liu HY, Lian QY, Chen A, You ZX, Li K, Cai YH, Lin YX, Pan JB, Zhang GX, Ju CR, You CX , He JX",The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients,Microbiology spectrum,2022,"16S rRNA, airway microbiota, infection, lung transplant, rejection",Experiment 3,China,Homo sapiens,Sputum,UBERON:0007311,Lung transplantation,EFO:0010721,Recipients with infection,Recipients with rejection,Lung transplant recipients (LTRs) with rejection,103,31,None,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 4C,26 March 2024,Scholastica,Scholastica,LEfSe analysis identifying the airway microbiota that were differentially altered among the transplant groups. Only those taxa with LDA scores 4.0 were ultimately considered.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|1239|91061|186826|186827|46123;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|1239|91061|186826|186827;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|201174|1760|85006|1268;2|201174|1760|85006;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2759|33090|35493|3398|72025|3803|3814|508215,Complete,Peace Sandy
bsdb:1045/1/1,Study 1045,prospective cohort,33407119,https://doi.org/10.1186/s12866-020-02056-3,NA,"Lu ZH, Liu YW, Ji ZH, Fu T, Yan M, Shao ZJ , Long Y",Alterations in the intestinal microbiome and mental health status of workers in an underground tunnel environment,BMC microbiology,2021,"16S rRNA, Brain-gut-microbiota axis, Gut microbiome, Mental distress, Underground tunnel environment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Workers before entry into an underground tunnel (Baseline status (BS)),Workers after entry into an underground tunnel (Exposed status (ES)),Tunnel workers who spent 3 (three) weeks working in the underground tunnel.,48,48,NA,16S,45,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,"Figure 3A, Text (page 3)",22 March 2024,Flo,"Flo,Scholastica",LEfSe and LDA analysis revealed changes in the taxonomic composition of the gut microbiota in ES (Exposed status) compared to BS (Baseline status) tunnel workers.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107;2|201174|84998|84999;2|28221;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|201174|1760|85006|85023|55968;2|201174|1760|85006|85023;2|1239|186801|3082720|186804;2|1224|1236|72274|135621;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:1045/1/2,Study 1045,prospective cohort,33407119,https://doi.org/10.1186/s12866-020-02056-3,NA,"Lu ZH, Liu YW, Ji ZH, Fu T, Yan M, Shao ZJ , Long Y",Alterations in the intestinal microbiome and mental health status of workers in an underground tunnel environment,BMC microbiology,2021,"16S rRNA, Brain-gut-microbiota axis, Gut microbiome, Mental distress, Underground tunnel environment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Workers before entry into an underground tunnel (Baseline status (BS)),Workers after entry into an underground tunnel (Exposed status (ES)),Tunnel workers who spent 3 (three) weeks working in the underground tunnel.,48,48,NA,16S,45,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,"Figure 3A, Text (page 3)",22 March 2024,Flo,Flo,LEfSe and LDA analysis revealed changes in the taxonomic composition of the gut microbiota in ES (Exposed status) compared to BS (Baseline status) tunnel workers.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:1046/1/1,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Aging,GO:0007568,PLWOH,PLWH on ART,People living with HIV(PLWH) on Anti-Retroviral Therapy(ART),23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig 4D,22 March 2024,Imaspecial,Imaspecial,"Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWoH and PLWH on ART.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2|976|200643|171549|171552|1283313;2|1239|526524|526525|2810280|135858,Complete,NA
bsdb:1046/1/2,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Aging,GO:0007568,PLWOH,PLWH on ART,People living with HIV(PLWH) on Anti-Retroviral Therapy(ART),23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig 4D,22 March 2024,Imaspecial,Imaspecial,"Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWoH and PLWH on ART.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|526524|526525|128827|331630,Complete,NA
bsdb:1046/2/1,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 2,United States of America,Homo sapiens,Ileum,UBERON:0002116,Aging,GO:0007568,PLWOH,PLWH on ART,People living with HIV(PLWH) on Anti-Retroviral Therapy(ART),23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4D,22 March 2024,Imaspecial,Imaspecial,"Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWoH and PLWH on ART.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2|976|200643|171549|171552|1283313;2|1239|526524|526525|2810280|135858,Complete,NA
bsdb:1046/2/2,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 2,United States of America,Homo sapiens,Ileum,UBERON:0002116,Aging,GO:0007568,PLWOH,PLWH on ART,People living with HIV(PLWH) on Anti-Retroviral Therapy(ART),23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 4D,22 March 2024,Imaspecial,Imaspecial,"Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWOH and PLWH on ART",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1239|186801|186802|216572|292632;2|1239|526524|526525|128827|331630,Complete,NA
bsdb:1046/3/1,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,PLWOH,PLWH on ART,People living with HIV(PLWH) on Anti-Retroviral Therapy (ART),23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4D,22 March 2024,Imaspecial,Imaspecial,"Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWOH and PLWH on ART.",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|526524|526525|2810280|135858;2|1239|186801|3085636|186803,Complete,NA
bsdb:1046/3/2,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,PLWOH,PLWH on ART,People living with HIV(PLWH) on Anti-Retroviral Therapy (ART),23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 4D,22 March 2024,Imaspecial,Imaspecial,"Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWOH and PLWH on ART.",decreased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,2|1239|526524|526525|128827|331630,Complete,NA
bsdb:1046/4/1,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 4,United States of America,Homo sapiens,"Colon,Feces","UBERON:0001155,UBERON:0001988",Aging,GO:0007568,Samples of PLWOH,Samples PLWH on ART,Colon vs fecal samples of People living with HIV on ART,23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4C,22 March 2024,Imaspecial,Imaspecial,"Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include colon vs. feces (red), ileum vs. feces (blue), and ileum vs. colon (green).",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|1407607;2|1239|526524|526525|128827|1573535;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263|438033;2|1239|91061|186826|1300|1301;2|1239|526524|526525|128827|331630,Complete,NA
bsdb:1046/4/2,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 4,United States of America,Homo sapiens,"Colon,Feces","UBERON:0001155,UBERON:0001988",Aging,GO:0007568,Samples of PLWOH,Samples PLWH on ART,Colon vs fecal samples of People living with HIV on ART,23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 4C,22 March 2024,Imaspecial,Imaspecial,"Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include colon vs. feces (red), ileum vs. feces (blue), and ileum vs. colon (green).",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|s__uncultured Firmicutes bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816;2|1224|1236|91347|543;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|2316020|33039;2|1239|344338,Complete,NA
bsdb:1046/5/1,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 5,United States of America,Homo sapiens,"Ileum,Feces","UBERON:0002116,UBERON:0001988",Aging,GO:0007568,Samples of PLWOH,Samples of PLWH on ART,Ileum vs Feces of people living with HIV on ART,23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4C,22 March 2024,Imaspecial,Imaspecial,"Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include colon vs. feces (red), ileum vs. feces (blue), and ileum vs. colon (green).",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|1239|186801|3085636|186803|1766253;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1407607;2|1239|526524|526525|128827|1573535;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263|438033;2|1239|526524|526525|128827|331630,Complete,NA
bsdb:1046/5/2,Study 1046,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A , Abdel-Mohsen M",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 5,United States of America,Homo sapiens,"Ileum,Feces","UBERON:0002116,UBERON:0001988",Aging,GO:0007568,Samples of PLWOH,Samples of PLWH on ART,Ileum vs Feces of people living with HIV on ART,23,25,Not stated,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 4C,22 March 2024,Imaspecial,Imaspecial,"Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include colon vs. feces (red), ileum vs. feces (blue), and ileum vs. colon (green).",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816;2|1224|1236|91347|543;2|32066|203490|203491|203492|848;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|2316020|33038;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|2316020|33039,Complete,NA
bsdb:1047/1/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS group,Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.,6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Verrucomicrobiota",2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|570;2|1224|1236;2|1224;2|976|200643|171549|815|816;2|976|200643|171549|815;2|976|200643;2|976|200643|171549;2|32066|203490;2|74201,Complete,NA
bsdb:1047/1/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS group,Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.,6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Bacillota,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Armatimonadota",2|1239|91061|1385;2|201174;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|200795|32061;2|1239;2|142182|219685;2|67819,Complete,NA
bsdb:1047/2/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS + XYS group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of XYS.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Mycoplasmatota",2|1239;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|544448,Complete,NA
bsdb:1047/2/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS + XYS group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of XYS.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174;2|67819;2|1239|91061|1385;2|1239;2|200795|32061;2|142182|219685;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1047/3/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS + FLX group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Atribacterota|g__Candidatus Caldatribacterium|s__Candidatus Caldatribacterium californiense,k__Bacteria|p__Planctomycetota|c__Planctomycetia",2|1239|526524|526525|128827|174708;2|1239|526524|526525|128827;2|1239|526524;2|1239|526524|526525;2|976|200643;2|1117;2|200930|68337;2|57723;2|1090;2|67818|1454725|1454726;2|203682|203683,Complete,NA
bsdb:1047/3/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS + FLX group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Armatimonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota,k__Bacteria|p__Chloroflexota|c__Chloroflexia,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174;2|67819;2|1239|91061|1385;2|1239;2|200795|32061;2|142182|219685;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1047/4/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS group,CUMS + XYS group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of XYS.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Mycoplasmatota",2|1239;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|544448,Complete,NA
bsdb:1047/4/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS group,CUMS + XYS group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of XYS.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Verrucomicrobiota",2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|570;2|1224|1236;2|1224;2|976|200643|171549|815|816;2|976|200643|171549|815;2|976|200643;2|976|200643|171549;2|32066|203490;2|74201,Complete,NA
bsdb:1047/5/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS group,CUMS + FLX group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Atribacterota|g__Candidatus Caldatribacterium|s__Candidatus Caldatribacterium californiense,k__Bacteria|p__Planctomycetota|c__Planctomycetia",2|1239|526524|526525|128827|174708;2|1239|526524|526525|128827;2|1239|526524;2|1239|526524|526525;2|976|200643;2|1117;2|200930|68337;2|57723;2|1090;2|67818|1454725|1454726;2|203682|203683,Complete,NA
bsdb:1047/5/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS group,CUMS + FLX group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Verrucomicrobiota",2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|570;2|1224|1236;2|1224;2|976|200643|171549|815|816;2|976|200643|171549|815;2|976|200643;2|976|200643|171549;2|32066|203490;2|74201,Complete,NA
bsdb:1047/6/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS + XYS group,CUMS + FLX group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Deferribacterota|c__Deferribacteres,k__Bacteria|p__Acidobacteriota,k__Bacteria|p__Chlorobiota,k__Bacteria|p__Atribacterota|g__Candidatus Caldatribacterium|s__Candidatus Caldatribacterium californiense,k__Bacteria|p__Planctomycetota|c__Planctomycetia",2|1239|526524|526525|128827|174708;2|1239|526524|526525|128827;2|1239|526524;2|1239|526524|526525;2|976|200643;2|1117;2|200930|68337;2|57723;2|1090;2|67818|1454725|1454726;2|203682|203683,Complete,NA
bsdb:1047/6/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS + XYS group,CUMS + FLX group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of FLX.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,Aleru Divine,LEfSe analysis of the differentially abundant taxa in each groups.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Mycoplasmatota",2|1239;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|544448,Complete,NA
bsdb:1047/7/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS,Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.,6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8G,22 March 2024,Aleru Divine,Aleru Divine,The representation of the differentially abundant taxa between the CUMS and the control group.,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1047/7/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS,Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.,6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8G,22 March 2024,Aleru Divine,Aleru Divine,The representation of the differentially abundant taxa between CUMS and control.,decreased,"k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1047/8/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,Control + FMT(CUMS) group,"Mice group with no stress stimulation for 8 weeks, followed by daily FMT (feces from CUMS group in the first experiment.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8i,22 March 2024,Aleru Divine,"Aleru Divine,Scholastica",The representation of the differentially abundant taxa between the Control + FMT(CUMS) group and the control group.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota",2|1239|526524|526525|128827|174708;2|976|200643|171549;2|976|200643;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976,Complete,NA
bsdb:1047/8/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,Control + FMT(CUMS) group,"Mice group with no stress stimulation for 8 weeks, followed by daily FMT (feces from CUMS group in the first experiment.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8i,22 March 2024,Aleru Divine,Aleru Divine,The representation of the differentially abundant taxa between the Control + FMT(CUMS) group and the control group.,decreased,k__Bacteria|p__Bacillota,2|1239,Complete,NA
bsdb:1047/9/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group,CUMS + FMT(XYS) group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily FMT (feces from CUMS + XYS group in the first experiment) for 4 weeks.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Text and Figure S5f,22 March 2024,Aleru Divine,Aleru Divine,Differential abundance in the Control group and the CUMS + FMT(XYS) group,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|1239|91061|186826|33958|1578;2|74201|203494|48461|1647988|239934,Complete,NA
bsdb:1047/10/1,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS group,CUMS + FMT(XYS) group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily FMT (feces from CUMS + XYS group in the first experiment) for 4 weeks.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8K,22 March 2024,Aleru Divine,Aleru Divine,The representation of the differentially abundant taxa between the CUMS and the CUMS + FMT(XYS) group.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria",2|976|200643|171549|171552|838;2,Complete,NA
bsdb:1047/10/2,Study 1047,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W, Ma Q, Wang L, Yuan N, Gan H, He L, Li X, Huang J , Chen J",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,CUMS group,CUMS + FMT(XYS) group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily FMT (feces from CUMS + XYS group in the first experiment) for 4 weeks.",6,6,NA,16S,34,NA,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8K,22 March 2024,Aleru Divine,Aleru Divine,The representation of the differentially abundant taxa between the Control + FMT(CUMS) group and the CUMS group.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|31979|49082;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|1263,Complete,NA
bsdb:1048/1/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 1,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 64 hours (-80°C),P1 sample spiked with a mock community and stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/2/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 2,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 64 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/3/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 3,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 64 hours (5°C),P1 sample spiked with a mock community and stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/4/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 4,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 64 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/5/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 5,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 16 hours (-80°C),P1 sample spiked with a mock community and stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/6/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 6,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 16 hours (5°C),P1 samplespiked with a mock community and stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/7/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 7,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 16 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/8/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 8,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 0 hour,Spiked pig feces(P1) at 16 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/9/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 9,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 64 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/10/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 10,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 64 hours (-80°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (-80°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/11/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 11,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 64 hours (-20°C),P1 samplespiked with a mock community and  stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/12/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 12,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 16 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/13/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 13,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 64 hours (5°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/14/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 14,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 16 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/15/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 15,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 16 hours (5°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/16/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 16,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-80°C),Spiked pig feces(P1) at 16 hours (5°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/17/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 17,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-80°C),Spiked pig feces(P1) at 16 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/18/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 18,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-80°C),Spiked pig feces(P1) at 64 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/19/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 19,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (5°C),Spiked pig feces(P1) at 64 hours (22°C),P1 sample spiked with a mock community and  stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/20/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 20,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-20°C),Spiked pig feces(P1) at 64 hours (22°C),P1 sample spiked with a mock community and  stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/21/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 21,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (22°C),Spiked pig feces(P1) at 64 hours (5°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/22/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 22,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-20°C),Spiked pig feces(P1) at 64 hours (22°C),P1 sample spiked with a mock community and  stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/23/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 23,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (22°C),Spiked pig feces(P1) at 64 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/24/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 24,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-80°C),Spiked pig feces(P1) at 16 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/25/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 25,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-20°C),Spiked pig feces(P1) at 16 hours (22°C),P1 sample spiked with a mock community and  stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/26/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 26,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-20°C),Spiked pig feces(P1) at 64 hours (5°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/27/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 27,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-80°C),Spiked pig feces(P1) at 64 hours (5°C),P1 sample spiked with a mock community and  stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/28/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 28,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-20°C),Spiked pig feces(P1) at 64 hours (5°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/29/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 29,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (5°C),Spiked pig feces(P1) at 64 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/30/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 30,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-80°C),Spiked pig feces(P1) at 16 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/31/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 31,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (-80°C),Spiked pig feces(P1) at 64 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/32/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 32,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (-20°C),Spiked pig feces(P1) at 64 hours (-20°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/33/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 33,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked P1 sample stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Bolanle,Bolanle,"Prevotella (class Bacteroidia), the most abundant genus in pig feces, was more abundant for P1 frozen samples than in samples undergoing immediate DNA isolation,  Phascolarctobacterium (class Negativicutes), also had higher abundance in stored samples than for samples processed immediately.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/33/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 33,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked P1 sample stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/34/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 34,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked P1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Bolanle,Bolanle,"Prevotella (class Bacteroidia), the most abundant genus in pig feces, was abundant for P1 frozen samples than in samples undergoing immediate DNA isolation, Phascolarctobacterium (class Negativicutes), also had higher abundance in stored samples than for samples processed immediately",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/34/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 34,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked P1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/35/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 35,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 1,Figure 4,30 March 2024,Bolanle,Bolanle,"Prevotella (class Bacteroidia), the most abundant genus in pig feces, was abundant for P1 frozen samples than in samples undergoing immediate DNA isolation, Phascolarctobacterium (class Negativicutes), also had higher abundance in stored samples than for samples processed immediately",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/35/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 35,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 2,Figure 4,30 March 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/36/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 36,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,30 March 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/36/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 36,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,30 March 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/37/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 37,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,Signature 1,Figure 4,30 March 2024,Bolanle,Bolanle,NA,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/37/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 37,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,Signature 2,Figure 4,1 April 2024,Bolanle,Bolanle,NA,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/38/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 38,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,decreased,NA,NA,Signature 1,Figure 4,1 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/38/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 38,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,decreased,NA,NA,Signature 2,Figure 4,1 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/39/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 39,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,1 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/39/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 39,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,1 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/40/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 40,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,1 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/40/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 40,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 0 hour,Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,1 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/41/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 41,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked P1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4,1 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/41/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 41,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked P1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 4,1 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/42/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 42,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,1 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/42/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 42,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,1 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/43/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 43,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/43/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 43,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/44/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 44,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/44/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 44,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/45/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 45,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/45/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 45,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/46/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 46,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/46/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 46,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/47/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 47,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed imm,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/47/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 47,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-80°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,lower abundance with increasing temperature and time was detected in samples processed immediately,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/48/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 48,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/48/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 48,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/49/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 49,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/49/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 49,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/50/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 50,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/50/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 50,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/51/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 51,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/51/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 51,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/52/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 52,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/52/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 52,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/53/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 53,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/53/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 53,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-80°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,lower abundance with increasing temperature and time was detected in samples processed immediately.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/54/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 54,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/54/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 54,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked P1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/55/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 55,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/55/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 55,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/56/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 56,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,2 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/56/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 56,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,2 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/57/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 57,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/57/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 57,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/58/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 58,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/58/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 58,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (-20°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/59/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 59,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (5°C),Spiked pig feces(P1) at 64 hours (5°C),P1 samplespiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/60/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 60,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (5°C),Spiked pig feces(P1) at 16 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/61/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 61,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 64 hours (5°C),Spiked pig feces(P1) at 16 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/62/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 62,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/62/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 62,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 16 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/63/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 63,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P1) at 16 hours (22°C),Spiked pig feces(P1) at 64 hours (22°C),P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/64/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 64,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/64/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 64,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/65/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 65,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/65/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 65,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/66/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 66,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/66/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 66,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (-20°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/67/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 67,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/67/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 67,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked pig feces(P1) at 64 hours (5°C),Unspiked P1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/68/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 68,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/68/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 68,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/69/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 69,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/69/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 69,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (5°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/70/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 70,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (5°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/70/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 70,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (5°C),Unspiked pig feces(P1) at 16 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/71/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 71,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (5°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/71/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 71,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 64 hours (5°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/72/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 72,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (22°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,higher abundance with increasing temperature and time was detected in samples processed immediately,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/72/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 72,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P1) at 16 hours (22°C),Unspiked pig feces(P1) at 64 hours (22°C),Unspiked P1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,3 April 2024,Bolanle,Bolanle,There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/73/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 73,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 64 hours (-80°C),P2 sample spiked with a mock community and stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/74/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 74,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 64 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/75/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 75,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 64 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/76/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 76,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 64 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/77/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 77,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 16 hours (-80°C),P2 sample spiked with a mock community and stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/78/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 78,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 16 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/79/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 79,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 16 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/80/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 80,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 0 hour,Spiked pig feces(P2) at 16 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/81/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 81,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 64 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/82/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 82,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 64 hours (-80°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (-80°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/83/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 83,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 64 hours (-20°C),P2 sample spiked with a mock community and  stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/84/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 84,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 16 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/85/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 85,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 64 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/86/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 86,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 16 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/87/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 87,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 16 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/88/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 88,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-80°C),Spiked pig feces(P2) at 16 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/89/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 89,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-80°C),Spiked pig feces(P2) at 16 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/90/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 90,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-80°C),Spiked pig feces(P2) at 64 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/91/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 91,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (5°C),Spiked pig feces(P2) at 64 hours (22°C),P2 sample spiked with a mock community and  stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/92/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 92,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-20°C),Spiked pig feces(P2) at 64 hours (22°C),P2 sample spiked with a mock community and  stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/93/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 93,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (22°C),Spiked pig feces(P2) at 64 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/94/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 94,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-20°C),Spiked pig feces(P2) at 64 hours (22°C),P2 sample spiked with a mock community and  stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/95/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 95,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (22°C),Spiked pig feces(P2) at 64 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/96/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 96,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-80°C),Spiked pig feces(P2) at 16 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/97/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 97,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-20°C),Spiked pig feces(P2) at 16 hours (22°C),P2 sample spiked with a mock community and  stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/98/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 98,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-20°C),Spiked pig feces(P2) at 64 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/99/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 99,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-80°C),Spiked pig feces(P2) at 64 hours (5°C),P2 sample spiked with a mock community and  stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/100/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 100,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-20°C),Spiked pig feces(P2) at 64 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/101/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 101,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (5°C),Spiked pig feces(P2) at 64 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/102/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 102,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-80°C),Spiked pig feces(P2) at 16 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/103/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 103,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (-80°C),Spiked pig feces(P2) at 64 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/104/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 104,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (-20°C),Spiked pig feces(P2) at 64 hours (-20°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/105/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 105,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (5°C),Spiked pig feces(P2) at 64 hours (5°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (5°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/106/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 106,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 16 hours (5°C),Spiked pig feces(P2) at 16 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/107/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 107,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,NA,NA,Spiked pig feces(P2) at 64 hours (5°C),Spiked pig feces(P2) at 16 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 16 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/108/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 108,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Spiked pig feces(P2) at 16 hours (22°C),Spiked pig feces(P2) at 64 hours (22°C),P2 sample spiked with a mock community and stored at a temperature of 64 hours (22°C),1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/109/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 109,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked P2 sample stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/109/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 109,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked P2 sample stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|186801|186802|216572|216851;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/110/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 110,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked P2 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,unchanged,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/110/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 110,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked P2 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,unchanged,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/111/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 111,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,unchanged,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/111/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 111,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,unchanged,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/112/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 112,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/112/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 112,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/113/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 113,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/113/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 113,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/114/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 114,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/114/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 114,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/115/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 115,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/115/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 115,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/116/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 116,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/116/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 116,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 0 hour,Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/117/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 117,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (80°C),Unspiked P2 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/117/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 117,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (80°C),Unspiked P2 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/118/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 118,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/118/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 118,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/119/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 119,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/119/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 119,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/120/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 120,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/120/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 120,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/121/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 121,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/121/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 121,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/122/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 122,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/122/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 122,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/123/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 123,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/123/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 123,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-80°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,27 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/124/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 124,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,28 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/124/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 124,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,28 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
bsdb:1048/125/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 125,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,28 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/125/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 125,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,28 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/126/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 126,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,28 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/126/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 126,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,28 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/127/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 127,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,28 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/127/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 127,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/128/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 128,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2.,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/128/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 128,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/129/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 129,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|203691|203692|136|2845253|157;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/129/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 129,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-80°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/130/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 130,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/130/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 130,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked P2 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/131/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 131,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/131/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 131,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/132/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 132,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/132/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 132,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/133/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 133,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/133/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 133,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/134/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 134,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/134/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 134,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (-20°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,29 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/135/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 135,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/135/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 135,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 16 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/136/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 136,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/136/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 136,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/137/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 137,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1239|186801|186802|216572|216851;2|203691|203692|136|2845253|157;2|1239|186801|3085636|186803|841;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/137/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 137,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/138/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 138,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/138/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 138,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (-20°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/139/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 139,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/139/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 139,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked pig feces(P2) at 64 hours (5°C),Unspiked P2 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/140/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 140,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/140/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 140,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/141/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 141,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/141/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 141,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (5°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/142/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 142,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (5°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157,Complete,NA
bsdb:1048/142/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 142,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (5°C),Unspiked pig feces(P2) at 16 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/143/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 143,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (5°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024,Complete,NA
bsdb:1048/143/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 143,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 64 hours (5°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/144/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 144,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (22°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,increased,"k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",2|203691|203692|136|2845253|157;2|1239|909932|1843488|909930|33024;2|1239|186801|3085636|186803|841,Complete,NA
bsdb:1048/144/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 144,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Microbiome,EFO:0004982,Unspiked pig feces(P2) at 16 hours (22°C),Unspiked pig feces(P2) at 64 hours (22°C),Unspiked P2 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,30 March 2024,Aleru Divine,Aleru Divine,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked pig feces P2,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/145/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 145,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked S1 sample stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 1,Figure 4,3 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/145/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 145,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked S1 sample stored at a temperature of -80°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,Signature 2,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1048/146/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 146,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked S1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/146/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 146,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked S1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/147/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 147,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 1,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/147/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 147,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 2,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/148/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 148,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 1,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|29547|3031852|213849|2808963|28196;2|1224|1236|135624|84642|642;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/148/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 148,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 2,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|976|200643|171549|2005525|375288;2|1224|1236|2887326|468|469,Complete,NA
bsdb:1048/149/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 149,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 1,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/149/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 149,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,increased,NA,NA,Signature 2,Figure 4,4 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1048/150/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 150,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,7 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/150/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 150,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,7 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469,Complete,NA
bsdb:1048/151/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 151,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,increased,NA,NA,Signature 1,Figure 4,7 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/151/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 151,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,increased,NA,NA,Signature 2,Figure 4,7 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469,Complete,NA
bsdb:1048/152/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 152,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 1,Figure 4,7 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/152/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 152,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 0 hours,Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,Signature 2,Figure 4,7 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1048/153/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 153,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked S1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,17 April 2024,Bolanle,Bolanle,NA,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/153/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 153,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked S1 sample stored at a temperature of -80°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/154/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 154,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,2|1224|1236|2887326|468|469,Complete,NA
bsdb:1048/154/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 154,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/155/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 155,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/155/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 155,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/156/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 156,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 1,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/156/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 156,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 2,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/157/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 157,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 1,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1048/157/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 157,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,Signature 2,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/158/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 158,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 1,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/158/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 158,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,unchanged,NA,NA,Signature 2,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/159/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 159,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,17 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/159/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 159,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,19 April 2024,Bolanle,Bolanle,NA,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1048/160/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 160,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,20 April 2024,Bolanle,Bolanle,NA,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/160/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 160,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,20 April 2024,Bolanle,Bolanle,NA,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/161/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 161,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,27 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/161/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 161,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,27 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/162/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 162,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,27 April 2024,Bolanle,Bolanle,"
: Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1
",increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838,Complete,NA
bsdb:1048/162/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 162,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,28 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/163/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 163,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/164/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 164,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/165/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 165,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-80°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/166/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 166,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked S1 sample stored at a temperature of -20°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/167/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 167,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/168/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 168,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/169/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 169,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/170/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 170,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (-20°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/171/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 171,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/172/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 172,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/173/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 173,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/174/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 174,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (-20°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/175/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 175,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked S1 sample stored at a temperature of 5°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/176/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 176,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/177/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 177,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (5°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/178/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 178,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 16 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/179/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 179,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 64 hours (5°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/180/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 180,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S1) at 16 hours (22°C),Unspiked sewage samples (S1) at 64 hours (22°C),Unspiked S1 sample stored at a temperature of 22°C for 64 hours,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/181/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 181,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked S2 sample stored at a temperature of -80°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/182/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 182,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked S2 sample stored at a temperature of -80°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/183/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 183,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked S2 sample stored at a temperature of -20°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/184/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 184,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked S2 sample stored at a temperature of -20°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/185/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 185,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/186/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 186,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/187/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 187,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/188/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 188,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 0 hour,Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/189/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 189,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked S2 sample stored at a temperature of -80°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/190/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 190,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked S2 sample stored at a temperature of -20°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/191/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 191,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked S2 sample stored at a temperature of -20°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/192/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 192,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/193/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 193,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/194/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 194,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/195/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 195,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-80°C),Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/196/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 196,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked S2 sample stored at a temperature of -20°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/197/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 197,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked S2 sample stored at a temperature of -20°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/198/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 198,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/199/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 199,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/200/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 200,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/201/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 201,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-80°C),Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/202/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 202,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked S2 sample stored at a temperature of -20°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/203/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 203,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/204/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 204,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/205/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 205,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/206/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 206,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (-20°C),Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/207/1,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 207,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 1,Figure 4,18 April 2024,Bolanle,Bolanle,NA,increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1048/207/2,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 207,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,Signature 2,Figure 4,18 April 2024,Bolanle,Bolanle,Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S2,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|29547|3031852|213849|2808963|28196;2|1224|1236|2887326|468|469;2|976|200643|171549|171552|838;2|1224|1236|135624|84642|642,Complete,NA
bsdb:1048/208/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 208,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/209/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 209,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/210/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 210,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (-20°C),Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/211/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 211,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked S2 sample stored at a temperature of 5°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/212/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 212,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/213/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 213,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (5°C),Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,unchanged,NA,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/214/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 214,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 16 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/215/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 215,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 64 hours (5°C),Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,increased,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1048/216/NA,Study 1048,laboratory experiment,34612701,10.1128%2FSpectrum.01387-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/,"Poulsen CS, Kaas RS, Aarestrup FM , Pamp SJ",Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns,Microbiology spectrum,2021,"antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community",Experiment 216,Denmark,Not specified,NA,NA,Microbiome,EFO:0004982,Unspiked sewage samples (S2) at 16 hours (22°C),Unspiked sewage samples (S2) at 64 hours (22°C),Unspiked S2 sample stored at a temperature of 22°C for 64 hours.,1,1,NA,WMS,NA,Illumina,DESeq2,0.01,FALSE,NA,NA,NA,decreased,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1049/1/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 1,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable.,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter",2|201174|1760|85006|1268|1663;2|201174|1760|85007|1653|1716;2|1224|28216|80840|80864|281915,Complete,NA
bsdb:1049/2/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 2,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella",2|201174|1760|85006|1268|1663;2|1239|91061|1385|186817|1386;2|1297|188787|118964|183710|1298;2|1224|1236|72274|135621|286;2|1224|28211|204441|2829815|204447,Complete,NA
bsdb:1049/2/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 2,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216;2|1224|28211|356|119045|407;2|201174|1760|85009|85015|1839;2|1224|28211|204455|31989|265;2|1224|28211|204441|433|125216;2|1224|28211|204455|2854170|295418;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:1049/3/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 3,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs,increased,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,2|976|768503|768507|1853232|89966,Complete,NA
bsdb:1049/3/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 3,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1224|28211|204441|433|434;2|32066|203490|203491|203492|848,Complete,NA
bsdb:1049/4/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 4,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Frederiksenia",2|1224|1236|2887326|468|469;2|1224|28216|80840|80864|281915;2|1224|1236|135625|712|1649317,Complete,NA
bsdb:1049/4/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 4,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1224|28211|204441|433|434;2|976|117743|200644|49546|1016;2|201174|1760|85009|85015|86795;2|1239|909932|909929|1843491|158846,Complete,NA
bsdb:1049/5/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 5,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera",2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1912216;2|1297|188787|118964|183710|1298;2|32066|203490|203491|203492|848;2|201174|1760|85009|85015|86795;2|201174|1760|85009|85015|1839;2|1224|28216|80840|80864|219181;2|1224|28211|204455|31989|265;2|1224|1236|72274|135621|286;2|1224|28211|204455|2854170|295418;2|1297|188787|2762275|332247|332248,Complete,NA
bsdb:1049/5/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 5,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,decreased,"k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|976|1853228|1853229|563835|398041;2|976|768503|768507|1853232|89966;2|1224|28211|356|119045|407;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|1224|28211|204441|2829815|204447;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1049/6/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 6,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Buchananella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85006|1268|1663;2|201174|1760|1643682|85030|38501;2|201174|1760|2037|2049|2767323;2|976|117743|200644|49546|1016;2|201174|1760|85009|31957|1912216;2|32066|203490|203491|203492|848;2|1239|91061|1385|539738|1378;2|201174|1760|85009|85015|1839;2|201174|84995|84996|84997|42255;2|976|768503|768507|89373|107;2|1239|91061|186826|1300|1301,Complete,NA
bsdb:1049/6/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 6,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|28211|204441|2829815|204447;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1049/7/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 7,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Bacteria|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella",2|1239|186801|3085636|186803|572511;2|1224|28216|80840|119060|47670;2|976|200643|171549|171551|836;2|201174|1760|85006|1268|1742993;2|201174|84995|84996|84997|42255;2|1224|28211|204441|2829815|204447,Complete,NA
bsdb:1049/7/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 7,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Conchiformibius,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",2|1224|1236|2887326|468|469;2|1224|28216|206351|481|334107;2|1224|28211|356|119045|407;2|201174|1760|85006|85023|33882;2|1224|1236|135625|712|745;2|1224|28216|80840|80864|34072,Complete,NA
bsdb:1049/8/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 8,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the phylum level between two groups; cADpre dogs and cADpost dogs,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|976|117743|200644|49546|1016;2|1224|1236|91347|543|547;2|1239|186801|3082720|3118655|44259;2|32066|203490|203491|203492|848;2|1224|28211|356|119045|186650;2|1224|1236|135625|712|745;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1049/8/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 8,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera",2|1224|28211|204441|433|434;2|201174|1760|2037|2049|1654;2|976|117743|200644|2762318|59735;2|201174|1760|85009|31957|1912216;2|1297|188787|118964|183710|1298;2|1224|28216|80840|119060|47670;2|1224|28211|356|119045|407;2|201174|1760|85009|31957|29404;2|1224|28216|206351|481|482;2|201174|1760|85009|85015|1839;2|1224|28216|80840|80864|219181;2|976|200643|171549|171551|836;2|1224|28211|204455|2854170|295418;2|201174|1760|2037|2049|2529408;2|1239|91061|186826|1300|1301;2|1297|188787|2762275|332247|332248,Complete,NA
bsdb:1049/9/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 9,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADpre dogs,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|976|200643|171549|171551|836;2759|33090|35493|3398|72025|3803|3814|508215,Complete,NA
bsdb:1049/9/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 9,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADpre dogs,decreased,"k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|976|768503|768507|1853232|89966;2|201174|1760|85009|85015|86795;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1049/10/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 10,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADtreat dogs,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|201174|1760|2037|2049|1654;2|976|117743|200644|2762318|501783;2|1224|1236|2887326|468|475,Complete,NA
bsdb:1049/10/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 10,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADtreat dogs,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1224|28216|80840|119060|47670;2|1224|28216|80840|75682|149698;2|976|200643|171549|171551|836;2|1224|28211|204441|433|125216;2|1239|91061|1385|90964|1279;2|1239|526524|526525|2810281|191303,Complete,NA
bsdb:1049/11/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 11,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|1643682|85030|38501;2|1239|186801|3085636|186803|572511;2|1297|188787|118964|183710|1298;2|976|1853228|1853229|563835|398041;2|1224|1236|91347|1903414|583;2|1224|28211|204455|2854170|295418;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1049/11/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 11,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,Deacme,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|201174|1760|85006|1268|1663;2|976|200643|171549|815|816;2|201174|1760|85009|31957|1912216;2|1224|28211|204458|76892|41275;2|1239|186801|3085636|186803|2005355;2|976|117743|200644|49546|237;2|1224|28216|80840|119060|47670;2|1224|28211|356|119045|407;2|201174|1760|85009|31957|29404;2|1224|28211|356|119045|186650;2|201174|1760|1643684|85031|53460;2|201174|1760|85009|85015|1839;2|976|200643|171549|171551|836;2|1224|28211|204441|2829815|204447;2|1224|28211|204457|41297|13687,Complete,NA
bsdb:1049/12/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 12,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable.,16S,34,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,30 March 2024,Barrakat,Barrakat,Differentially abundant faecal bacterial taxa at the genus level between two groups cADpre and Healthy dogs,increased,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,2|32066|203490|203491|203492|848,Complete,NA
bsdb:1049/12/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 12,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable.,16S,34,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,30 March 2024,Barrakat,Barrakat,Differentially abundant faecal bacterial taxa at the genus level between two groups cADpre and Healthy dogs,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|526524|526525|128827|2749267;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|946234;2|976|200643|171549|171551|836;2|1239|91061|1385|90964|1279;2|1239|186801|186802|31979|1485,Complete,NA
bsdb:1049/13/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 13,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,cADpre,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable.,16S,34,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,30 March 2024,Barrakat,"Barrakat,MyleeeA",Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|526524|526525|128827|2749267;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803|2005355;2|1239|186801|186802|216572|946234;2|1239|186801|3082720|186804|1505652;2|1239|526524|526525|2810280|3025755;2|1239|186801|186802|31979|1485,Complete,NA
bsdb:1049/13/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 13,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,cADpre,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable.,16S,34,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,30 March 2024,Barrakat,Barrakat,Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|3118652|2039240;2|1239|186801|3085636|186803|2719313;2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836;2|1224|1236|91347|1903414|583;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|91061|1385|90964|1279;2|1239|186801|3085636|186803,Complete,NA
bsdb:1049/14/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 14,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable.,16S,34,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,30 March 2024,Barrakat,Barrakat,Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|1239|186801|3085636|3118652|2039240;2|1239|186801|3085636|186803|2005355;2|201174|1760|85007|1653|1716,Complete,NA
bsdb:1049/14/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 14,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable.,16S,34,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,30 March 2024,Barrakat,"Barrakat,MyleeeA",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|186802|31979|1485;2|1239|526524|526525|2810281|191303,Complete,NA
bsdb:1049/15/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 15,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy controls,cAD Pre,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,MyleeeA,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/16/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 16,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,cAD Pre,cAD post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,N/A,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S4 and Fig 3,1 April 2024,MyleeeA,MyleeeA,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus coagulans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi",2|1239|91061|1385|90964|1279|283734;2|1239|91061|1385|90964|1279|74706;2|1239|91061|1385|90964|1279|1295,Complete,NA
bsdb:1049/17/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 17,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,N/A,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,MyleeeA,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,2|1239|91061|1385|90964|1279|246432,Complete,NA
bsdb:1049/17/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 17,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,N/A,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,MyleeeA,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,2|1239|91061|1385|90964|1279|1282,Complete,NA
bsdb:1049/18/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 18,Japan,Canis lupus familiaris,Axilla skin,UBERON:0015474,Atopic eczema,EFO:0000274,Healthy,cAD Pre,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,N/A,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,MyleeeA,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/19/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 19,Japan,Canis lupus familiaris,Axilla skin,UBERON:0015474,Atopic eczema,EFO:0000274,cAD Pre,cAD post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,N/A,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,MyleeeA,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,2|1239|91061|1385|90964|1279|246432,Complete,NA
bsdb:1049/19/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 19,Japan,Canis lupus familiaris,Axilla skin,UBERON:0015474,Atopic eczema,EFO:0000274,cAD Pre,cAD post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,N/A,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,MyleeeA,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,2|1239|91061|1385|90964|1279|1290,Complete,NA
bsdb:1049/20/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 20,Japan,Canis lupus familiaris,Axilla skin,UBERON:0015474,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus",2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1283,Complete,NA
bsdb:1049/21/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 21,Japan,Canis lupus familiaris,Brachialis muscle,UBERON:0001506,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/22/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 22,Japan,Canis lupus familiaris,Brachialis muscle,UBERON:0001506,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi",2|1239|91061|1385|90964|1279|246432;2|1239|91061|1385|90964|1279|1295,Complete,NA
bsdb:1049/23/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 23,Japan,Canis lupus familiaris,Lateral lumbar region of abdomen,UBERON:0000180,Atopic eczema,EFO:0000274,Healthy controls,cAD Pre,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S4 and Fig 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/24/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 24,Japan,Canis lupus familiaris,Lateral lumbar region of abdomen,UBERON:0000180,Atopic eczema,EFO:0000274,Healthy controls,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus coagulans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi",2|1239|91061|1385|90964|1279|74706;2|1239|91061|1385|90964|1279|246432;2|1239|91061|1385|90964|1279|1295,Complete,NA
bsdb:1049/24/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 24,Japan,Canis lupus familiaris,Lateral lumbar region of abdomen,UBERON:0000180,Atopic eczema,EFO:0000274,Healthy controls,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,5 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,2|1239|91061|1385|90964|1279|1283,Complete,NA
bsdb:1049/25/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 25,Japan,Canis lupus familiaris,Lateral lumbar region of abdomen,UBERON:0000180,Atopic eczema,EFO:0000274,cADpre,cAD Post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Fig 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,2|1239|91061|1385|90964|1279|1290,Complete,NA
bsdb:1049/26/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 26,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy controls,cAD Pre,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,Barrakat,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/27/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 27,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy controls,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,2|1239|91061|1385|90964|1279|246432,Complete,NA
bsdb:1049/28/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 28,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,cADpre,cAD Post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus coagulans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",2|1239|91061|1385|90964|1279|74706;2|1239|91061|1385|90964|1279|1295;2|1239|91061|1385|90964|1279|1292,Complete,NA
bsdb:1049/29/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 29,Japan,Canis lupus familiaris,Hindlimb skin,UBERON:0003532,Atopic eczema,EFO:0000274,Healthy controls,cAD Pre,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/30/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 30,Japan,Canis lupus familiaris,Hindlimb skin,UBERON:0003532,Atopic eczema,EFO:0000274,Healthy controls,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus coagulans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi",2|1239|91061|1385|90964|1279|74706;2|1239|91061|1385|90964|1279|1283;2|1239|91061|1385|90964|1279|1295,Complete,NA
bsdb:1049/31/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 31,Japan,Canis lupus familiaris,Hindlimb skin,UBERON:0003532,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",2|1239|91061|1385|90964|1279|29380;2|1239|91061|1385|90964|1279|283734;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|28035;2|1239|91061|1385|90964|1279|1292,Complete,NA
bsdb:1049/31/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 31,Japan,Canis lupus familiaris,Hindlimb skin,UBERON:0003532,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,NA
bsdb:1049/32/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 32,Japan,Canis lupus familiaris,Inguinal part of abdomen,UBERON:0008337,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not Applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/33/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 33,Japan,Canis lupus familiaris,Inguinal part of abdomen,UBERON:0008337,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,5 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,2|1239|91061|1385|90964|1279|246432,Complete,NA
bsdb:1049/34/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 34,Japan,Canis lupus familiaris,Pinna,UBERON:0001757,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,5 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",2|1239|91061|1385|90964|1279|246432;2|1239|91061|1385|90964|1279|1292,Complete,NA
bsdb:1049/35/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 35,Japan,Canis lupus familiaris,Pinna,UBERON:0001757,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,5 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",2|1239|91061|1385|90964|1279|246432;2|1239|91061|1385|90964|1279|1295;2|1239|91061|1385|90964|1279|1292,Complete,NA
bsdb:1049/36/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 36,Japan,Canis lupus familiaris,Pinna,UBERON:0001757,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,5 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,2|1239|91061|1385|90964|1279|1292,Complete,NA
bsdb:1049/37/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 37,Japan,Canis lupus familiaris,Skin of palmar/plantar part of autopod,UBERON:0013776,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum",2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|246432,Complete,NA
bsdb:1049/37/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 37,Japan,Canis lupus familiaris,Skin of palmar/plantar part of autopod,UBERON:0013776,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/38/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 38,Japan,Canis lupus familiaris,Skin of palmar/plantar part of autopod,UBERON:0013776,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",2|1239|91061|1385|90964|1279|246432;2|1239|91061|1385|90964|1279|1292,Complete,NA
bsdb:1049/39/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 39,Japan,Canis lupus familiaris,Skin of palmar/plantar part of autopod,UBERON:0013776,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,2|1239|91061|1385|90964|1279|1290,Complete,NA
bsdb:1049/40/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 40,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus sciuri,2|1239|91061|1385|90964|2803850|1296,Complete,NA
bsdb:1049/40/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 40,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/41/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 41,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus coagulans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi",2|1239|91061|1385|90964|1279|74706;2|1239|91061|1385|90964|1279|283734;2|1239|91061|1385|90964|1279|1295,Complete,NA
bsdb:1049/42/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 42,Japan,Canis lupus familiaris,Perineum,UBERON:0002356,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,2|1239|91061|1385|90964|1279|1292,Complete,NA
bsdb:1049/43/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 43,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,2|1239|91061|1385|90964|1279|283734,Complete,NA
bsdb:1049/44/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 44,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,2|1239|91061|1385|90964|1279|246432,Complete,NA
bsdb:1049/44/2,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 44,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis",2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1290,Complete,NA
bsdb:1049/45/1,Study 1049,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M, Künstner A, Wohlers I, Olbrich M, Lenfers T, Osumi T, Shimazaki Y, Nishifuji K, Ibrahim SM, Watson A, Busch H , Hirose M",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 45,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,Not applicable,16S,12,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,Deacme,Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,2|1239|91061|1385|90964|1279|1290,Complete,NA
bsdb:1050/1/1,Study 1050,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L, Yin J, Zhao J, Ma SR, Wang HR, Wang M, Chen W , Wei WQ",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 1,China,Homo sapiens,"Oral cavity,Esophagus","UBERON:0000167,UBERON:0001043",Taxonomic microbiome measurement,EFO:0007883,Oral cavity,Esophagus,"Healthy individual who are esophageal disease-free, confirmed by endoscopic examination and then biopsy-based pathological diagnosis if necessary.",27,27,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,increased,decreased,NA,NA,Signature 1,"Figure 3, Supplementary Figure S1",2 May 2024,Scholastica,Scholastica,Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Saprospira,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1224|28211|204441|433;2|1224|1236|2887326|468|469;2|1224|1236|135625|712|713;2|1239|526524|526525|128827|174708;2|1224|28211;2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061;2|1239;2|1239|186801|3085636|186803|572511;2|1224|28211|356|41294|374;2|1224|28211|356|118882;2|1224|28211|204458|76892;2|1224|28211|204458;2|976|1853228|1853229|563835;2|976|117743|200644|2762318|59732;2|1239|186801|3085636|186803|33042;2|1224|28211|356|212791;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|1239|91061|1385|539738;2|1224|28211|356;2|201174|1760|85006|85021;2|1239|91061|186826;2|1224|1236|135614|32033;2|1224|1236|135614;2|1224|28211|356|119045;2|1224|28211|356|119045|407;2|1224|28211|356|41294;2|1224|28211|204457|41297|165696;2|1224|28211|356|118882|528;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|1224|28216|80840|75682;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|28211|204458|76892|20;2|201174|1760|85009|31957|1743;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1224|28216|80840|119060|48736;2|1224|28211|204441|41295;2|1224|28211|204441;2|976|1937959|1936988|89374|1007;2|976|1937959|1936988;2|976|1853228|1853229|563835|504481;2|1224|28211|204457|41297|165695;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1224|1236|135614|32033|40323;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|28211|204441|433;2|1224|28211|356|41294;2|1224|28211|204458|76892;2|1224|1236|91347|543;2|1224|28211|356|119045;2|1239|186801|186802|216572;2|1224|28216|80840|75682;2|1224|28211|204441|41295;2|976|200643|171549|2005473,Complete,Svetlana up
bsdb:1050/1/2,Study 1050,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L, Yin J, Zhao J, Ma SR, Wang HR, Wang M, Chen W , Wei WQ",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 1,China,Homo sapiens,"Oral cavity,Esophagus","UBERON:0000167,UBERON:0001043",Taxonomic microbiome measurement,EFO:0007883,Oral cavity,Esophagus,"Healthy individual who are esophageal disease-free, confirmed by endoscopic examination and then biopsy-based pathological diagnosis if necessary.",27,27,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,increased,decreased,NA,NA,Signature 2,"Figure 3, Supplementary Figure S1",2 May 2024,Scholastica,Scholastica,Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Candidatus Saccharibacteria",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|976|200643|171549;2|976|200643;2|976;2|1224|28216;2|1224|1236|135615|868;2|1224|1236|135615;2|1224|1236|135615|868|2717;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|976|200643|171549|2005523|346096;2|1239|909932|909929|1843491|970;2|95818,Complete,Svetlana up
bsdb:1050/2/1,Study 1050,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L, Yin J, Zhao J, Ma SR, Wang HR, Wang M, Chen W , Wei WQ",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 2,China,Homo sapiens,Oral cavity,UBERON:0000167,Taxonomic microbiome measurement,EFO:0007883,Saliva and tongue dorsum,Supragingival plaque,Supragingival plaque samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.,27,27,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 5,4 May 2024,Scholastica,Scholastica,Significantly higher relative abundance in the supragingival plaques compared to other two sites,increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Spirochaetota|c__Spirochaetia,k__Bacteria|p__Spirochaetota",2|976;2|29547|3031852;2|976|117743;2|32066;2|32066|203490;2|203691|203692;2|203691,Complete,Svetlana up
bsdb:1050/3/1,Study 1050,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L, Yin J, Zhao J, Ma SR, Wang HR, Wang M, Chen W , Wei WQ",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 3,China,Homo sapiens,Oral cavity,UBERON:0000167,Taxonomic microbiome measurement,EFO:0007883,Tongue dorsum and supragingival plaque,Saliva,Saliva samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.,27,27,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2024,Scholastica,Scholastica,Significantly higher relative abundance in the saliva compared to other two sites,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Synergistota",2|976|200643;2|201174|84998;2|508458|649775;2|508458,Complete,Svetlana up
bsdb:1050/4/1,Study 1050,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L, Yin J, Zhao J, Ma SR, Wang HR, Wang M, Chen W , Wei WQ",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 4,China,Homo sapiens,Oral cavity,UBERON:0000167,Taxonomic microbiome measurement,EFO:0007883,Supragingival plaque and Saliva,Tongue dorsum,Tongue dorsum samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.,27,27,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2024,Scholastica,Scholastica,Significantly higher relative abundance in the tongue dorsum compared to other two sites,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Clostridia",2|1239|526524;2|1239|186801,Complete,Svetlana up
bsdb:1051/1/1,Study 1051,"cross-sectional observational, not case-control",38166904,10.1186/s12890-023-02825-6,NA,"Luan J, Zhang F, Suo L, Zhang W, Li Y, Yu X, Liu B , Cao H",Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites,BMC pulmonary medicine,2024,"Biomarkers, Gut microbiota, Lung cancer, Metabolomics, Pulmonary function",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,Benign pulmonary diseases (N group),Lung cancer (L group),"Lung cancer patients graded according to the American Thoracic Society/ European Respiratory Society (ATS/ERS) five level classification method for pulmonary ventilation impairment and divided into 3 groups, including 20 patients with normal lung ventilation, 23 patients with mild pulmonary ventilation dysfunction and 12 patients with moderate or above pulmonary ventilation dysfunction.",28,55,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 2b,21 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Differential taxa at the genus level analyzed by linear discriminant analysis (LDA) scores in lung cancer patients (C) versus benign diseases patients(N),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|815|816;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:1051/1/2,Study 1051,"cross-sectional observational, not case-control",38166904,10.1186/s12890-023-02825-6,NA,"Luan J, Zhang F, Suo L, Zhang W, Li Y, Yu X, Liu B , Cao H",Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites,BMC pulmonary medicine,2024,"Biomarkers, Gut microbiota, Lung cancer, Metabolomics, Pulmonary function",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,Benign pulmonary diseases (N group),Lung cancer (L group),"Lung cancer patients graded according to the American Thoracic Society/ European Respiratory Society (ATS/ERS) five level classification method for pulmonary ventilation impairment and divided into 3 groups, including 20 patients with normal lung ventilation, 23 patients with mild pulmonary ventilation dysfunction and 12 patients with moderate or above pulmonary ventilation dysfunction.",28,55,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 2b,21 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica",Differential taxa at the genus level analyzed by linear discriminant analysis (LDA) scores in lung cancer patients (C) versus benign diseases patients(N),decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Kurthia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae",2|1239|186801|3085636|186803|572511;2|1239|91061|186826|186828|2747;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|1407607;2|1239|91061|1385|186818|1649;2|1239|186801|3085636|186803|1164882;2|201174|1760|85009|31957|1743;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|216572|292632;2|201174|84998|84999|1643824,Complete,Svetlana up
bsdb:1052/1/1,Study 1052,case-control,34384375,10.1186/s12866-021-02286-z,NA,"Xi J, Ding D, Zhu H, Wang R, Su F, Wu W, Xiao Z, Liang X, Zhao Q, Hong Z, Fu H , Xiao Q",Disturbed microbial ecology in Alzheimer's disease: evidence from the gut microbiota and fecal metabolome,BMC microbiology,2021,"Alzheimer’s disease, Fecal markers, Fecal metabolome, Gut microbiota, Inflammatory cytokines",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Cognitively normal control (NC),Alzheimer’s Disease (AD),Participants with Alzheimer’s Disease (AD); the most prevalent neurodegenerative disorder.,44,21,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,Fig. 1B,21 March 2024,Scholastica,Scholastica,Taxonomic differences of gut microbiota bacterial in Alzheimer’s disease (AD) versus cognitively normal control (NC) participants analyzed by Linear discriminant analysis (LDA) effect size (LEfSe),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|3085636|186803|1766253;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|508458|649775|649776|649777|508459;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1410626;2|1239|1737404|1737405|1570339|543311;2|1224|1236|72274|135621|286;2|1239|526524|526525|128827|123375;2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:1052/1/2,Study 1052,case-control,34384375,10.1186/s12866-021-02286-z,NA,"Xi J, Ding D, Zhu H, Wang R, Su F, Wu W, Xiao Z, Liang X, Zhao Q, Hong Z, Fu H , Xiao Q",Disturbed microbial ecology in Alzheimer's disease: evidence from the gut microbiota and fecal metabolome,BMC microbiology,2021,"Alzheimer’s disease, Fecal markers, Fecal metabolome, Gut microbiota, Inflammatory cytokines",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Cognitively normal control (NC),Alzheimer’s Disease (AD),Participants with Alzheimer’s Disease (AD); the most prevalent neurodegenerative disorder.,44,21,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,Fig. 1B,21 March 2024,Scholastica,Scholastica,Taxonomic differences of gut microbiota bacterial in Alzheimer’s disease (AD) versus cognitively normal control (NC) participants analyzed by Linear discriminant analysis (LDA) effect size (LEfSe),decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",2|1239|526524|526525|2810280|3025755;2|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:1053/1/1,Study 1053,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, Xiao KF , Guo JN",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Nephrolithiasis,EFO:0004253,HB group - Bladder urine from healthy controls.,KB group - Bladder urine from kidney stone patients.,Bladder urine collected from nephrolithiasis (Kidney stone) patients.,21,22,30 days.,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Fig. 5A & 5B,22 March 2024,Victoria,Victoria,"A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green), and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05).",increased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|976;2|1239;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186807;2|1224|1236|135614|1775411|231454;2|32066|203490|203491;2|32066|203490;2|32066;2|1224|1236|91347|1903411|34037;2|1239|186801|186802|186807|2740;2|1224|28211|204457|41297|165697;2|1224|28211|356|69277|31988;2|1239|91061|1385|186822|44249;2|976|200643|171549|171551;2|1224|1236|135624;2|976|200643|171549|2005525|375288;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231,Complete,Peace Sandy
bsdb:1053/1/2,Study 1053,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, Xiao KF , Guo JN",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Nephrolithiasis,EFO:0004253,HB group - Bladder urine from healthy controls.,KB group - Bladder urine from kidney stone patients.,Bladder urine collected from nephrolithiasis (Kidney stone) patients.,21,22,30 days.,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,Fig. 5A & 5B,22 March 2024,Victoria,Victoria,"A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",2|1224|1236|2887326|468;2|1224|1236|2887326|468|469;2|1224|1236|72274;2|1224|1236;2|1224;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492,Complete,Peace Sandy
bsdb:1053/2/1,Study 1053,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, Xiao KF , Guo JN",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 2,China,Homo sapiens,Renal pelvis/ureter,UBERON:0036295,Nephrolithiasis,EFO:0004253,KB group - Bladder urine from kidney stone patients.,KP group - Renal pelvis urine from kidney stone patients.,Renal pelvis urine collected from nephrolithiasis (Kidney stone) patients.,22,22,Participants using antibiotics within 30days were excluded.,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5A & 5B,22 March 2024,Victoria,Victoria,"A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1224;2|1224|1236;2|1224|1236|2887326|468;2|1224|1236|2887326|468|469;2|1224|1236|72274,Complete,Peace Sandy
bsdb:1053/2/2,Study 1053,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, Xiao KF , Guo JN",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 2,China,Homo sapiens,Renal pelvis/ureter,UBERON:0036295,Nephrolithiasis,EFO:0004253,KB group - Bladder urine from kidney stone patients.,KP group - Renal pelvis urine from kidney stone patients.,Renal pelvis urine collected from nephrolithiasis (Kidney stone) patients.,22,22,Participants using antibiotics within 30days were excluded.,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5A & 5B,22 March 2024,Victoria,Victoria,"A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus",2|201174|1760|2037;2|1239|91061|1385|186817|150247,Complete,Peace Sandy
bsdb:1054/1/1,Study 1054,case-control,36544085,10.1186/s12866-022-02730-8,NA,"Shabayek S, Abdellah AM, Salah M, Ramadan M , Fahmy N",Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester,BMC microbiology,2022,"Group B Streptococcus, Healthy, Microbiome, Pregnant, Streptococcus agalactiae, Third trimester, Vagina",Experiment 1,Egypt,Homo sapiens,Vagina,UBERON:0000996,Streptococcal infection,EFO:1001476,GBS culture-negative pregnant women,GBS culture-positive pregnant women,Pregnant women who tested positive for Group B Streptococcus (GBS) by culture during the third trimester,22,22,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,parity",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figs. 3 and 4,21 March 2024,Ayibatari,"Ayibatari,Scholastica",Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing taxa with significant differential abundance in GBS culture-negative versus GBS culture-positive pregnant Egyptian women,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus coleohominis",2|1239;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|147802;2|1239|91061|186826|33958|1578|147802;2|1239|91061|186826|33958|2742598|181675,Complete,Svetlana up
bsdb:1054/1/2,Study 1054,case-control,36544085,10.1186/s12866-022-02730-8,NA,"Shabayek S, Abdellah AM, Salah M, Ramadan M , Fahmy N",Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester,BMC microbiology,2022,"Group B Streptococcus, Healthy, Microbiome, Pregnant, Streptococcus agalactiae, Third trimester, Vagina",Experiment 1,Egypt,Homo sapiens,Vagina,UBERON:0000996,Streptococcal infection,EFO:1001476,GBS culture-negative pregnant women,GBS culture-positive pregnant women,Pregnant women who tested positive for Group B Streptococcus (GBS) by culture during the third trimester,22,22,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,parity",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figs. 3 and 4,21 March 2024,Ayibatari,"Ayibatari,Scholastica",Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing taxa with significant differential abundance in GBS culture-negative versus GBS culture-positive pregnant Egyptian women,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella pickettii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",2|201174;2|201174|1760|85004|31953;2|29547|3031852|213849|72294|194;2|29547|3031852|213849|72294;2|29547;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|32066|203490;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|2701|2914924;2|32066|203490|203491|1129771;2|544448|31969|2085|2092;2|544448;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1224;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|544448|2790996|2790998|2129;2|544448|2790996|2790998|2129|134821;2|201174|1760|85007|1653|1716|43771;2|1239|186801|3082720|186804|1257|1261,Complete,Svetlana up
bsdb:1055/1/1,Study 1055,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T , Reunanen J",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 1,Finland,Homo sapiens,Amniotic fluid,UBERON:0000173,Pregnancy,EFO:0002950,Amniotic fluid (AM),Amniotic fluid-derived extracellular vesicles (AM EVs),Amniotic fluid EV group,10,24,NA,16S,45,Ion Torrent,"Kruskall-Wallis,ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,Iman-Ngwepe,Differential abundance taxa of AM and AM_EV pair,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816;2|1224|28211|356|41294|374;2|1297|188787|118964|183710|1298;2|201174|1760|85006|145357|57495;2|1239|91061|186826|186828|29393;2|1224|1236|91347|543|1940338;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|201174|1760|85007|2805586|1847725;2|1224|28216|206351|481|482;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1055/2/1,Study 1055,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T , Reunanen J",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 2,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Pregnancy,EFO:0002950,Amniotic fluid (AM),Maternal feces (FE),Contrasts in the AM and FE pair,10,22,NA,16S,45,Ion Torrent,"ANCOM,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,decreased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,Iman-Ngwepe,Differential abundance taxa of AM and FE pair,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|28211|356|41294|374;2|201174|1760|85006|145357|57495;2|1239|186801|186802|216572|216851;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1055/3/NA,Study 1055,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T , Reunanen J",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 3,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Pregnancy,EFO:0002950,Amniotic fluid (AM),Feces-derived extracellular vesicles (FE EV),Contrasts between AM and FE_EV pair,10,22,NA,16S,45,Ion Torrent,"ANCOM,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1055/4/NA,Study 1055,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T , Reunanen J",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 4,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Pregnancy,EFO:0002950,Amniotic fluid-derived extracellular vesicles (AM EV),Maternal feces (FE),Differences between AM_EV and FE pair,24,22,NA,16S,45,Ion Torrent,"ANCOM,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1055/5/1,Study 1055,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T , Reunanen J",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 5,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Pregnancy,EFO:0002950,Amniotic fluid-derived extracellular vesicles (AM EV),Feces-derived extracellular vesicles (FE EV),Differences in AM_EV and FE_EV pair,24,22,NA,16S,45,Ion Torrent,"ANCOM,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,Iman-Ngwepe,Differential abundance taxa of FE_EV and AM_EV pair,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|976|200643|171549|815|816;2|1239|1737404|1737405|1570339|150022;2|32066|203490|203491|203492|848,Complete,NA
bsdb:1055/6/1,Study 1055,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T , Reunanen J",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Pregnancy,EFO:0002950,Maternal feces (FE),Feces-derived extracellular vesicles (FE EV),Differences in FE and FE_EV,22,22,NA,16S,45,Ion Torrent,"ANCOM,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,Iman-Ngwepe,Differential abundance taxa of FE and FE_EV pair,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|1980681;2|1297|188787|118964|183710|1298;2|1239|91061|186826|186828|29393;2|1239|91061|186826|186827|171412;2|1239|186801|186802|186806|1730|290054;2|1239|1737404|1582879;2|1239|186801|186802|216572|216851;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|201174|1760|85007|2805586|1847725;2|201174|1760|85006|1268|1269;2|1224|28216|206351|481|482;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|1239|909932|1843489|31977|29465;2|1239|186801|3085636|186803,Complete,NA
bsdb:1056/1/1,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 1,Iran,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,RNAlater - Day 0,RNAlater - Day 4,"RNAlater fecal samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran",69,64,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional files 2 Table S2,25 March 2024,EGO,"EGO,Scholastica","Differential abundance analysis of phylum and genus level changes comparing RNAlater  fecal samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|201174;2|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:1056/1/2,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 1,Iran,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,RNAlater - Day 0,RNAlater - Day 4,"RNAlater fecal samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran",69,64,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional files 2 Table S2,25 March 2024,EGO,"EGO,Scholastica","Differential abundance analysis of phylum and genus level changes comparing RNAlater  fecal samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran",decreased,NA,NA,Complete,Svetlana up
bsdb:1056/2/1,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 2,Iran,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,RNAlater - Day 0,Fecal occult blood test [FOBT] cards - Day 0,"Fecal occult blood test [FOBT] cards fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran",69,70,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional files 2 Table S4,26 March 2024,EGO,"EGO,Scholastica","Differential abundance analysis of phylum and genus level changes comparing RNAlater to FOBT card fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran",increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__Eggerthellaceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",2|201174;2|1239;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|580024;2|201174|84998|84999|84107|1473205;2|201174|84998|1643822|1643826|1972561;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1301;2|1239|186801|186802|31979|1485;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|543314|2137877;2|1239|186801|3085636|186803|207244;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|1263|438033;2|1239|186801|3085636|186803|2316020|33038;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|3085636|186803;2|1239|186801|3082720|186804|1505657;2|1239|186801|3082720|186804|1501226;2|1239|186801|3082720|186804|1505652;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|216572|216851;2|1239|1980693;2|1239|186801|186802|216572|707003;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|292632;2|1239|186801|186802|186806|1730|290054;2|1239|526524|526525|128827|1573535;2|1239|526524|526525|128827|123375;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225,Complete,Svetlana up
bsdb:1056/2/2,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 2,Iran,Homo sapiens,Feces,UBERON:0001988,Microbiome measurement,EFO:0007882,RNAlater - Day 0,Fecal occult blood test [FOBT] cards - Day 0,"Fecal occult blood test [FOBT] cards fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran",69,70,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional files 2 Table S8,26 March 2024,EGO,"EGO,Scholastica","Differential abundance analysis of phylum level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran",decreased,"k__Bacteria|p__Bacteroidota,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,s__metagenome,s__gut metagenome,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Mycoplasmatota|c__Candidatus Izimaplasma|o__Candidatus Izemoplasmatales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes,k__Bacteria|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae",2|976;2|1117;2|256845;2|1224;2|544448;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|283168;256318;749906;2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|370804;2|976|200643|171549|171550|239759;2|976|200643|171549|2005525|375288;2|1798710|1906119;2|1239|186801|3085636|186803|830;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|297314;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|1470353;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|707003;2|1239|186801|186802;2|544448|31969|186332|186333|2152;2|256845|1313211|278082|255528|172900;2|1224|28211|204441;2|200940|3031449|213115|194924|35832;2|200940|3031449|213115|194924|872;2|1224|1236|135624|83763|83770;2|1224|28216|80840|995019|577310;2|1224|28216|80840|995019|40544;2|1224|28216|80840|119060;2|544448|1912503|2975519;2|544448|31969;2|74201|414999|415001|415002,Complete,Svetlana up
bsdb:1056/3/1,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 3,Iran,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Scope mouthwash - Day 0,Scope mouthwash - Day 4,"Scope mouthwash samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran",70,55,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional files 2 Table S6,23 July 2024,Scholastica,Scholastica,"Differential abundance analysis of phylum and genus level changes comparing Scope mouthwash samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1239;2|201174|1760|2037|2049;2|201174|1760|85004|31953|1678;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|707003;2|1239|526524|526525|128827|123375;2|1239|909932|1843489|31977;2|1224|28216|80840|119060|47670;2|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:1056/3/2,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 3,Iran,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,Scope mouthwash - Day 0,Scope mouthwash - Day 4,"Scope mouthwash samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran",70,55,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional files 2 Table S6,23 July 2024,Scholastica,Scholastica,"Differential abundance analysis of phylum and genus level changes comparing Scope mouthwash samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran",decreased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1224;2|201174|1760|85006|1268|32207;2|976|200643|171549|171551|836;2|976|200643|171549|171552|1283313;2|1239|91061|1385|539738|1378;2|1224|28216|206351|481|482;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:1056/4/1,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 4,Iran,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,OMNIgene ORAL kit,Scope mouthwash,"Scope mouthwash oral samples from Gonbad and Yazd, Iran",77,125,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional files 2 Table S8,23 July 2024,Scholastica,Scholastica,"Differential abundance analysis of phylum and genus level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Campylobacterota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Candidatus Absconditabacteria|s__candidate division SR1 bacterium MGEHA",2|1239|91061|186826|186827|46123;2|201174|1760|85004|31953|419014;2|976;2|29547|3031852|213849|72294|194;2|29547;2|976|117743|200644|49546|1016;2|1239|91061|1385|539738|1378;2|1239|91061|1385|186817|129337;2|1239|91061|186826|33958|1578;2|1224|28216|80840|119060|47670;2;2|976|200643|171549|815|909656;2|1224|1236|72274|135621|286;2|201174|1760|85004|31953|196081;2|1239|909932|909929|1843491|970;2|203691;2|1239|909932|1843489|31977;2|1239|186801|186802|216572|707003;2|221235|1293577,Complete,Svetlana up
bsdb:1056/4/2,Study 1056,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9,"Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R , Vogtmann E",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 4,Iran,Homo sapiens,Saliva,UBERON:0001836,Microbiome measurement,EFO:0007882,OMNIgene ORAL kit,Scope mouthwash,"Scope mouthwash oral samples from Gonbad and Yazd, Iran",77,125,None,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional files 2 Table S8,23 July 2024,Scholastica,Scholastica,"Differential abundance analysis of phylum and genus level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran",decreased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1224;2|201174|1760|85006|1268|32207;2|976|200643|171549|171552|1283313;2|1239|186801|186802|543314|35517;2|1239|186801|186802|543314|35518;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803|265975;2|1239|526524|526525|128827|123375;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:1057/1/1,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Female subjects situated in Bushbuckridge,Female subjects situated in Soweto,Female subjects (both obese and lean) living in Soweto whose microbiota was studied to reflect transitional changes in microbiome on account of the adoption of a more Westernized lifestyle (in terms of diet and activity levels). Soweto represented the urban site of the two; the other (Bushbuckridge) being more relatively rural.,119,51,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5a and Supplementary Table 2A,23 March 2024,Ehi,"Ehi,Deacme,Scholastica",Phylum and Genus level significant differential abundance of taxa between Bushbuckbridge and Soweto cohorts (site differences).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Bacillota",2|1239|186801|186802|216572|258514;2|1239,Complete,Svetlana up
bsdb:1057/1/2,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Female subjects situated in Bushbuckridge,Female subjects situated in Soweto,Female subjects (both obese and lean) living in Soweto whose microbiota was studied to reflect transitional changes in microbiome on account of the adoption of a more Westernized lifestyle (in terms of diet and activity levels). Soweto represented the urban site of the two; the other (Bushbuckridge) being more relatively rural.,119,51,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5a and Supplementary Table 2A,23 March 2024,Ehi,"Ehi,Deacme,Scholastica",Phylum and Genus level significant differential abundance of taxa between Bushbuckbridge and Soweto cohorts (site differences).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Mycoplasmatota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio",2|976|200643|171549|171550|239759;2|544448|31969|186332|186333|2086;2|1239;2|976;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|544448;2|1224|28216|80840|995019|577310;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|1798710|3118680|2211217|213484,Complete,Svetlana up
bsdb:1057/2/1,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Bushbuckridge,Lean female subjects in Soweto,Lean females subjects living in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.,21,9,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5b and Supplementary Table 2B,24 March 2024,Ehi,"Ehi,Deacme,Scholastica",Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|201174;2|1239;2|976;2|201174|1760|85004|31953|1678;2|1239|526524|526525|2810280|135858;2|1239|909932|1843488|909930|33024;2|1224;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|976|200643|171549|171552|838;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:1057/2/2,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Bushbuckridge,Lean female subjects in Soweto,Lean females subjects living in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.,21,9,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5b and Supplementary Table 2B,24 March 2024,Ehi,"Ehi,Deacme",Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota",2|1239;2|976|200643|171549|815|816;2|976;2|1239|909932|1843489|31977|39948;2|1224,Complete,Svetlana up
bsdb:1057/3/1,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Obese female subjects in Bushbuckridge,Obese female subjects in Soweto,Obese females in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.,66,40,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5c and Supplementary Table 2C,24 March 2024,Ehi,"Ehi,Deacme",Phylum and Genus level significant differences between obese groups in the Soweto and Bushbuckridge cohorts.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota",2|1239|186801|186802|216572|1263;2|1239,Complete,Svetlana up
bsdb:1057/4/1,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in both cohorts,Obese female subjects in both cohorts,Obese female subjects in both the Bushbuckridge and Soweto cohorts.,30,106,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5d and Supplementary Table 2D,24 March 2024,Ehi,"Ehi,Deacme",Phylum and Genus level inter-cohort differential abundance between lean and obese groups (BMI differences).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota",2|1239|186801|186802|1392389;2|976|200643|171549|171552|838;2|1239;2|976,Complete,Svetlana up
bsdb:1057/5/1,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 5,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Bushbuckridge,Obese female subjects in Bushbuckridge,Obese females in Bushbuckridge whose microbiota is studied for transitional differences between lean and obese subjects in both Cohorts (Bushbuckridge and Soweto).,21,66,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 5e and Supplementary Table 2E,24 March 2024,Ehi,"Ehi,Deacme,Scholastica",Phylum and Genus level differential abundance between lean and obese groups in the Bushbuckridge cohort (BMI differences).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Bacteria|p__Verrucomicrobiota",2|1239|186801|186802|216572|258514;2|74201|203494|48461|1647988|239934;2|1239;2|976;2|1239|526524|526525|2810280|135858;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|1224;2|1224|28216|80840|995019|40544;2|1798710|3118680|2211217|213484;2|74201,Complete,Svetlana up
bsdb:1057/6/1,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 6,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Soweto,Obese female subjects in Soweto,Obese females in Soweto whose microbiota is studied to observe transitional changes between lean and obese groups in the Soweto cohort.,9,40,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5f and Supplementary Table 2F,24 March 2024,Ehi,"Ehi,Deacme,Scholastica",Phylum and Genus level differential abundance between lean and obese groups in the Soweto cohort (BMI differences).,increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|1239;2|976;2|1224|1236|91347|543|561;2|1224|1236|135625|712|724;2|1239|186801|186802|1392389;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1224;2|1239|186801|186802|216572|44748,Complete,Svetlana up
bsdb:1057/6/2,Study 1057,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS , Hazelhurst S",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 6,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Soweto,Obese female subjects in Soweto,Obese females in Soweto whose microbiota is studied to observe transitional changes between lean and obese groups in the Soweto cohort.,9,40,None,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5f and Supplementary Table 2F,24 March 2024,Ehi,"Ehi,Deacme,Scholastica",Phylum and Genus level differential abundance between lean and obese groups in the Soweto cohort (BMI differences).,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Lentisphaerota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239;2|976;2|256845;2|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:1058/1/1,Study 1058,case-control,37924005,10.1186/s12866-023-03071-w,NA,"Chen L, Mou X, Li J, Li M, Ye C, Gao X, Liu X, Ma Y, Xu Y , Zhong Y",Alterations in gut microbiota and host transcriptome of patients with coronary artery disease,BMC microbiology,2023,"Biomarkers, Coronary artery disease, Gut microbe, Risk genes, Transcriptome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Coronary artery disease,EFO:0001645,Healthy controls,Patient with coronary artery disease,patients with coronary artery disease between the age of 25 - 80 years and show greater than 70% stenosis in at least one major branch of the coronary artery.,21,31,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 2 & supplementary figure S1,22 March 2024,Idiaru angela,"Idiaru angela,Scholastica",Differential abundance of gut microbiota between coronary artery disease patients and controls at all taxa levels,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus rubiinfantis,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacteria|p__Bacillota|g__Negativibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",2|201174|1760|2037|2049|1654|1655;2|1239|186801|186802|216572|244127|1720200;2|1239|186801;2|1239|186801|186802|2109688;2|1239|186801|186802|1980681;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|909932|1843489|31977|39948|308994;2|1239|526524|526525|128827|1573534;2|1239|91061|186826|33958|2767881;2|1239|186801|3085636|186803|2109691;2|1239|1980693;2|1239|186801|186802|216572;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836|281920;2|1224|28211|356|82115;2|1239|526524|526525|128827|123375;2|1239|526524|526525|128827|123375|102148;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|877420;2|1239|186801|3085636|186803|2569097|39488,Complete,Svetlana up
bsdb:1058/1/2,Study 1058,case-control,37924005,10.1186/s12866-023-03071-w,NA,"Chen L, Mou X, Li J, Li M, Ye C, Gao X, Liu X, Ma Y, Xu Y , Zhong Y",Alterations in gut microbiota and host transcriptome of patients with coronary artery disease,BMC microbiology,2023,"Biomarkers, Coronary artery disease, Gut microbe, Risk genes, Transcriptome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Coronary artery disease,EFO:0001645,Healthy controls,Patient with coronary artery disease,patients with coronary artery disease between the age of 25 - 80 years and show greater than 70% stenosis in at least one major branch of the coronary artery.,21,31,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 2 & supplementary figure S1,23 March 2024,Idiaru angela,Idiaru angela,Differential abundance of gut microbiota between coronary artery disease patients and controls at all taxa levels,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacteria|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|186806;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186806|1730|1736;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085656|3085657;2|1239|186801|3085656;2|1239|186801|3085656|3085657|2039302;2|976|200643|171549|2005525|375288|46503,Complete,Svetlana up
bsdb:1059/1/1,Study 1059,time series / longitudinal observational,36997838,10.1186/s12866-023-02822-z,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02822-z,"Jacky D, Bibi C, Meng LMC, Jason F, Gwendoline T, Jeremy L , Wie CC",Effects of OsomeFood Clean Label plant-based meals on the gut microbiome,BMC microbiology,2023,"Intervention, Metagenomic, Microbiota, Nutrition",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants before the AWE diet - D0,Participants after the AWE diet - D21,Participants who strictly adhered to OsomeFoods plant-based meal plans for five consecutive days (Monday through to Friday; 'AWE') for 3 weeks.,10,10,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 2c,25 March 2024,ModinatG,ModinatG,Species differentially abundant between baseline and day 21 (End of the intervention period),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc garlicum",2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|371601;2|1239|91061|186826|33958|1243|255248,Complete,Svetlana up
bsdb:1059/1/2,Study 1059,time series / longitudinal observational,36997838,10.1186/s12866-023-02822-z,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02822-z,"Jacky D, Bibi C, Meng LMC, Jason F, Gwendoline T, Jeremy L , Wie CC",Effects of OsomeFood Clean Label plant-based meals on the gut microbiome,BMC microbiology,2023,"Intervention, Metagenomic, Microbiota, Nutrition",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants before the AWE diet - D0,Participants after the AWE diet - D21,Participants who strictly adhered to OsomeFoods plant-based meal plans for five consecutive days (Monday through to Friday; 'AWE') for 3 weeks.,10,10,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 2c,25 March 2024,ModinatG,ModinatG,Species differentially abundant between baseline and day 21 (End of the intervention period),decreased,"k__Viruses|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Bacteroides phage B124-14,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",10239|2731360|2731618|2731619|1105171;2|201174|84998|84999|84107|102106|147207;2|1239|186801|3082720|186804|1501226|1115758;2|1239|91061|186826|33958|46255|1583,Complete,Svetlana up
bsdb:1060/1/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 1,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Kwepe,"The Kwepe are small stock herders possibly linked to early pastoral migrations from eastern to southern Africa. They dwell in the coastal lowlands of the Angola Namib Desert, which is characterized by an arid and warm climate.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei",2|1239|526524|526525|128827|118747;2|1239|186801|3085636|186803|177971;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877,Complete,NA
bsdb:1060/1/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 1,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Kwepe,"The Kwepe are small stock herders possibly linked to early pastoral migrations from eastern to southern Africa. They dwell in the coastal lowlands of the Angola Namib Desert, which is characterized by an arid and warm climate.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,2|1224|1236|91347|543|544|545,Complete,NA
bsdb:1060/2/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 2,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Himba,The Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1591;2|201174|1760|85009|31957|2801844|1750;2|201174|1760|85009|31957|2801844,Complete,NA
bsdb:1060/2/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 2,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Himba,The Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|158483|158484,Complete,NA
bsdb:1060/3/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 3,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",2|508458|649775|649776|3029088|638847;2|508458|649775|649776|3029088|638847|638849;2|1224|1236|91347|543|544|133448,Complete,NA
bsdb:1060/3/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 3,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|1903412|568;2|1224|1236|91347|1903412|568|1873498,Complete,NA
bsdb:1060/4/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 4,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis",2|1224|1236|91347|543|544|133448;2|1239|526524|526525|2810280|1279384|31973,Complete,NA
bsdb:1060/4/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 4,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between Population according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|544|1896336,Complete,NA
bsdb:1060/5/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 5,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor",2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|133448;2|1239|526524|526525|2810280|1279384;2|1239|526524|526525|2810280|1279384|31973;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|3082720|3118655|44259|143361;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|576;2|201174|84998|84999|1643824|2767353|1383;2|976|200643|171549|171551|836;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|306;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1224|1236|91347|1903411|613;2|1224|1236|91347|1903411|613|616;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877;2|1239|186801|3082720|3118655|44259,Complete,NA
bsdb:1060/5/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 5,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848|860;2|1239|91061|1385|539738|1378|84135;2|976|200643|171549|171552|577309|454154;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|577309;2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836,Complete,NA
bsdb:1060/6/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 6,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Tshwa,"They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] saphenum,k__Bacteria|p__Bacteroidota|s__Bacteroidetes oral taxon 274,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__Peptoanaerobacter stomatis",2|976|200643;2|1224|1236|135615|868|2717|194702;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|43996|43997;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|133448;2|201174|1760|85007|1653|1716|43768;2|1239|526524|526525|2810280|1279384;2|1239|526524|526525|2810280|1279384|31973;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|42895;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|3082720|3118655|44259;2|1239|186801|3082720|3118655|44259|143361;2|32066|203490|203491|203492|848|851;2|1224|1236|91347|1903412|568;2|1224|1236|91347|1903412|568|1873498;2|1239|186801|3085636|186803|43994;2|1239|186801|3085636|186803|43994|43995;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|576;2|1239|186801|3082720|3118655|1913599;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1904861;2|1224|1236|72274|135621|286|306;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877;2|1239|186801|186802|543314|51123;2|976|652708;2|1239|186801|3082720|3118655|1913599|796937,Complete,NA
bsdb:1060/6/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 6,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Tshwa,"They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp.",2|201174|1760|2037|2049|1654|55565;2|1224|1236|135625|712|724|1078480;2|1224|28216|206351|481|32257|504;2|1239|186801|3085636|186803|1164882;2|976|200643|171549|171552|577309;2|976|200643|171549|171551|836;2|1224|28216|206351|481|71;2|1224|28216|206351|481|71|72;2|1239|186801|3085636|186803|1164882|2049030,Complete,NA
bsdb:1060/7/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 7,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|1224|1236|91347|543|544|133448;2|1239|526524|526525|2810280|1279384;2|1239|526524|526525|2810280|1279384|31973;2|1239|186801|3082720|3118655|1913599;2|201174|1760|85009|31957|1743;2|1239|186801|3085636|186803|177971;2|976|200643,Complete,NA
bsdb:1060/7/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 7,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|46125;2|1239|91061|1385|186817|1386;2|1224|1236|91347|543|544|546;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1870884|1496;2|1239|91061|186826|81852|1350;2|1239|91061|1385|539738|1378|84135;2|1224|1236|135625|712|724|736;2|1239|91061|186826|186827|46123|76631,Complete,NA
bsdb:1060/8/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 8,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Himba,the Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|576;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1898203;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877,Complete,NA
bsdb:1060/8/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 8,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Himba,the Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1591;2|1239|91061|186826|1300|1301|1305;2|201174|1760|85009|31957|2801844;2|201174|1760|85009|31957|2801844|1750,Complete,NA
bsdb:1060/9/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 9,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,2|1224|1236|91347|543|544|133448,Complete,NA
bsdb:1060/9/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 9,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella",2|1224|1236|91347|543|544|546;2|1224|1236|91347|1903412|568|1873498;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|1903412|568;2|1239|526524|526525|128827|118747;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158876,Complete,NA
bsdb:1060/10/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 10,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.",2|1224|1236|91347|543|544|133448;2|1224|1236|2887326|468|475|479,Complete,NA
bsdb:1060/10/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 10,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|29317;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1898203;2|1239|91061|186826|1300|1301|1318;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|158483,Complete,NA
bsdb:1060/11/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 11,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,24 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",2|1224|1236|91347|543|544;2|1224|1236|91347|543|547;2|1224|1236|72274|135621|286;2|1224|1236|91347|543|561;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|544|133448,Complete,NA
bsdb:1060/12/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 12,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|544|133448;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|186828|117563|137732;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|570|571;2|1224|1236|72274|135621|286|306;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|257758;2|1239|186801|3082720|3118655|1913599|39498,Complete,NA
bsdb:1060/12/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 12,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|55565;2|201174|1760|2037|2049|1654|29317;2|1224|28216|206351|481|32257|504;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1898203;2|1239|909932|1843489|31977|906;2|201174|1760|2037|2049|2529408|1660,Complete,NA
bsdb:1060/13/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 13,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,2|1224|1236|91347|543|544|133448,Complete,NA
bsdb:1060/13/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 13,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria)",2|1224|1236|91347|543|544|546;2|1239|186801|3082720|186804|1870884|1496;2|1239|91061|1385|539738|1378|84135;2|1224|1236|91347|543|570|573;2|1239|1737404|1737405|1570339|543311|33033;2|201174|1760|85006|1268|32207|1885016,Complete,NA
bsdb:1060/14/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 14,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba.,7,4,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|590,Complete,NA
bsdb:1060/14/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 14,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba.,7,4,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia",2|1224|1236|91347|1903412|568|1873498;2|1224|1236|91347|1903412|568,Complete,NA
bsdb:1060/15/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 15,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",2|1224|1236|91347|543|590;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|590|599;2|203691|203692|136|2845253|157|53418;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|544|133448,Complete,NA
bsdb:1060/15/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 15,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|1239|91061|186826|33958|1578,Complete,NA
bsdb:1060/16/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 16,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",2|1224|1236|91347|543|590;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|544;2|1224|1236|91347|543|561;2|1224|1236|91347|1903412|568;2|29547|3031852|213849|72294|194;2|1224|1236|91347|1903411|613;2|1239|909932|909929|1843491|970;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|544|133448;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|561|562,Complete,NA
bsdb:1060/16/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 16,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|976|200643|171549|171552|577309|454154;2|976|200643|171549|171552|577309,Complete,NA
bsdb:1060/17/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 17,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tshwa,"They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|1224|1236|91347|543|590;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|547;2|1224|1236|91347|543|544;2|1224|1236|91347|543|158876;2|1224|1236|91347|1903412|568;2|1224|1236|91347|1903412|568|1873498;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|1884818;2|1239|186801|3082720|186804;2|976|200643,Complete,NA
bsdb:1060/17/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 17,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tshwa,"They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia",2|201174|1760|2037|2049|1654|55565;2|201174|1760|85009|31957|2801844|1750;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1591;2|201174|1760|85009|31957|2801844,Complete,NA
bsdb:1060/18/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 18,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.",2|1224|1236|91347|543|590;2|29547|3031852|213849|72294|194;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336,Complete,NA
bsdb:1060/18/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 18,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes)",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|76631;2|1239|91061|1385|186817|1386;2|976|117743|200644|49546|1016|1017;2|1224|1236|91347|543|544|546;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561|562;2|1239|91061|1385|539738|1378|1379;2|1239|91061|1385|539738|1378|84135;2|1224|1236|135625|712|724|735;2|201174|1760|85009|31957|2801844;2|1239|186801|186802|543314|35517;2|1239|91061|1385|186817|1386|1409,Complete,NA
bsdb:1060/19/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 19,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,Tshwa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",2|32066|203490|203491|203492|848|851;2|1239|186801|3082720|3118655|1913599|39498,Complete,NA
bsdb:1060/19/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 19,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,Tshwa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1224|28216|206351|481|71|72;2|201174|1760|2037|2049|1654|55565;2|1224|28216|206351|481|71;2|201174|1760|2037|2049|1654,Complete,NA
bsdb:1060/20/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 20,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1239|186801|3082720|186804|1870884;2|201174|1760|85007|1653|1716|1720;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|42895;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|35783;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|576;2|1224|1236|72274|135621|286;2759|33090|35493|3398|72025|3803|3814|508215;2|1224|1236|91347|543|590;2|201174|1760|2037|2049|2529408|52768;2|1224|1236|91347|1903411|613;2|1224|1236|91347|1903411|613|616;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877,Complete,NA
bsdb:1060/21/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 21,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tshwa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",5,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri",2|1224|28216|206351|481|71;2|201174|1760|85009|31957|1743;2|201174|1760|2037|2049|1654|55565;2|1224|28216|206351|481|32257|504;2|1224|28216|206351|481|71|72,Complete,NA
bsdb:1060/21/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 21,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tshwa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",5,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides",2|1224|1236|91347|543|544|546;2|1239|91061|186826|81852|1350|35783;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|561|562;2|201174|1760|85006|1268|32207|172042;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|544|545;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1239|91061|1385|539738|1378|84135;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|158876|158877;2|1239|91061|186826|1300|1301|1304;2|1224|1236|91347|543|158483|158484;2|1239|91061|1385|539738|1378|1379;2|32066|203490|203491|203492|848|851;2|1224|28216|80840|119060|47670|47671;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|547|42895;2|1239|1737404|1737405|1570339|543311|33033;2|1224|1236|91347|1903411|613;2|1239|91061|1385|539738|1378;2|1224|28216|80840|119060|47670;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|544;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2|1224|1236|91347|543|590;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158483;2|1239|186801|3082720|186804|1870884,Complete,NA
bsdb:1060/22/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 22,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,4,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia",2|1224|1236|91347|543|544|546;2|1224|1236|91347|1903412|568|1873498;2|1224|1236|91347|1903412|568,Complete,NA
bsdb:1060/22/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 22,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,4,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens",2|508458|649775|649776|3029088|638847;2|508458|649775|649776|3029088|638847|638849,Complete,NA
bsdb:1060/23/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 23,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",4,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",2|1224|1236|91347|1903412|568;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|561;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|573,Complete,NA
bsdb:1060/24/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 24,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",4,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.",2|1224|1236|91347|1903412|568;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|544;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|561;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|547|42895;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|1903412|568|1873498,Complete,NA
bsdb:1060/24/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 24,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",4,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,2|201174|1760|2037|2049|1654|55565,Complete,NA
bsdb:1060/25/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 25,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",4,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|1224|1236|91347|1903412|568;2|1224|1236|91347|1903412|568|1873498;2|201174|1760|85009|31957|1743,Complete,NA
bsdb:1060/26/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 26,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|544,Complete,NA
bsdb:1060/26/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 26,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis",2|1224|1236|2887326|468|475|479;2|976|117743|200644|49546|1016|1017,Complete,NA
bsdb:1060/27/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 27,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",8,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|547;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|570|571;2|32066|203490|203491|203492|848|851;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|590|599;2|1239|186801|3082720|3118655|1913599|39498,Complete,NA
bsdb:1060/27/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 27,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",8,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|976|117743|200644|49546|1016|1017;2|1224|1236|2887326|468|475|479;2|1224|28216|206351|481|32257|504;2|1224|28216|206351|481|71|72;2|1224|28216|206351|481|71;2|1224|1236|2887326|468|475,Complete,NA
bsdb:1060/28/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 28,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|201174|1760|85009|31957|1743,Complete,NA
bsdb:1060/28/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 28,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes)",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|76631;2|1239|91061|1385|186817|1386;2|976|117743|200644|49546|1016|1017;2|1224|1236|91347|543|544|546;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|91061|1385|539738|1378|1379;2|1239|91061|1385|539738|1378|84135;2|1224|1236|135625|712|724|735;2|1239|186801|186802|543314|35517;2|1239|91061|1385|186817|1386|1409,Complete,NA
bsdb:1060/29/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 29,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Foragers,"They are the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",21,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,26 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia",2|1224|1236|91347|543|544|133448;2|201174|1760|85004|31953|1678|1685;2|1239|526524|526525|2810280|1279384|31973;2|1224|1236|91347|543|547|42895;2|1239|526524|526525|2810280|1279384,Complete,NA
bsdb:1060/29/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 29,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Foragers,"They are the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",21,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,26 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|46125;2|1239|91061|186826|186827|46123|76631;2|1239|91061|1385|186817|1386;2|1224|1236|91347|543|158483|158484;2|201174|1760|85006|1268|32207|1885016;2|1224|1236|91347|543|544|546;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|35783;2|1239|91061|1385|539738|1378|84135;2|1239|91061|186826|186828|117563|2049028;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1304;2|1239|91061|1385|186817|1386|1409;2759|33090|35493|3398|72025|3803|3814|508215;2|201174|1760|2037|2049|2529408|52768,Complete,NA
bsdb:1060/30/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 30,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Peripatetics,"Includes the Twa, Tjimba, Kwisi, and Kwepe in southwestern Angola, these groups have a mobile lifestyle without a fixed settlement. They inhabit coastal lowlands and may have mixed livelihoods, combining aspects of both pastoralism and foraging.",21,24,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,26 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus sp. (in: enterobacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii",2|1224|1236|91347|543|544;2|1224|1236|91347|543|570;2|1224|1236|91347|543|561;2|1224|1236|91347|543|590;2|1224|1236|91347|1903412|568|1873498;2|1224|1236|91347|1903412|568;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|547|158836;2|1224|1236|91347|543|547|69218;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|306;2|1239|526524|526525|2810280|1279384;2|1239|526524|526525|2810280|1279384|31973;2|976|117743|200644|2762318|1013;2|976|200643;2|1239|186801|3082720|186804;2|1224|1236|91347|1903414|583;2|1224|1236|91347|1903414|583|229037;2|1224|1236|91347|543|544|133448;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|570|1134687;2|32066|203490|203491|1129771|32067|157688;2|201174|1760|85007|1653|1716|43768,Complete,NA
bsdb:1060/30/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 30,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Peripatetics,"Includes the Twa, Tjimba, Kwisi, and Kwepe in southwestern Angola, these groups have a mobile lifestyle without a fixed settlement. They inhabit coastal lowlands and may have mixed livelihoods, combining aspects of both pastoralism and foraging.",21,24,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,26 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|1239|526524|526525|128827|123375;2|1239|186801|3085636|186803|1164882;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|577309,Complete,NA
bsdb:1060/31/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 31,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Peripatetics,Foragers,"They are represented by the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",24,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,26 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve",2|201174|1760|85009|31957|1743;2|201174|1760|85004|31953|1678|1685,Complete,NA
bsdb:1060/31/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 31,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Peripatetics,Foragers,"They are represented by the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",24,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,29 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between subsistence methods according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria)",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|46125;2|1239|91061|186826|186827|46123|76631;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817|1386|1409;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1224|1236|91347|543|547|69218;2|1224|1236|91347|543|547|158836;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|35783;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|91061|1385|539738|1378|1379;2|1239|91061|1385|539738|1378|84135;2|1224|1236|91347|543|570;2|1224|1236|91347|543|570|1134687;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|576;2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060|47670|47671;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1239|186801|186802|543314|35517;2|201174|1760|2037|2049|2529408|52768;2|201174|1760|85006|1268|32207|1885016,Complete,NA
bsdb:1061/1/1,Study 1061,"cross-sectional observational, not case-control",38373985,https://doi.org/10.1186/s13195-024-01402-1,NA,"Qiu C, Zhou W, Shen H, Wang J, Tang R, Wang T, Xie X, Hong B, Ren R, Wang G , Song Z",Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer's disease,Alzheimer's research & therapy,2024,"Alzheimer’s disease, Metabolome, Microbiome, Mild cognitive impairment, Multiomics, Periodontitis",Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Alzheimer's disease,MONDO:0004975,Cognitively normal (CN) and amnestic mild cognitive impairment (aMCI),Alzheimer’s Disease (AD),Patients with Alzheimer’s Disease (AD) dementia who were diagnosed following the National Institute on Aging and Alzheimer’s Association guidelines for probable AD dementia with the support of magnetic resonance imaging,64,32,3 months,16S,NA,PacBio RS,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 1f,23 March 2024,Aananditaa,"Aananditaa,Scholastica","LEfSe analysis revealed significant bacterial differences in subgingival microbiota among the cognitively normal (CN), amnestic mild cognitive impairment (aMCI), and Alzheimer’s Disease (AD) groups",increased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia|s__Afipia genosp. 6,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis lipophila,k__Bacteria|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter pittii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Steroidobacterales|f__Steroidobacteraceae|g__Steroidobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Steroidobacterales|f__Steroidobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales",2|1239;2|1239|909932;2|976|200643|171549|171552|838;2|1239|909932|1843489;2|1239|909932|1843489|31977;2|976|200643|171549|171552;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|29466;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|851;2|976|200643|171549|171552|838|28129;2|1224|1236|72274|135621|286;2|1224|1236|72274;2|1224|1236|72274|135621;2|976|200643|171549|171552|838|28132;2|1239|91061|186826|1300|1301|1309;2|29547|3031852|213849|72294|194|824;2|1239|91061|186826|1300|1301|1303;2|1224|28211|356|41294|1033;2|1239|909932|1843489|31977|156454;2|1239|909932|1843489|31977|156454|156456;2|1239|91061|186826|1300|1301|1328;2|1224|28211|356|41294|1033|56981;2|1224|28211;2|1224|28211|356|119045|2282523;2|201174|84998|84999;2|201174|84998;2|201174|84998|84999|1643824;2|1224|28211|356;2|544448|2790996|2895623|2767358|2117;2|544448|2790996|2895623|2767358;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906|187326;2|1224|28211|356|41294|374;2|1224|28211|356|41294;2|976|200643|171549|171552|2974251|28136;2|201174|84998|84999|1643824|2767353;2|1224|1236|2887326|468|469|48296;2|1239|186801|3085636|186803|1213720;2|1239|186801|3085636|186803|1213720|796942;2|1224|28211|356|119045;2|201174|84998|84999|1643824|2767353|1383;2|201174|84998|84999|1643824|2767353|1382;2|203691|203692|136|2845253|157|59892;2|1239|909932|909929|1843491|970|135080;2|1239|91061|186826|33958;2|1239|186801|186802|186806;2|1239|91061|186826|1300|1301|1304;2|1224|1236|3060226|2689614|469322;2|1224|1236|3060226|2689614;2|1224|1236|1775403,Complete,Svetlana up
bsdb:1061/2/1,Study 1061,"cross-sectional observational, not case-control",38373985,https://doi.org/10.1186/s13195-024-01402-1,NA,"Qiu C, Zhou W, Shen H, Wang J, Tang R, Wang T, Xie X, Hong B, Ren R, Wang G , Song Z",Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer's disease,Alzheimer's research & therapy,2024,"Alzheimer’s disease, Metabolome, Microbiome, Mild cognitive impairment, Multiomics, Periodontitis",Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Alzheimer's disease,MONDO:0004975,Cognitively normal (CN) and Alzheimer’s Disease (AD),Amnestic mild cognitive impairment (aMCI),"Patients with aMCI who met the previously published National Institute on Aging and Alzheimer’s Association criteria (2011) for “MCI due to AD,” with memory deficits as the only complaint of cognitive impairment.",64,32,3 months,16S,NA,PacBio RS,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 1f,23 March 2024,Aananditaa,"Aananditaa,Scholastica","LEfSe analysis revealed significant bacterial differences in subgingival microbiota among the cognitively normal (CN), amnestic mild cognitive impairment (aMCI), and Alzheimer’s Disease (AD) groups",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter segnis",2|1224|28216;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|1224|28216|206351;2|1224|28216|206351|481|482|495;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006;2|976|117743|200644|49546|1016|1018;2|1224|28216|80840|119060|48736|329;2|1224|28216|80840|119060|48736;2|1239|91061|1385;2|201174|1760|85007|1653|1716|61592;2|1224|28216|206351|481|32257|502;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1318;2|1224|1236|135625|712|724|726;2|1224|28211|204458|76892;2|1224|28211|204458;2|1224|28211|204458|76892|75;2|1224|28211|204458|76892|75|88688,Complete,Svetlana up
bsdb:1061/3/1,Study 1061,"cross-sectional observational, not case-control",38373985,https://doi.org/10.1186/s13195-024-01402-1,NA,"Qiu C, Zhou W, Shen H, Wang J, Tang R, Wang T, Xie X, Hong B, Ren R, Wang G , Song Z",Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer's disease,Alzheimer's research & therapy,2024,"Alzheimer’s disease, Metabolome, Microbiome, Mild cognitive impairment, Multiomics, Periodontitis",Experiment 3,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Alzheimer's disease,MONDO:0004975,Cognitively normal (CN),Alzheimer’s Disease (AD) and Amnestic mild cognitive impairment (aMCI),"Patients with AD dementia who were diagnosed following the National Institute on Aging and Alzheimer’s Association guidelines for probable AD dementia with the support of magnetic resonance imaging and all patients with aMCI who met the previously published National Institute on Aging and Alzheimer’s Association criteria (2011) for “MCI due to AD,” with memory deficits as the only complaint of cognitive impairment.",32,64,3 months,16S,NA,PacBio RS,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 1f,23 March 2024,Aananditaa,"Aananditaa,Scholastica","LEfSe analysis revealed significant bacterial differences in subgingival microbiota among the cognitively normal (CN), amnestic mild cognitive impairment (aMCI), and Alzheimer’s Disease (AD) groups",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus qingshengii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia rubra,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella cardium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia",2|1224|28216|80840;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|28216|80840|80864;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|561;2|1224|28216|206351|481|482|28449;2|1224|1236|135625|712|724|729;2|1224|1236|135625|712|724;2|32066|203490|203491|1129771|32067|40542;2|201174|1760|85007|85025|1827;2|201174|1760|85009;2|201174|1760|85009|31957;2|201174|1760|85007|85025|1827|334542;2|201174|1760|85009|31957|2801844;2|201174|1760|85007|85025;2|1239|91061|186826|1300|1301|1305;2|201174|1760|85009|31957|2801844|1750;2|29547|3031852|213849|72294|194|204;2|976|117743|200644|49546|1016|1019;2|201174|1760|85009|31957|2801844|1547448;2|976|117743|200644|2762318;2|976|117743|200644|2762318|59735;2|1239|186801|3082720|3118655|1913599;2|201174|1760|2037|2049|1654|461393;2|976|117743|200644|2762318|59735|1585976;2|1239|186801|3085636|186803|43996;2|1239|186801|3085636|186803|43996|43997;2|1239|186801|3085636|186803|43994|43995;2|32066|203490|203491|1129771|2755140|157692;2|32066|203490|203491|1129771|2755140,Complete,Svetlana up
bsdb:1062/1/1,Study 1062,"cross-sectional observational, not case-control",37715296,10.1186/s40168-023-01636-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503196/,"Mills M, Lee S, Piperata BA, Garabed R, Choi B , Lee J",Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua,Microbiome,2023,"Animals, Breastfeeding duration, Dirt floor, E. coli as antibiotic resistance host, Microbial source tracking, Multi-drug resistance, One Health",Experiment 1,Nicaragua,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants,Children,Participants between 2.0 – 6.0 years of age,26,31,None,WMS,NA,Nanopore,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,NA,NA,NA,Signature 1,Figure 2b,23 March 2024,Aishat,"Aishat,Scholastica",Bacterial families with different abundances in children versus infants identified with linear discriminant analysis effect size (LEfSe),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|3085636|186803;2|976|200643|171549|171552;2|203691|203692|136|137;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:1062/1/2,Study 1062,"cross-sectional observational, not case-control",37715296,10.1186/s40168-023-01636-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503196/,"Mills M, Lee S, Piperata BA, Garabed R, Choi B , Lee J",Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua,Microbiome,2023,"Animals, Breastfeeding duration, Dirt floor, E. coli as antibiotic resistance host, Microbial source tracking, Multi-drug resistance, One Health",Experiment 1,Nicaragua,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants,Children,Participants between 2.0 – 6.0 years of age,26,31,None,WMS,NA,Nanopore,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,NA,NA,NA,Signature 2,Figure 2b,23 March 2024,Aishat,"Aishat,Scholastica",Bacterial families with different abundances in children versus infants identified with linear discriminant analysis effect size (LEfSe),decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|1224|1236|91347|543,Complete,Svetlana up
bsdb:1062/2/1,Study 1062,"cross-sectional observational, not case-control",37715296,10.1186/s40168-023-01636-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503196/,"Mills M, Lee S, Piperata BA, Garabed R, Choi B , Lee J",Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua,Microbiome,2023,"Animals, Breastfeeding duration, Dirt floor, E. coli as antibiotic resistance host, Microbial source tracking, Multi-drug resistance, One Health",Experiment 2,Nicaragua,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,No - antibiotics,Yes - antibiotics,Infants and young children (ages 4 days - 6 years) in rural Nicaragua who had ever received antibiotics,11,11,None,WMS,NA,Nanopore,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S5,5 July 2024,Scholastica,Scholastica,Differentially abundant taxa identified in children and infants who had compared to those who had not received antibiotics using linear discriminant analysis effect size (LEfSe).,decreased,"k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale",2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311;2|1239|91061|186826|33958|46255;2|1239|909932|909929|1843491|158846|158847,Complete,Svetlana up
bsdb:1063/1/1,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy Control,Oral lichen planus (both erosive and non-erosive ),"Oral lichen planus (OLP) is a common oral mucosal disease with or without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,20,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Table 5, Supplemental figure (Excel sheet) and Text",25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients with and without erosive lesions (E and NE) versus control group,increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",2|1224|28211|204457|335929|361177;2|201174|1760|85006|1268|1663;2|1239|909932|1843489|31977|906;2|201174|1760|2037|2049|2050;2|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:1063/1/2,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy Control,Oral lichen planus (both erosive and non-erosive ),"Oral lichen planus (OLP) is a common oral mucosal disease with or without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,20,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Table 5, Supplemental figure (Excel sheet) and Text",25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients with and without erosive lesions (E and NE) versus control group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|91061|186826|186827|46123;2|544448|31969|186329|2146|2147;2|1224|1236|135625|712|416916;2|976|200643|171549|815|816;2|1224|28216|206351|481|538;2|1239|1737404|1582879;2|976|117743|200644|1853230|332102;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|976|1853228|1853229|563835|504481;2|1224|28216|32003|2008793|1054211;2|976|200643|171549|2005525|195950;2|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:1063/2/NA,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,OLP patients without erosive lesions (NE),Patients with oral aphthous ulcer (RAU/U),"Recurrent aphthous ulceration (RAU) is a common oral mucosal disease also characterized by multiple oral ulcers, a feature similar to erosive OLP but different from OLP in the pattern of the clinical lesions and the pathogenesis mechanism",10,10,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1063/3/NA,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,Patients with oral aphthous ulcer (U/RAU),"Recurrent aphthous ulceration (RAU) is a common oral mucosal disease also characterized by multiple oral ulcers, a feature similar to erosive OLP but different from OLP in the pattern of the clinical lesions and the pathogenesis mechanism",10,10,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1063/4/1,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients with erosive lesions (E) versus control group,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia",2|1239|186801|3085636|186803|265975;2|203691|203692|136;2|203691|203692,Complete,Svetlana up
bsdb:1063/4/2,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients with erosive lesions (E) versus control group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:1063/5/1,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients without erosive lesions (NE),"Non-erosive OLP is a common oral mucosal disease without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,10,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients without erosive lesions (NE) versus control group,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:1063/5/2,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients without erosive lesions (NE),"Non-erosive OLP is a common oral mucosal disease without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,10,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients without erosive lesions (NE) versus control group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827;2|203691|203692|136;2|203691|203692,Complete,Svetlana up
bsdb:1063/6/NA,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 6,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Patients with oral aphthous ulcer (U/RAU),OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1063/7/1,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 7,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,OLP patients without erosive lesions (NE),OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients with (E) compared to patients without (NE) erosive lesions,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetota|c__Spirochaetia",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827;2|203691|203692|136;2|203691|203692,Complete,Svetlana up
bsdb:1063/7/2,Study 1063,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B , Ren XY",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 7,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,OLP patients without erosive lesions (NE),OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica",The differential taxa of bacteria in oral lichen planus (OLP) patients with (E) compared to patients without (NE) erosive lesions,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:1064/1/1,Study 1064,case-control,36864380,10.1186/s12866-023-02791-3,https://pubmed.ncbi.nlm.nih.gov/36864380/,"Mahdy MS, Azmy AF, Dishisha T, Mohamed WR, Ahmed KA, Hassan A, Aidy SE , El-Gendy AO",Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity,BMC microbiology,2023,"Anticancer, Beta-glucuronidase, Colon, Inflammation, Irinotecan, Probiotics",Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Response to irinotecan,EFO:0004829,Healthy individuals,Colon cancer and Irinotecan treated patients,"Patients with colorectal cancer and Irinotecan treated patients. Irinotecan is a chemotherapeutic agent used to treat a variety of tumors, including colorectal cancer (CRC).",5,10,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 4a,18 June 2024,Scholastica,Scholastica,"The differences in the relative abundance of taxa between the colon cancer patients, Irinotecan treated, and healthy individuals as detected by the linear discriminant analysis effect size (LEfSe)",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|186801|186802|204475;2|1239|186801|186802|216572|1263;2|1239|909932|1843488|909930|33024;2|200940|3031449|213115|194924|872;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|976|200643|171549|2005473,Complete,Svetlana up
bsdb:1064/2/1,Study 1064,case-control,36864380,10.1186/s12866-023-02791-3,https://pubmed.ncbi.nlm.nih.gov/36864380/,"Mahdy MS, Azmy AF, Dishisha T, Mohamed WR, Ahmed KA, Hassan A, Aidy SE , El-Gendy AO",Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity,BMC microbiology,2023,"Anticancer, Beta-glucuronidase, Colon, Inflammation, Irinotecan, Probiotics",Experiment 2,Egypt,Homo sapiens,Feces,UBERON:0001988,Response to irinotecan,EFO:0004829,Healthy individuals and colon cancer (CRC) patients,Irinotecan treated patients,"Patients treated with Irinotecan, a chemotherapeutic agent used to treat a variety of tumors, including colorectal cancer (CRC).",10,5,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 4a,18 June 2024,Scholastica,Scholastica,"The differences in the relative abundance of taxa between the colon cancer patients, Irinotecan treated, and healthy individuals as detected by the linear discriminant analysis effect size (LEfSe)",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|186801|186802|3085642|580596;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1064/3/1,Study 1064,case-control,36864380,10.1186/s12866-023-02791-3,https://pubmed.ncbi.nlm.nih.gov/36864380/,"Mahdy MS, Azmy AF, Dishisha T, Mohamed WR, Ahmed KA, Hassan A, Aidy SE , El-Gendy AO",Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity,BMC microbiology,2023,"Anticancer, Beta-glucuronidase, Colon, Inflammation, Irinotecan, Probiotics",Experiment 3,Egypt,Homo sapiens,Feces,UBERON:0001988,Response to irinotecan,EFO:0004829,Healthy individuals and Irinotecan treated patients,Colon cancer patients,Patients with colon cancer,10,5,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4a,18 June 2024,Scholastica,Scholastica,"The differences in the relative abundance of taxa between the colon cancer patients, Irinotecan treated, and healthy individuals as detected by the linear discriminant analysis effect size (LEfSe)",increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543;2|1224|1236|91347,Complete,Svetlana up
bsdb:1065/1/1,Study 1065,case-control,38327745,10.3389/fonc.2024.1279132,NA,"Zeber-Lubecka N, Kulecka M, Jagiełło-Gruszfeld A, Dąbrowska M, Kluska A, Piątkowska M, Bagińska K, Głowienka M, Surynt P, Tenderenda M, Mikula M , Ostrowski J",Breast cancer but not the menopausal status is associated with small changes of the gut microbiota,Frontiers in oncology,2024,"breast cancer, gut dysbiosis, menopausal status, microbiome, shotgun",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,pre-menopausal controls,pre-menopausal breast cancer (BC) patients,Newly diagnosed pre- or perimenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.,51,47,2 months,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,31 March 2024,Keamy,"Keamy,Scholastica",Taxa differentiating premenopausal breast cancer (BC) patients from premenopausal controls assessed using the LInear model for Differential Abundance (LINDA) method for compositional data,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis",2|201174|1760|2037|2049;2|201174;2|1239|186801|186802|3082771|1924093;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107;2|201174|84998|1643822|1643826;2|1239|186801|186802|204475;2|1239|186801|186802|204475|745368;2|1239|186801|186802|216572|1905344;2|201174|84998|84999|84107|1472762|1232426,Complete,Svetlana up
bsdb:1065/2/1,Study 1065,case-control,38327745,10.3389/fonc.2024.1279132,NA,"Zeber-Lubecka N, Kulecka M, Jagiełło-Gruszfeld A, Dąbrowska M, Kluska A, Piątkowska M, Bagińska K, Głowienka M, Surynt P, Tenderenda M, Mikula M , Ostrowski J",Breast cancer but not the menopausal status is associated with small changes of the gut microbiota,Frontiers in oncology,2024,"breast cancer, gut dysbiosis, menopausal status, microbiome, shotgun",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,post-menopausal controls,post-menopausal BC patients,Newly diagnosed postmenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.,35,41,2 months,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Table 4,31 March 2024,Keamy,"Keamy,Scholastica",Taxa differentiating postmenopausal breast cancer (BC) patients from postmenopausal controls assessed using the Linear model for Differential Abundance (LINDA) method for compositional data,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",2|1239|186801|186802|3085642|2048137;2|201174|84998|84999|84107|102106|147207;2|1239|186801|186802|216572|1892380;2|201174|1760|85006|1268,Complete,Svetlana up
bsdb:1065/2/2,Study 1065,case-control,38327745,10.3389/fonc.2024.1279132,NA,"Zeber-Lubecka N, Kulecka M, Jagiełło-Gruszfeld A, Dąbrowska M, Kluska A, Piątkowska M, Bagińska K, Głowienka M, Surynt P, Tenderenda M, Mikula M , Ostrowski J",Breast cancer but not the menopausal status is associated with small changes of the gut microbiota,Frontiers in oncology,2024,"breast cancer, gut dysbiosis, menopausal status, microbiome, shotgun",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,post-menopausal controls,post-menopausal BC patients,Newly diagnosed postmenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.,35,41,2 months,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Table 4,31 March 2024,Keamy,"Keamy,Scholastica",Taxa differentiating postmenopausal breast cancer (BC) patients from postmenopausal controls assessed using the Linear model for Differential Abundance (LINDA) method for compositional data,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",2|976|200643|171549|815|816|818;2|976|200643|171549|2005519;2|1239|186801|3085636|186803|572511|40520;2|976|200643|171549|2005519|1348911;2|976|200643|171549|2005519|1348911|1099853;2|1239|186801|3085636|186803|189330;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|823;2|1239|909932|1843488|909930|33024|33025,Complete,Svetlana up
bsdb:1066/1/1,Study 1066,case-control,37702484,10.1128/spectrum.02360-23,NA,"Chen K, Geng H, Liu J , Ye C",Alteration in gut mycobiota of patients with polycystic ovary syndrome,Microbiology spectrum,2023,"Aspergillus, Lentinula, Saccharomyces, gut mycobiota, polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Controls,Polycystic ovary syndrome (PCOS) patients,Women with PCOS diagnosed according to the 2003 Rotterdam criteria.,17,17,NA,PCR,NA,Illumina,LEfSe,0.05,TRUE,4,age,NA,decreased,decreased,unchanged,decreased,NA,decreased,Signature 1,Figure 7,25 March 2024,Linda Uchenwoke,Linda Uchenwoke,Differences in microbial genera identified by LEfSe analysis.,increased,"k__Eukaryota|k__Fungi|p__Ascomycota,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Omphalotaceae|g__Lentinula,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Omphalotaceae|g__Lentinula|s__Lentinula edodes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Marasmiaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces",2759|4751|4890;2759|4751|5204|155619|5338|72117|5352;2759|4751|5204|155619|5338|72117|5352|5353;2759|4751|5204|155619|5338|654128;2759|4751|4890|4891|4892|4893|4930;2759|4751|4890|4891|4892|4893|4930|4932;2759|4751|4890|4891|4892|4893;2759|4751|4890|4891|4892;2759|4751|4890|4891;2759|4751|4890|4891|4892|4893|4930,Complete,Peace Sandy
bsdb:1066/1/2,Study 1066,case-control,37702484,10.1128/spectrum.02360-23,NA,"Chen K, Geng H, Liu J , Ye C",Alteration in gut mycobiota of patients with polycystic ovary syndrome,Microbiology spectrum,2023,"Aspergillus, Lentinula, Saccharomyces, gut mycobiota, polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Controls,Polycystic ovary syndrome (PCOS) patients,Women with PCOS diagnosed according to the 2003 Rotterdam criteria.,17,17,NA,PCR,NA,Illumina,LEfSe,0.05,TRUE,4,age,NA,decreased,decreased,unchanged,decreased,NA,decreased,Signature 2,Figure 7,25 March 2024,Linda Uchenwoke,Linda Uchenwoke,Differences in microbial genera identified by LEfSe analysis.,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Arachnida|o__Ricinulei|f__Ricinoididae|g__Cryptocellus|s__Cryptocellus magnus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota",2759|4751|4890|147545|5042|1131492|5052;2759|33208|6656|6854|58139|88345|118523|3072159;2759|4751|4890|147545|5042;2759|4751|4890|147545|5042|28568;2759|4751|5204|155616;2759|4751|5204,Complete,Peace Sandy
bsdb:1067/1/1,Study 1067,case-control,32727366,https://doi.org/10.1186/s12866-020-01918-0,NA,"Wang J, Xu J, Han Q, Chu W, Lu G, Chan WY, Qin Y , Du Y",Changes in the vaginal microbiota associated with primary ovarian failure,BMC microbiology,2020,"16S rRNA, Female reproductive tract, Pathogenesis, Primary ovarian failure, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Acquired primary ovarian failure,MONDO:0019851,Healthy controls,Primary ovarian failure (POF),Women of reproductive age with follicular failure,29,22,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 2a,25 March 2024,Ndruscilla,"Ndruscilla,Scholastica",Differential genera in vaginal microbiota in patients with primary ovarian failure (POF) compared to control group,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Caryophanon,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|976|200643|171549|171552|838;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|1678;2|32066|203490|203491|1129771|168808;2|976|200643|171549|171551|836;2|1224|1236|91347|543|1940338;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|29465;2|29547|3031852|213849|72294|194;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|31983;2|1224|1236|91347|1903414|586;2|201174|1760|85007|1653|1716;2|1224|28216|80840|995019|577310;2|1239|186801|186802|31979|1485;2|1224|1236|91347|1903411|613;2|29547|3031852|213849|2808963|28196;2|1239|91061|1385|186817|182709;2|976|117743|200644|2762318|59732;2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|150022;2|1239|186801|186802|404402;2|1239|186801|3085636|186803|572511;2|1224|1236|135614|32033|83614;2|1239|91061|1385|186818|33976;2|1224|1236|72274|2887365|2742;2|1224|1236|135624|83763|83770;2|1239|1737404|1737405|1570339|1161127;2|1224|1236|135619|28256|2745;2|1239|909932|1843488|909930|904;2|1239|91061|1385|539738|1378;2|1239|909932|1843489|31977|909928;2|1239|186801|186802|204475;2|201174|1760|85006|1268|32207;2|1224|28216|80840|506|90243;2|1239|91061|186826|81852|1350;2|201174|1760|2037|2049|28263;2|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:1067/1/2,Study 1067,case-control,32727366,https://doi.org/10.1186/s12866-020-01918-0,NA,"Wang J, Xu J, Han Q, Chu W, Lu G, Chan WY, Qin Y , Du Y",Changes in the vaginal microbiota associated with primary ovarian failure,BMC microbiology,2020,"16S rRNA, Female reproductive tract, Pathogenesis, Primary ovarian failure, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Acquired primary ovarian failure,MONDO:0019851,Healthy controls,Primary ovarian failure (POF),Women of reproductive age with follicular failure,29,22,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 2a,25 March 2024,Ndruscilla,"Ndruscilla,Scholastica",Differential genera in vaginal microbiota in patients with primary ovarian failure (POF) compared to control group,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|91061|186826|33958|1578;2|1224|28211|204458|76892|41275;2|1239|1737404|1737405|1570339|543311;2|1239|186801|3085636|186803|841;2|1224|28211|356|118882|528;2|201174|84998|84999|1643824|1380;2|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:1068/1/1,Study 1068,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye KM, Swaggerty CL, Kogut MH, Ricke SC, Piva A , Grilli E",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 1,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(300 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 300g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3 A&B,7 September 2024,Victoria,Victoria,Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:1068/1/2,Study 1068,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye KM, Swaggerty CL, Kogut MH, Ricke SC, Piva A , Grilli E",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 1,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(300 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 300g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3 A&B,7 September 2024,Victoria,Victoria,Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1239|91061|186826|186827;2|1239|91061|1385|90964,Complete,Svetlana up
bsdb:1068/2/1,Study 1068,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye KM, Swaggerty CL, Kogut MH, Ricke SC, Piva A , Grilli E",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 2,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3. A&C,7 September 2024,Victoria,Victoria,Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|91061|186826|33958;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:1068/2/2,Study 1068,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye KM, Swaggerty CL, Kogut MH, Ricke SC, Piva A , Grilli E",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 2,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3 A&C,7 September 2024,Victoria,Victoria,Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1239|186801|3082720|186804;2|1239|91061|186826|186827;2|1224|1236|91347|543;2|1239|91061|1385|90964,Complete,Svetlana up
bsdb:1068/3/1,Study 1068,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye KM, Swaggerty CL, Kogut MH, Ricke SC, Piva A , Grilli E",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 3,United States of America,Gallus gallus,"Ileum,Jejunum","UBERON:0002116,UBERON:0002115",Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4,7 September 2024,Victoria,Victoria,"Linear discriminant analysis effect size (LEfSE) analysis. Missing operational taxonomic units (OUT) are not defined within the Family taxonomical designation and are labelled as unclassified. The 500 and NTC groups are relative to 300. An LDA > +/− 2 with a Q < 0.05 is considered significant and is graphically represented. All comparisons are relative to 300 g/MT, which was selected as it is the intermediary dose and describes the potential dose effect.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",2|1239|186801|186802|31979;2|201174|1760|85006|1268,Complete,Svetlana up
bsdb:1068/3/2,Study 1068,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye KM, Swaggerty CL, Kogut MH, Ricke SC, Piva A , Grilli E",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 3,United States of America,Gallus gallus,"Ileum,Jejunum","UBERON:0002116,UBERON:0002115",Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4,7 September 2024,Victoria,Victoria,"Linear discriminant analysis effect size (LEfSE) analysis. Missing operational taxonomic units (OUT) are not defined within the Family taxonomical designation and are labelled as unclassified. The 500 and NTC groups are relative to 300. An LDA > +/− 2 with a Q < 0.05 is considered significant and is graphically represented. All comparisons are relative to 300 g/MT, which was selected as it is the intermediary dose and describes the potential dose effect.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae",2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|1239|91061|186826|186827,Complete,Svetlana up
bsdb:1069/1/1,Study 1069,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M, Krumbeck JA, Wu G, Tang S, Prem A, Gupta AK , Dawson TL",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 1,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis media,Otitis externa","EFO:0004992,EFO:0009560",Healthy group,Otitis media and otitis externa,Adults patients affected by otitis externa (OE) and otitis media (OM),92,70,Patients receiving any antimicrobial treatment at time of sample collection,16S,123,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3A,30 May 2024,Scholastica,Scholastica,Taxa significantly different in healthy versus otitis externa (OE) and otitis media (OM) groups at the phylum to genus level for bacteria.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli",2|201174|1760|85009|31957;2|201174|1760|85009;2|201174;2|1239|91061|1385|90964;2|1239|91061|1385;2|1239|91061|186826|186828;2|1239|91061,Complete,Svetlana up
bsdb:1069/2/1,Study 1069,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M, Krumbeck JA, Wu G, Tang S, Prem A, Gupta AK , Dawson TL",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 2,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis media,Otitis externa,Adults patients affected by otitis externa (OE),140,22,Patients receiving any antimicrobial treatment at time of sample collection,16S,123,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3A,30 May 2024,Scholastica,Scholastica,Taxa significantly different in healthy and otitis media (OM) versus otitis externa (OE) groups at the phylum to genus level for bacteria.,increased,"k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcidiopsidales|f__Chroococcidiopsidaceae,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcidiopsidales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|1117|3028117|1890505|1890528;2|1117|3028117|1890505;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|72274|135621;2|1224|1236|72274;2|1224|1236,Complete,Svetlana up
bsdb:1069/3/1,Study 1069,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M, Krumbeck JA, Wu G, Tang S, Prem A, Gupta AK , Dawson TL",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 3,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis externa,Otitis media,Adults patients affected by otitis media (OM),114,48,Patients receiving any antimicrobial treatment at time of sample collection,16S,123,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3A,30 May 2024,Scholastica,Scholastica,Taxa significantly different in healthy and otitis externa (OE) versus otitis media (OM) groups at the phylum to genus level for bacteria.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacillota|c__Tissierellia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae",2|1239|91061|186826|81852;2|1239|1737404|1737405|1570339;2|1239|1737404|1737405;2|1239|1737404;2|1224|28216|80840|506;2|29547|3031852|213849|72294;2|29547|3031852|213849;2|29547|3031852;2|1224|1236|91347|1903411,Complete,Svetlana up
bsdb:1069/4/1,Study 1069,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M, Krumbeck JA, Wu G, Tang S, Prem A, Gupta AK , Dawson TL",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 4,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis media,Otitis externa","EFO:0004992,EFO:0009560",Healthy group,Otitis media and otitis externa,Adults patients affected by otitis externa (OE) and otitis media (OM),92,70,Patients receiving any antimicrobial treatment at time of sample collection,ITS / ITS2,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Fig. 3B,30 May 2024,Scholastica,Scholastica,Taxa significantly different in healthy versus otitis externa (OE) and otitis media (OM) groups at the phylum to genus level for fungi.,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae",2759|4751|5204|1538075|162474;2759|4751|5204|1538075;2759|4751|5204|1538075|162474|742845,Complete,Svetlana up
bsdb:1069/5/1,Study 1069,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M, Krumbeck JA, Wu G, Tang S, Prem A, Gupta AK , Dawson TL",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 5,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis media,Otitis externa,Adults patients affected by otitis externa (OE),140,22,Patients receiving any antimicrobial treatment at time of sample collection,ITS / ITS2,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3B,30 May 2024,Scholastica,Scholastica,Taxa significantly different in healthy and otitis media (OM) versus otitis externa (OE) groups at the phylum to genus level for fungi.,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes",2759|4751|4890|147545|5042|1131492;2759|4751|4890|147545|5042;2759|4751|4890|147545;2759|4751|4890|147550;2759|4751|5204|155619|139380;2759|4751|5204|155619|5303;2759|4751|5204|155619;2759|4751|5204|155616|5234;2759|4751|5204|155616,Complete,Svetlana up
bsdb:1069/6/1,Study 1069,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M, Krumbeck JA, Wu G, Tang S, Prem A, Gupta AK , Dawson TL",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 6,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis externa,Otitis media,Adults patients affected by otitis media (OM),114,48,Patients receiving any antimicrobial treatment at time of sample collection,ITS / ITS2,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Fig. 3B,30 May 2024,Scholastica,Scholastica,Taxa significantly different in healthy and otitis externa (OE) versus otitis media (OM) groups at the phylum to genus level for fungi.,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae",2759|4751|4890|147541;2759|4751|4890|3239874|2916678|766764;2759|4751|4890|4891|4892;2759|4751|4890|4891;2759|4751|5204|155619|452342|103376;2759|4751|5204|155619|452342;2759|4751|5204|155616|90883;2759|4751|5204|155616|90886|5408,Complete,Svetlana up
bsdb:1070/1/NA,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 1,China,Homo sapiens,"Subgingival dental plaque,Saliva","UBERON:0016484,UBERON:0001836",Hypertension,EFO:0000537,Saliva samples,Subgingival plague samples,"Subgingival plague samples from participants with Hypertension (HTN); n = 36
and without Hypertension (No HTN); n = 24",60,60,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,unchanged,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1070/2/NA,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 2,China,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Hypertension,EFO:0000537,Saliva samples,Fecal samples,Fecal samples from participants with Hypertension (HTN); n = 36 and without Hypertension (No HTN); n = 24,60,60,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1070/3/NA,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 3,China,Homo sapiens,"Subgingival dental plaque,Feces","UBERON:0016484,UBERON:0001988",Hypertension,EFO:0000537,Subgingival plague samples,Fecal samples,Fecal samples from participants with Hypertension (HTN); n = 36 and without Hypertension (No HTN); n = 24,60,60,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1070/4/1,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 3 (A),12 April 2024,Rahila,Rahila,Different fungal enrichments between the HTN and no-HTN groups.  (a) Saliva.,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Exophiala|s__Exophiala spinifera,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Tetrapisispora,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Agaricaceae|g__Agaricus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Agaricaceae|g__Agaricus|s__Agaricus bisporus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Agaricaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae|g__Saccharomycopsis|s__Saccharomycopsis fibuligera,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum orchidophilum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Thermochaetoides|s__Thermochaetoides thermophila",2759|4751|4890|4891|4892|4893|4910;2759|4751|4890|147545|34395|43219|5583|91928;2759|4751|4890|4891|4892|4893|113604;2759|4751|5204|155619|5338|5339|5340;2759|4751|5204|155619|5338|5339|5340|5341;2759|4751|5204|155619|5338|5339;2759|4751|4890|4891|2926619|34366|4943|4944;2759|4751|4890|147550|1028384|681950|5455|1209926;2759|4751|4890|147550|5139|35718|2944547|209285,Complete,NA
bsdb:1070/4/2,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 3 (A),12 April 2024,Rahila,Rahila,Different fungal enrichments between the HTN and no-HTN groups. (a) Saliva.,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus bombycis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae|g__Melampsora,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae|g__Melampsora|s__Melampsora laricis-populina,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Metarhizium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella lignohabitans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria|s__Zymoseptoria tritici,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Magnaporthaceae|g__Magnaporthe",2759|4751|4890|147545|5042|1131492|5052|109264;2759|4751|5204|162484|5258|5259|5260;2759|4751|5204|162484|5258|5259|5260|203908;2759|4751|5204|162484|5258|5259;2759|4751|4890|147550|5125|34397|5529;2759|4751|4890|3239873|3243772|410830|410829;2759|4751|4890|3239873|3243772|410830|410829|796027;2759|4751|4890|3239873|3243772|410830;2759|4751|4890|147541|2726947|93133|1047167;2759|4751|4890|147541|2726947|93133|1047167|1047171;2759|4751|4890|147550;2759|4751|4890|147550|639021|81093|148303,Complete,NA
bsdb:1070/5/1,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,decreased,Signature 1,FIG 3 (B),12 April 2024,Rahila,Rahila,Different fungal enrichments between the HTN and no-HTN groups. (b) Subgingival plaques.,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Nannizzia|s__Nannizzia gypsea,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Nannizzia,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Verticillium|s__Verticillium dahliae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Ajellomycetaceae|g__Blastomyces|s__Blastomyces gilchristii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Ajellomycetaceae|g__Blastomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Kwoniella|s__Kwoniella pini,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia mellicola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma gamsii",2759|4751|4890|147545|33183;2759|4751|4890|147545|33183|34384;2759|4751|4890|147545|33183|34384|1915381|63402;2759|4751|4890|147545|33183|34384|1915381;2759|4751|4890|147550|1028384|1033978|1036719|27337;2759|4751|5204|431957;2759|4751|4890|147545|33183|299071|229219|1681229;2759|4751|4890|147545|33183|299071|229219;2759|4751|5204|431957|431958|431959|148959;2759|4751|5204|431957|431958;2759|4751|5204|155619|452342;2759|4751|5204|431957|431958|431959;2759|4751|5204|155616|5234|1884633|490731|453459;2759|4751|5204|431957|431958|431959|148959|1708541;2759|4751|4890|147550|5125|5129|5543|398673,Complete,NA
bsdb:1070/5/2,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,decreased,Signature 2,FIG 3 (B),12 April 2024,Rahila,Rahila,Different fungal enrichments between the HTN and no-HTN groups. (b) Subgingival plaques.,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria alternata,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Chaetomium|s__Chaetomium globosum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus|s__Cryptococcus neoformans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Magnaporthaceae|g__Gaeumannomyces|s__Gaeumannomyces tritici,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Leptosphaeriaceae|g__Leptosphaeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Leptosphaeriaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Magnaporthaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales|f__Sporocadaceae|g__Pestalotiopsis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales|f__Sporocadaceae|g__Pestalotiopsis|s__Pestalotiopsis fici,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Leptosphaeriaceae|g__Plenodomus|s__Plenodomus biglobosus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae|g__Saccharomycopsis|s__Saccharomycopsis fibuligera,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__Scheffersomyces stipitis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales|f__Sporocadaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae|g__Saccharomycopsis",2759|4751|4890|147541|92860|28556|5598|5599;2759|4751|4890|147550|5139|35718|5149|38033;2759|4751|5204|155616|5234|1884633|5206|5207;2759|4751|4890|147550|639021|81093|29849|36779;2759|4751|4890|147541|92860|34374|5021;2759|4751|4890|147541|92860|34374;2759|4751|4890|147550|639021|81093;2759|4751|4890|147550|639021;2759|4751|4890|147550|37989|1812776|37840;2759|4751|4890|147550|37989|1812776|37840|393283;2759|4751|4890|147541|92860|34374|118259|220672;2759|4751|4890|4891|2926619|34366;2759|4751|4890|4891|2926619|34366|4943|4944;2759|4751|4890|3239874|2916678|766764|766733;2759|4751|4890|3239874|2916678|766764|766733|4924;2759|4751|4890|147550|5139;2759|4751|4890|147550|37989|1812776;2759|4751|4890|4891|4892|4893|4948;2759|4751|4890|4891|4892|4893|4948|4950;2759|4751|4890|147550|37989;2759|4751|4890|147550|5125;2759|4751|4890|4891|2926619|34366|4943,Complete,NA
bsdb:1070/6/1,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,FIG 3 (C),12 April 2024,Rahila,Rahila,Different fungal enrichments between the HTN and no-HTN groups. (c) Feces,increased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus terreus,k__Eukaryota|k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales|f__Spizellomycetaceae|g__Spizellomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora,k__Eukaryota|k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales|f__Spizellomycetaceae|g__Spizellomyces|s__Spizellomyces punctatus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum higginsianum,k__Eukaryota|k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales|f__Spizellomycetaceae,k__Eukaryota|k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Komagataella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma reesei,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Komagataella|s__Komagataella phaffii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus nomiae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus fumigatus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma virens",2759|4751|5204|155616|5234|1884633;2759|4751|5204|155616|5234;2759|4751|5204|155616|5234|1884633|5206;2759|4751|5204|155616|5234|1884633|5206;2759|4751|5204|155616;2759|4751|4890|147550|1028384|681950|5455;2759|4751|4890|147550|1028384|681950;2759|4751|4890|147545|5042|1131492|5052|33178;2759|4751|4761|451435|34478|34479|4815;2759|4751|4890|147541;2759|4751|4890|4891|4892|4893|4948;2759|4751|4761|451435|34478|34479|4815|109760;2759|4751|4890|4891|4892|4893|4948|4950;2759|4751|4890|147550|1028384|681950|5455|80884;2759|4751|4761|451435|34478|34479;2759|4751|4761|451435|34478;2759|4751|4890|3239874|3243775|1156497|460517;2759|4751|4890|147550|5125|5129|5543|51453;2759|4751|4890|3239874|3243775|1156497|460517|460519;2759|4751|4890|147545|5042|1131492|5052|41061;2759|4751|4890|147545|5042|1131492|5052|746128;2759|4751|4890|147550|5125|5129|5543|29875,Complete,NA
bsdb:1070/6/2,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,FIG 3 (C),12 April 2024,Rahila,Rahila,Different fungal enrichments between the HTN and no-HTN groups. (c) Feces,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces pinophilus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Coniophoraceae,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Coniophoraceae|g__Coniophora|s__Coniophora puteana,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Coniophoraceae|g__Coniophora",2759|4751|4890|147545|34395|43219;2759|4751|4890|147545|34395;2759|4751|4890|147550|5139;2759|4751|4890|147545|5042|28568|5094|128442;2759|4751|5204|155619|68889|80634;2759|4751|5204|155619|68889|80634|80635|80637;2759|4751|5204|155619|68889|80634|80635,Complete,NA
bsdb:1070/7/NA,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 7,China,Homo sapiens,"Subgingival dental plaque,Saliva","UBERON:0016484,UBERON:0001836",Hypertension,EFO:0000537,Saliva samples (No HTN),Subgingival plague samples (No HTN),Subgingival plague samples from participants without Hypertension (No HTN),24,24,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1070/8/NA,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 8,China,Homo sapiens,"Saliva,Subgingival dental plaque","UBERON:0001836,UBERON:0016484",Hypertension,EFO:0000537,Saliva samples (HTN),Subgingival plague samples (HTN),Subgingival plague samples from participants with Hypertension (HTN),36,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1070/9/NA,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 9,China,Homo sapiens,"Subgingival dental plaque,Feces","UBERON:0016484,UBERON:0001988",Hypertension,EFO:0000537,Subgingival plague samples (No HTN),Fecal samples (No HTN),Fecal samples from participants without Hypertension (No HTN),24,24,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1070/10/NA,Study 1070,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen BY, Lin WZ, Li YL, Bi C, Du LJ, Liu Y, Zhou LJ, Liu T, Xu S, Shi CJ, Zhu H, Wang YL, Sun JY, Liu Y, Zhang WC, Zhang Z, Zhang HL, Zhu YQ , Duan SZ",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 10,China,Homo sapiens,"Subgingival dental plaque,Feces","UBERON:0016484,UBERON:0001988",Hypertension,EFO:0000537,Subgingival plague samples (HTN),Fecal samples (HTN),Fecal samples from participants with Hypertension (HTN),36,36,2 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1071/1/1,Study 1071,case-control,33685393,10.1186/s12866-021-02125-1,https://rdcu.be/dCvoU,"Zhang X, Shi L, Sun T, Guo K , Geng S",Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients,BMC microbiology,2021,"16S, Cytokines, Gut microbiome, Microbiota, Psoriasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy Control (HC),Psoriasis,"Patients with a clinical diagnosis of psoriasis who were attending a dermatology outpatient clinic in the Second Affiliated Hospital of Xi ‘an Jiaotong University, among them 24 were diagnosed with psoriasis vulgaris (PV), 6 with pustular psoriasis (PP).",30,30,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2 e/f,28 March 2024,PraiseAgbetuyi,PraiseAgbetuyi,Differentially abundant taxa between the psoriasis group (P) and healthy control group (N) which was generated from LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Synergistota|c__Synergistia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae",2|1239|186801|186802|216572|216851;2|1239|186801|186802|204475;2|1239|909932|909929|1843491|158846;2|508458|649775|649776|3029088|638847;2|508458|649775|649776;2|508458|649775|649776|649777|2753;2|508458|649775;2|1239|909932|1843489|31977;2|508458|649775|649776|3029088,Complete,Svetlana up
bsdb:1071/1/2,Study 1071,case-control,33685393,10.1186/s12866-021-02125-1,https://rdcu.be/dCvoU,"Zhang X, Shi L, Sun T, Guo K , Geng S",Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients,BMC microbiology,2021,"16S, Cytokines, Gut microbiome, Microbiota, Psoriasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy Control (HC),Psoriasis,"Patients with a clinical diagnosis of psoriasis who were attending a dermatology outpatient clinic in the Second Affiliated Hospital of Xi ‘an Jiaotong University, among them 24 were diagnosed with psoriasis vulgaris (PV), 6 with pustular psoriasis (PP).",30,30,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2 e/f,28 March 2024,PraiseAgbetuyi,PraiseAgbetuyi,Differentially abundant taxa between the psoriasis group (P) and healthy control group (N) which was generated from LEfSe analysis,decreased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:1071/2/1,Study 1071,case-control,33685393,10.1186/s12866-021-02125-1,https://rdcu.be/dCvoU,"Zhang X, Shi L, Sun T, Guo K , Geng S",Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients,BMC microbiology,2021,"16S, Cytokines, Gut microbiome, Microbiota, Psoriasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Pustular Psoriasis (PP),Psoriasis Vulgaris (PV),Patients with psoriasis diagnosed with psoriasis vulgaris (PV),6,24,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4C,29 March 2024,KwennB,KwennB,Differentially abundant taxa between the psoriasis group (PP) and Psoriasis Vulgaris (PV) which was generated from LEfSe analysis,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|526524|526525|128827|118966;2|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:1071/2/2,Study 1071,case-control,33685393,10.1186/s12866-021-02125-1,https://rdcu.be/dCvoU,"Zhang X, Shi L, Sun T, Guo K , Geng S",Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients,BMC microbiology,2021,"16S, Cytokines, Gut microbiome, Microbiota, Psoriasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Pustular Psoriasis (PP),Psoriasis Vulgaris (PV),Patients with psoriasis diagnosed with psoriasis vulgaris (PV),6,24,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4C,29 March 2024,KwennB,KwennB,Differentially abundant taxa between the psoriasis group (P) and Psoriasis Vulgaris (PV) which was generated from LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria",2|1239|909932|1843489|31977;2|1224|1236,Complete,Svetlana up
bsdb:1072/1/1,Study 1072,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J, Talavera-Rodríguez A, Díaz-Álvarez J, Rosas Cancio-Suárez M, Rodríguez JM, Alba C, Montes ML, Martín-Mateos R, Burgos-Santamaría D, Moreno S, Serrano-Villar S , Sánchez-Conde M",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV- MASLD+,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,20,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,5 May 2024,Aleru Divine,Aleru Divine,LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|186801|3085636|186803|877406;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1506577;2|1239|186801|3082720|3030910|86331;2|1239|526524|526525|128827|123375;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|877420;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|186807|2740;2157|28890|183925|2158|2159|2172;2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803|2316020|33038;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|572511;2|77133;2|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:1072/1/2,Study 1072,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J, Talavera-Rodríguez A, Díaz-Álvarez J, Rosas Cancio-Suárez M, Rodríguez JM, Alba C, Montes ML, Martín-Mateos R, Burgos-Santamaría D, Moreno S, Serrano-Villar S , Sánchez-Conde M",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV- MASLD+,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,20,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,5 May 2024,Aleru Divine,Aleru Divine,LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",2|1239|186801|186802|216572|1508657;2|1239|91061|186826|81852|1350;2|1224|1236|91347|1903409|53335;2|1239|186801|186802|31979|1485|1262798;2|1224|1236|91347|1903411|629;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1766253;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|292632;2|1239|91061|186826|33958|46255;2|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:1072/2/1,Study 1072,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J, Talavera-Rodríguez A, Díaz-Álvarez J, Rosas Cancio-Suárez M, Rodríguez JM, Alba C, Montes ML, Martín-Mateos R, Burgos-Santamaría D, Moreno S, Serrano-Villar S , Sánchez-Conde M",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,30,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,5 May 2024,Aleru Divine,Aleru Divine,LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|s__uncultured bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|186801|3085636|186803|877406;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1506577;2|1239|186801|3082720|3030910|86331;2|1239|526524|526525|128827|123375;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|877420;2|1239|186801|3085636|186803|2316020|33039;2|1239|186801|186802|186807|2740;2157|28890|183925|2158|2159|2172;2|1239|186801|3085636|186803|248744;2|1239|186801|3085636|186803|2316020|33038;2|1239|526524|526525|128827|1573535;2|1239|186801|3085636|186803|572511;2|77133;2|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:1072/2/2,Study 1072,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J, Talavera-Rodríguez A, Díaz-Álvarez J, Rosas Cancio-Suárez M, Rodríguez JM, Alba C, Montes ML, Martín-Mateos R, Burgos-Santamaría D, Moreno S, Serrano-Villar S , Sánchez-Conde M",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,30,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,5 May 2024,Aleru Divine,Aleru Divine,LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|909932|1843488|909930|904;2|976|200643|171549|171552|1283313;2|1239|909932|909929|1843491|82373;2|544448|31969|186332|186333|2152;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552|838|1486938;2|1224|1236|135624|83763|83770;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:1072/3/1,Study 1072,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J, Talavera-Rodríguez A, Díaz-Álvarez J, Rosas Cancio-Suárez M, Rodríguez JM, Alba C, Montes ML, Martín-Mateos R, Burgos-Santamaría D, Moreno S, Serrano-Villar S , Sánchez-Conde M",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV- MASLD+,Participants with Metabolic dysfunction-associated steatotic liver disease (MASLD) without HIV infection.,30,20,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,5 May 2024,Aleru Divine,Aleru Divine,LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1239|186801|186802|216572|1508657;2|1239|91061|186826|81852|1350;2|1224|1236|91347|1903409|53335;2|1239|186801|186802|31979|1485|1262798;2|1224|1236|91347|1903411|629;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1766253;2|1224|1236|91347|543|1940338;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|292632;2|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:1072/3/2,Study 1072,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J, Talavera-Rodríguez A, Díaz-Álvarez J, Rosas Cancio-Suárez M, Rodríguez JM, Alba C, Montes ML, Martín-Mateos R, Burgos-Santamaría D, Moreno S, Serrano-Villar S , Sánchez-Conde M",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV- MASLD+,Participants with Metabolic dysfunction-associated steatotic liver disease (MASLD) without HIV infection.,30,20,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,5 May 2024,Aleru Divine,Aleru Divine,LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|909932|1843488|909930|904;2|976|200643|171549|171552|1283313;2|1239|909932|909929|1843491|82373;2|544448|31969|186332|186333|2152;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552|838|1486938;2|1224|1236|135624|83763|83770;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815|816,Complete,Svetlana up
bsdb:1073/1/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 1,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Healthy sea urchins,Diseased sea urchins,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,"Figure 6 & Supplementary Data file 2,  Table S7.",15 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa with significantly different abundances in the microbiomes on sea urchins,increased,"k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Amoebophilaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Amylibacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Aureispira,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Donghicola,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Fusibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Granulosicoccaceae|g__Granulosicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Halocynthiibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Luteibaculaceae|g__Luteibaculum,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomicrobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Poseidonibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudoteredinibacter,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Reichenbachiellaceae|g__Reichenbachiella,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Roseobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Saccharospirillaceae,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae",2|976|768503|768507|1501348;2|1224|28211|204455|31989|1617805;2|29547|3031852|213849|2808963;2|976|1937959|1936988|89374|365032;2|1224|1236|135622|267889|28228;2|976|117743|200644|246874;2|1224|28211|204455|2854170|393277;2|976|117743|200644|49546;2|1239|186801|186802|543313|76008;2|1224|1236|135613|449719|437504;2|1224|1236|1706369|1706372;2|1224|28211|204455|31989|1579315;2|74201|203494|48461|203557|574899;2|1224|1236|72273|135617|45247;2|976|117743|200644|2772533|1649465;2|976|117743|200644|49546|449810;2|1224|28211|204455|31989;2|203682|203683|112|126|1779141;2|29547|3031852|213849|2808963|2321187;2|1224|1236|1706369|1706371|1122284;2|976|768503|768507|2762302|156993;2|203682|203683|2691354|2691357|265488;2|1224|28211|766|775;2|1224|28211|766;2|976|200643|1970189|1471398|1827484;2|1224|28211|204455|2854170|2433;2|1224|1236|135619|255527;2|976|1937959|1936988|89374;2|1224|1236|1706369|1706375,Complete,NA
bsdb:1073/1/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 1,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Healthy sea urchins,Diseased sea urchins,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,"Figure 6 & Supplementary Data file 2,  Table S7.",16 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Agarivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Candidatus Tectimicrobiota|c__Candidatus Entotheonellia|o__Candidatus Entotheonellales|f__Candidatus Entotheonellaceae|g__Candidatus Entotheonella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Riegeria,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flagellimonas,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Halioglobus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Parvularculales|f__Parvularculaceae|g__Hyphococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Jannaschia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Ahrensiaceae|g__Pseudahrensia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Psychroflexus,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Rubidimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Terasakiellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Ulvibacter",2|1224|1236|135622|72275|261825;2|976|200643;2|1802339|3277336|3277337|3277338|93171;2|1224|28211|204441|41295|1068873;2|976|1853228|1853229;2|1239|186801|3082768|990719;2|1239|186801;2|200940|3031451|3024411|213121|893;2|200940|3031451|3024411|2886822|109168;2|1224|28211|356|2831106|46913;2|976|200643|1970189|1471398|1471399;2|976|117743|200644|49546|444459;2|976|117743|200644|49546;2|1224|1236|1706369|1706372|1217416;2|1224|28211|255473|255474|2038635;2|1224|28211|2800060|69657;2|1224|28211|204455|2854170|188905;2|1239|186801|3085636|186803;2|976|200643|1970189|1573805;2|1224|28211|356|2829814|1434035;2|976|117743|200644|49546|83612;2|203682|203683|2691354|2691357|265488;2|976|200643|1970189|1471398|1827484;2|976|1937959|1936988|89374|1147735;2|1224|1236|135622|267890|22;2|1224|28211|204441|2813951;2|976|117743|200644|49546|237444,Complete,NA
bsdb:1073/2/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 2,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Healthy sea urchins,Recovered sea urchins,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,unchanged,Signature 1,"Figure 6 & Supplementary Data file 2,  Table S7.",16 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Aestuariicella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Pleioneaceae|g__Aliikangiella,k__Bacteria|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulforhopalus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae|g__Oceanicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Rubritaleaceae|g__Rubritalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Thalassotalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",2|1224|1236|1706369|1706371|1635133;2|1224|1236|135619|2823145|1920241;2|3018035|3031419|2024979|263369;2|976|1853228|1853229;2|1239|186801|3082768|990719;2|1239|186801;2|1224|1236|118969|118968|776;2|200940|3024418|213118|213119;2|200940|3031451|3024411|2886822|40413;2|200940|3031449|213115|194924|872;2|1224|1236;2|1224|28211|2800060|69657;2|1239|186801|3085636|186803;2|1224|1236|1706369|1706375|1084558;2|1239|186801|186802|216572;2|1224|28211|766;2|74201|203494|48461|203557|518755;2|74201|203494|48461|1648490|361050;2|1224|1236|1706369|1706375;2|1224|1236|135622|267889|1518149;2|1224|1236|135623|641|662,Complete,NA
bsdb:1073/2/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 2,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Healthy sea urchins,Recovered sea urchins,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,unchanged,Signature 2,"Figure 6 & Supplementary Data file 2,  Table S7.",16 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Candidatus Tectimicrobiota|c__Candidatus Entotheonellia|o__Candidatus Entotheonellales|f__Candidatus Entotheonellaceae|g__Candidatus Entotheonella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Halocynthiibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Parvularculales|f__Parvularculaceae|g__Hyphococcus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Jannaschia,k__Bacteria|p__Kiritimatiellota|c__Kiritimatiellia|o__Kiritimatiellales|f__Kiritimatiellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Luteibaculaceae|g__Luteibaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Ahrensiaceae|g__Pseudahrensia,k__Bacteria|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Roseobacter,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Rubidimonas,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Terasakiellaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Ulvibacter",2|976|200643;2|1802339|3277336|3277337|3277338|93171;2|200940|3031451|3024411|2886822|109168;2|1224|28211|356|2831106|46913;2|976|200643|1970189|1471398|1471399;2|976|117743|200644|49546;2|1224|28211|204455|31989|1579315;2|74201|203494|48461|203557|574899;2|1224|28211|255473|255474|2038635;2|1224|28211|2800060|69657;2|1224|28211|204455|2854170|188905;2|134625|1921781|1921782|1921783;2|976|117743|200644|2772533|1649465;2|976|200643|1970189|1573805;2|1224|28211|356|2829814|1434035;2|3018035|3031418|213481|213483;2|1224|28211|204455|2854170|2433;2|976|1937959|1936988|89374|1147735;2|976|1937959|1936988|89374;2|1224|1236|135622|267890|22;2|1224|28211|204441|2813951;2|976|117743|200644|49546|237444,Complete,NA
bsdb:1073/3/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 3,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Recovered sea urchins,Diseased sea urchins,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 6 & Supplementary Data file 2, Table S7.",17 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.,increased,"k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Amoebophilaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Amylibacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Aureispira,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Donghicola,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Fusibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Granulosicoccaceae|g__Granulosicoccus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Halocynthiibacter,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Luteibaculaceae|g__Luteibaculum,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomicrobium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Poseidonibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudoteredinibacter,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Reichenbachiellaceae|g__Reichenbachiella,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Roseobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Saccharospirillaceae,k__Bacteria|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae",2|976|768503|768507|1501348;2|1224|28211|204455|31989|1617805;2|29547|3031852|213849|2808963;2|976|1937959|1936988|89374|365032;2|1224|1236|135622|267889|28228;2|976|117743|200644|246874;2|1224|28211|204455|2854170|393277;2|976|117743|200644|49546;2|1239|186801|186802|543313|76008;2|1224|1236|135613|449719|437504;2|1224|1236|1706369|1706372;2|1224|28211|204455|31989|1579315;2|74201|203494|48461|203557|574899;2|1224|1236|72273|135617|45247;2|976|117743|200644|2772533|1649465;2|976|117743|200644|49546|449810;2|1224|28211|204455|31989;2|203682|203683|112|126|1779141;2|29547|3031852|213849|2808963|2321187;2|1224|1236|1706369|1706371|1122284;2|976|768503|768507|2762302|156993;2|203682|203683|2691354|2691357|265488;2|1224|28211|766|775;2|1224|28211|766;2|976|200643|1970189|1471398|1827484;2|1224|28211|204455|2854170|2433;2|1224|1236|135619|255527;2|976|1937959|1936988|89374;2|1224|1236|1706369|1706375,Complete,NA
bsdb:1073/3/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 3,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Recovered sea urchins,Diseased sea urchins,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 6 & Supplementary Data file 2,  Table S7.",17 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa with significantly different abundances in the microbiomes on sea urchins in each groups,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Aestuariicella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Pleioneaceae|g__Aliikangiella,k__Bacteria|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae|g__Oceanicoccus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Rubritaleaceae|g__Rubritalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Thalassotalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|1236|1706369|1706371|1635133;2|1224|1236|135619|2823145|1920241;2|3018035|3031419|2024979|263369;2|976|1853228|1853229;2|1239|186801;2|1224|1236|118969|118968|776;2|200940|3024418|213118|213119;2|200940|3031449|213115|194924|872;2|1224|1236;2|1224|28211|2800060|69657;2|1239|186801|3085636|186803;2|1224|1236|1706369|1706375|1084558;2|1224|28211|766;2|74201|203494|48461|203557|518755;2|74201|203494|48461|1648490|361050;2|1224|1236|1706369|1706375;2|1224|1236|135622|267889|1518149;2|1224|1236|135623|641|662;2|1239|186801|3082768|990719;2|1239|186801|186802|216572,Complete,NA
bsdb:1073/4/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 4,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Sea water from healthy sea urchins aquarium,Sea water from diseased sea urchins aquarium,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,2,2,NA,16S,34,"Illumina,Non-quantitative PCR",LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,"Supplementary Data File 2,Table S6",22 April 2024,Carita Ndibe,Carita Ndibe,Relative abundance of the most abundant genera in the seawater samples.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae",2|1224|1236|135622|267889|28228;2|1224|1236|91347|1903409;2|1224|1236;2|1224|1236|72273|135617|45247;2|976|117743|200644|49546|358023;2|1224|1236|1706369|1706375,Complete,NA
bsdb:1073/4/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 4,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Sea water from healthy sea urchins aquarium,Sea water from diseased sea urchins aquarium,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,2,2,NA,16S,34,"Illumina,Non-quantitative PCR",LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,"Supplementary Data File 2, Table S6",22 April 2024,Carita Ndibe,Carita Ndibe,Relative abundance of the most abundant genera in the seawater samples,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Ahrensiaceae|g__Pseudahrensia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",2|1224|28211;2|1224|1236|135622|72275;2|976|200643;2|200940|3031451|3024411|2886822|109168;2|976|200643|1970189|1573805;2|1224|28211|356|2829814|1434035;2|1224|1236|135622|267888|53246;2|1224|1236|135622|267894|67572;2|976|200643|1970189|1471398|1827484;2|1224|1236|135623|641|662,Complete,NA
bsdb:1073/5/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 5,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Sea water from healthy sea urchins aquarium,Sea water from recovered sea urchins aquarium,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",2,2,NA,16S,34,"Illumina,Non-quantitative PCR",LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Supplementary Data File 2, Table S6",22 April 2024,Carita Ndibe,Carita Ndibe,Relative abundance of the most abundant genera in the seawater samples,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria",2|1224|1236|135622|267894|67572;2|1224|1236;2|1224|1236|1706369|1706375;2|1224|1236|135622|72275;2|1224|28211,Complete,NA
bsdb:1073/5/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 5,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Sea water from healthy sea urchins aquarium,Sea water from recovered sea urchins aquarium,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",2,2,NA,16S,34,"Illumina,Non-quantitative PCR",LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,"Supplementary Data File 2, Table S6",23 April 2024,Carita Ndibe,Carita Ndibe,Relative abundance of the most abundant genera in the seawater samples,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Ahrensiaceae|g__Pseudahrensia",2|1224|1236|135623|641|662;2|1224|1236|135622|267889|28228;2|1224|1236|72273|135617|45247;2|976|200643|1970189|1573805;2|200940|3031451|3024411|2886822|109168;2|976|200643;2|1224|1236|135622|267888|53246;2|976|200643|1970189|1471398|1827484;2|976|117743|200644|49546|358023;2|1224|28211|356|2829814|1434035,Complete,NA
bsdb:1073/6/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 6,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Recovered sea urchins,Diseased sea urchins,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,4,4,NA,PCR,NA,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Supplementary Data file 3, figure 6A & TableS4-5.",17 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa have different abundances in microbiomes from samples collected from diseased sea urchins compared to recovered sea urchins,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Cognaticolwellia|s__Cognaticolwellia aestuarii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia|s__Colwellia psychrerythraea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia rhapontici,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix|s__Leucothrix mucor,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter|s__Lutibacter agarilyticus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas|s__Psychromonas arctica,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Octadecabacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Blastopirellula,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Polaribacter",2|1224|1236|135622|267889|2848171|329993;2|1224|1236|135622|267889|28228;2|1224|1236|135622|267889|28228|28229;2|1224|1236|91347|1903409|551;2|1224|1236|91347|1903409|551|55212;2|1224|1236|72273|135617|45247;2|1224|1236|72273|135617|45247|45248;2|976|117743|200644|49546|358023;2|976|117743|200644|49546|358023|1109740;2|1224|1236|135622|267894|67572|168275;2|1224|1236|135623|641|662;2|1224|1236|135619|135620;2|976|117743|200644|1853230|332102;2|1224|28211|204455|2854170|53945;2|29547|3031852|213849|2808963|28196;2|203682|203683|2691354|2691357|265487;2|976|117743|200644|49546|52959,Complete,NA
bsdb:1073/6/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 6,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Recovered sea urchins,Diseased sea urchins,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,4,4,NA,PCR,NA,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Supplementary Data file 3, figure 6A & TableS4-5.",17 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa have different abundances in microbiomes from samples collected from diseased sea urchins compared to recovered sea urchins,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Cobetia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurimonadaceae|g__Sulfurimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas|s__Psychromonas kaikoae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas|s__Psychromonas profunda,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio panuliri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Arenicellales|f__Arenicellaceae|g__Arenicella|s__Arenicella xantha,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus|s__Roseibacillus ponti,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrosopumilales|f__Nitrosopumilaceae|g__Nitrosarchaeum|s__Nitrosarchaeum koreense,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Roseibium|s__Roseibium aquae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Rubritaleaceae|g__Rubritalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Kordiimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Arenicellales|f__Arenicellaceae|g__Arenicella,k__Archaea|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrosopumilales|f__Nitrosopumilaceae|g__Nitrosarchaeum,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Winogradskyella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Roseibium",2|1224|1236|135619|28256|204286;2|200940|3031451|3024411|2886822|109168;2|29547|3031852|213849|2771471|202746;2|1224|1236|135622|72275|226;2|1224|1236|135622|267894|67572;2|1224|1236|135622|267894|67572|145373;2|1224|1236|135622|267894|67572|174037;2|1224|1236|1706369|1706371;2|1224|1236|135623|641|662|1381081;2|1224|1236|1617890|1617891|904708|644221;2|74201|203494|48461|203557|518755|454147;2157|651137|1643678|31932|338190|1007082|1088740;2|1224|28211|356|2821832|150830|1323746;2|74201|203494|48461|1648490|361050;2|1224|1236|72273|34064|262;2|1224|28211|362534|1331809|288021;2|1224|28211|204457|335929|361177;2|1224|1236|118969|118968|776;2|1224|1236|1617890|1617891|904708;2157|651137|1643678|31932|338190|1007082;2|74201|203494|48461|203557|518755;2|976|117743|200644|49546|286104;2|1224|28211|356|2821832|150830,Complete,NA
bsdb:1073/7/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 7,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Sea water from recovered sea urchins aquarium,Sea water diseased sea urchins aquarium,The sample collected from the water in the aquarium where the sea urchins with Bald sea urchin disease (BSUD) were cultured.,2,2,NA,16S,34,"Illumina,Non-quantitative PCR",LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Supplementary Data File 2, Table S6",23 April 2024,Carita Ndibe,Carita Ndibe,Relative abundance of the most abundant genera in the seawater samples,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter",2|1224|1236|135623|641|662;2|1224|1236|135622|267889|28228;2|1224|1236|72273|135617|45247;2|1224|1236|91347|1903409;2|976|117743|200644|49546|358023,Complete,NA
bsdb:1073/7/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 7,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Sea water from recovered sea urchins aquarium,Sea water diseased sea urchins aquarium,The sample collected from the water in the aquarium where the sea urchins with Bald sea urchin disease (BSUD) were cultured.,2,2,NA,16S,34,"Illumina,Non-quantitative PCR",LEfSe,0.05,FALSE,3,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,"Supplementary Data File 2, Table S6",23 April 2024,Carita Ndibe,Carita Ndibe,Relative abundance of the most abundant genera in the seawater samples,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Ahrensiaceae|g__Pseudahrensia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae",2|1224|28211;2|1224|1236|135622|72275;2|976|200643;2|200940|3031451|3024411|2886822|109168;2|1224|1236;2|976|200643|1970189|1573805;2|1224|28211|356|2829814|1434035;2|1224|1236|135622|267888|53246;2|1224|1236|135622|267894|67572;2|976|200643|1970189|1471398|1827484;2|1224|1236|1706369|1706375,Complete,NA
bsdb:1073/8/1,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 8,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Healthy sea urchins,Recovered sea urchins,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",4,4,NA,PCR,NA,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Supplementary Data file 3, figure 6B & TableS4-5.",17 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa have different abundances in microbiomes from samples collected from recovered sea urchins compared to healthy sea urchins,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Cobetia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas|s__Psychromonas kaikoae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas|s__Psychromonas profunda,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurimonadaceae|g__Sulfurimonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio panuliri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Arenicellales|f__Arenicellaceae|g__Arenicella|s__Arenicella xantha,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus|s__Roseibacillus ponti,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Roseibium|s__Roseibium aquae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Rubritaleaceae|g__Rubritalea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Kordiimonas,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Arenicellales|f__Arenicellaceae|g__Arenicella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Winogradskyella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Roseibium",2|1224|1236|135622|72275|226;2|1224|1236|135619|28256|204286;2|200940|3031451|3024411|2886822|109168;2|1224|1236|135622|267894|67572;2|1224|1236|135622|267894|67572|145373;2|1224|1236|135622|267894|67572|174037;2|29547|3031852|213849|2771471|202746;2|1224|1236|135623|641|662|1381081;2|1224|1236|1617890|1617891|904708|644221;2|74201|203494|48461|203557|518755|454147;2|1224|28211|356|2821832|150830|1323746;2|74201|203494|48461|1648490|361050;2|1224|1236|72273|34064|262;2|1224|28211|362534|1331809|288021;2|1224|28211|204457|335929|361177;2|1224|1236|118969|118968|776;2|1224|1236|1617890|1617891|904708;2|200940|3031449|213115|194924|872;2|74201|203494|48461|203557|518755;2|976|117743|200644|49546|286104;2|1224|28211|356|2821832|150830,Complete,NA
bsdb:1073/8/2,Study 1073,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA , Smith LC",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 8,United States of America,Strongylocentrotus purpuratus,Cellular bone tissue,UBERON:4000118,Bacterial disease,EFO:0000771,Healthy sea urchins,Recovered sea urchins,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",4,4,NA,PCR,NA,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Supplementary Data file 3, figure 6B & TableS4-5.",17 April 2024,Omojokunoluwatomisin,Omojokunoluwatomisin,Taxa have different abundances in microbiomes from samples collected from recovered sea urchins compared to healthy sea urchins,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Echinimonadaceae|g__Neiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Parvularculales|f__Parvularculaceae|g__Parvularcula,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas|s__Psychromonas heitensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter|s__Prolixibacter sp.,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Oceanispirochaeta|s__Oceanispirochaeta litoralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter salarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio litoralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas|s__Halomonas sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella olleyana,k__Bacteria|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Marinosulfonomonas|s__Marinosulfonomonas methylotropha,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium hippocampi,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Oceaniovalibus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Loktanella,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Litoribacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Marinosulfonomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Saccharicrinis,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Sulfitobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Gilvibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Psychroflexus",2|1224|1236|135622|267889|28228;2|1224|1236|135622|3046600|1434025;2|1224|28211|255473|255474|208215;2|1224|1236|135622|267888|53246;2|1224|1236|135622|267894|67572|479650;2|1224|1236|135623|641|662;2|976|200643|1970189|1471398|314318|1954466;2|203691|203692|136|137|2035349|151;2|1224|1236|72274|2887365|2742|1420917;2|1224|1236|135623|641|662|335972;2|1224|1236|135619|28256|2745|1486246;2|1224|1236|135622|267890|22|135626;2|203682|203683|112|126|118;2|1224|28211|204455|31989|50056|50058;2|201174|1760|85007|1762|1866885|659824;2|1224|1236|135622|267894|67572;2|1224|1236|135622|267890|22;2|976|200643|1970189|1471398|314318;2|1224|28211|204455|2854170|1207070;2|1224|1236|72274|2887365|2742;2|1224|28211|204455|2854170|245186;2|203691|203692|136|137|146;2|1224|1236|135619|135620|1264044;2|1224|28211|204455|31989|50056;2|976|200643|1970189|558415|1618113;2|1224|28211|204455|2854170|60136;2|976|200643|1970189|1471398|1471399;2|1224|28216|32003|206379|35798;2|976|117743|200644|49546|379070;2|201174|1760|85007|1762|1763;2|976|117743|200644|49546|83612,Complete,NA
bsdb:1074/1/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls,Patients at baseline - SVR,Patients at baseline with HCV monoinfection and HCV/HIV coinfection  who achieved sustained virological response (SVR),20,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/2/1,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Baseline - SVR,Follow-up at week 72 (FUw72) -SVR,Patients at week 72 after treatment completion who achieved sustained virological response (SVR),NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,increased,NA,NA,Signature 1,Table 2,5 April 2024,Scholastica,Scholastica,Significant taxa (≥ 1%) at genus levels in patients with SVR,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|3085636|186803|572511;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|189330;2|1239|909932|909929|1843491|158846;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|207244;2|1239|909932|1843489|31977|906;2|1239|526524|526525|128827|1573535;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:1074/2/2,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Baseline - SVR,Follow-up at week 72 (FUw72) -SVR,Patients at week 72 after treatment completion who achieved sustained virological response (SVR),NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,increased,NA,NA,Signature 2,Table 2,5 April 2024,Scholastica,Scholastica,Significant taxa (≥ 1%) at genus levels in patients with SVR,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|1506553;2|1224|28216|80840|995019|40544;2|1239|186801|3085636|186803|28050,Complete,Svetlana up
bsdb:1074/3/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls,Follow-up at week 72 (FUw72) -SVR,Patients at week 72 after treatment completion who achieved sustained virological response (SVR),20,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/4/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 4,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with mild fibrosis at baseline (F0–F1),Patients with mild fibrosis at FUw72 (F0–F1),Patients with mild fibrosis (F0–F1) at week 72 after treatment completion,NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/5/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 5,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with significant fibrosis to cirrhosis at baseline (F2–F4),Patients with significant fibrosis to cirrhosis at FUw72 (F2–F4),Patients with significant fibrosis to cirrhosis (F2–F4) at week 72 after treatment completion (FUw72),NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/6/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 6,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV monoinfection & (F2-F4) fibrosis at baseline,Patients with HCV monoinfection & (F2-F4) fibrosis at FUw72,Patients with HCV monoinfection and significant fibrosis to cirrhosis (F2-F4) at week 72 after treatment completion (FUw72).,NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/7/1,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV/HIV coinfection at baseline,Patients with HCV/HIV coinfection at FUw72,Patients with HCV/HIV coinfection at week 72 after treatment completion (FUw72),24,19,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,Signature 1,Table S4,4 April 2024,Idiaru angela,Idiaru angela,Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV/HIV coinfection,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|1766253;2|201174|1760|85004|31953|1678;2|1239|909932|909929|1843491|158846;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:1074/7/2,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV/HIV coinfection at baseline,Patients with HCV/HIV coinfection at FUw72,Patients with HCV/HIV coinfection at week 72 after treatment completion (FUw72),24,19,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,Signature 2,Table S3,4 April 2024,Idiaru angela,Idiaru angela,Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV/HIV coinfection,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:1074/8/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 8,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV monoinfection + mild fibrosis at baseline,Patients with HCV monoinfection + mild fibrosis at FUw72,Patients with HCV monoinfection who had F0–F1 fibrosis stage at week 72 after treatment completion (FUw72),NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/9/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 9,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV monoinfection + significant fibrosis at baseline,Patients with HCV monoinfection + significant fibrosis at FUw72,Patients with HCV monoinfection who had F2–F4 fibrosis stage at week 72 after treatment completion (FUw72),NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/10/NA,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 10,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV/HIV coinfection + mild fibrosis at baseline,Patients with HCV/HIV coinfection + mild fibrosis at FUw72,Patients with HCV/HIV coinfection who had F0–F1 fibrosis stage at week 72 after treatment completion (FUw72),NA,NA,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1074/11/1,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 11,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,patients with HCV monoinfection at baseline,patients with HCV monoinfection at FUw72,patients with HCV monoinfection at week 72 after treatment completion (FUw72),62,50,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,increased,NA,NA,Signature 1,Table S3,4 April 2024,Idiaru angela,Idiaru angela,Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV monoinfection,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:1074/11/2,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 11,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,patients with HCV monoinfection at baseline,patients with HCV monoinfection at FUw72,patients with HCV monoinfection at week 72 after treatment completion (FUw72),62,50,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,increased,NA,NA,Signature 2,Table S3,4 April 2024,Idiaru angela,Idiaru angela,Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV monoinfection,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|976|200643|171549|815|816;2|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:1074/12/1,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 12,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,healthy control,patients with HCV monoinfection at baseline,patients with HCV monoinfection at baseline,20,50,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,3 April 2024,Idiaru angela,"Idiaru angela,Scholastica",Gut microbiota composition at baseline comparing Healthy controls vs patients with HCV monoinfection,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|186801|3085636|186803|28050;2|976|200643|171549|2005525|375288;2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|877420;2|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:1074/13/1,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 13,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls,patients with HCV/HIV coinfection at baseline,Patients with HIV/HCV coinfection at baseline,20,19,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,4 April 2024,Idiaru angela,Idiaru angela,Gut microbiota composition at baseline comparing Healthy controls vs patients with HCV/HIV coinfection,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2|976|200643|171549|171552|1283313;2|1239|526524|526525|2810280|135858,Complete,Svetlana up
bsdb:1074/13/2,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 13,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls,patients with HCV/HIV coinfection at baseline,Patients with HIV/HCV coinfection at baseline,20,19,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,4 April 2024,Idiaru angela,Idiaru angela,Gut microbiota composition at baseline comparing Healthy controls vs patients with HCV/HIV coinfection,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3085636|186803|572511;2|201174|84998|84999|84107|102106;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|292632;2|1239|186801|3085636|186803|1407607;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:1074/14/1,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 14,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,patients with HCV monoinfection at baseline,patients with HCV/HIV coinfection at baseline,patients with HCV/HIV coinfection at baseline,50,19,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,4 April 2024,Idiaru angela,Idiaru angela,Gut microbiota composition at baseline comparing patients with HCV monoinfection vs patients with HCV/HIV coinfection,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|976|200643|171549|171552|1283313;2|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:1074/14/2,Study 1074,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y , Tangkijvanich P",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 14,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,patients with HCV monoinfection at baseline,patients with HCV/HIV coinfection at baseline,patients with HCV/HIV coinfection at baseline,50,19,Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,4 April 2024,Idiaru angela,Idiaru angela,Gut microbiota composition at baseline comparing patients with HCV monoinfection vs patients with HCV/HIV coinfection,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",2|1239|186801|3085636|186803|572511;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:1075/1/1,Study 1075,"cross-sectional observational, not case-control",33143658,https://doi.org/10.1186/s12866-020-02021-0,NA,"Yuan X, Chen R, Zhang Y, Lin X , Yang X",Gut microbiota: effect of pubertal status,BMC microbiology,2020,"16 s rRNA, Adolescent, Children, Gut microbiota, Puberty",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Puberty,EFO:0001382,Non-pubertal,Pubertal,Male children who have undergone puberty.,42,47,None,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,28 March 2024,Nityasinghal 14,"Nityasinghal 14,Junie",Differential biomarkers associated with genders in pubertal subjects and non-pubertal subjects.,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",2|1224|28216;2|1224|28216|80840,Complete,Svetlana up
bsdb:1075/1/2,Study 1075,"cross-sectional observational, not case-control",33143658,https://doi.org/10.1186/s12866-020-02021-0,NA,"Yuan X, Chen R, Zhang Y, Lin X , Yang X",Gut microbiota: effect of pubertal status,BMC microbiology,2020,"16 s rRNA, Adolescent, Children, Gut microbiota, Puberty",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Puberty,EFO:0001382,Non-pubertal,Pubertal,Male children who have undergone puberty.,42,47,None,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,28 March 2024,Nityasinghal 14,"Nityasinghal 14,Junie",Differential biomarkers associated with genders in pubertal subjects and non-pubertal subjects.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales",2|1224|1236|135625;2|1239|186801|186802|31979;2|1224|1236|135625|712|724;2|1239|526524|526525|2810280|100883;2|1239|186801|186802,Complete,Svetlana up
bsdb:1076/1/1,Study 1076,case-control,35069544,10.3389/fimmu.2021.771136,NA,"Yuan Y, Wang C, Wang G, Guo X, Jiang S, Zuo X, Wang X, Hsu AC, Qi M , Wang F",Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis,Frontiers in immunology,2021,"allergic rhinitis, biomarkers, metabolomics, microbiome, multiomics",Experiment 1,China,Homo sapiens,Inferior nasal concha,UBERON:0005922,Allergic rhinitis,EFO:0005854,healthy controls (HC),Allergic rhinitis (AR),Patients with allergic rhinitis (AR),15,28,NA,16S,34,Ion Torrent,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3. C, D.",30 March 2024,Ayibatari,"Omojokunoluwatomisin,Ayibatari",The distribution of taxa in phylum and genus levels of AR and HC groups. (C) the statistical results of top 10 phyla. (D) the statistical results of top 35 genera.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Cyanobacteriota|s__uncultured cyanobacterium",2|201174;2|1239;2|976|200643;2|1224|28216|80840|80864|80865;2|1239|1737404|1737405|1570339|150022;2|1224|1236|91347|543|570;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279;2|1224|1236|135623|641|662;2|1117|1211,Complete,Svetlana up
bsdb:1076/1/2,Study 1076,case-control,35069544,10.3389/fimmu.2021.771136,NA,"Yuan Y, Wang C, Wang G, Guo X, Jiang S, Zuo X, Wang X, Hsu AC, Qi M , Wang F",Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis,Frontiers in immunology,2021,"allergic rhinitis, biomarkers, metabolomics, microbiome, multiomics",Experiment 1,China,Homo sapiens,Inferior nasal concha,UBERON:0005922,Allergic rhinitis,EFO:0005854,healthy controls (HC),Allergic rhinitis (AR),Patients with allergic rhinitis (AR),15,28,NA,16S,34,Ion Torrent,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3 D.,30 March 2024,Ayibatari,"Ayibatari,Svetlana up",The distribution of taxa in phylum and genus levels of AR and HC groups. (D) the statistical results of top 35 genera.,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,2|1224|28216|80840|2975441|93681,Complete,Svetlana up
bsdb:1077/1/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 1,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3D,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|544448|31969|186332|186333|2086;2|976|200643|171549|815|816;2|1239|186801|186802|186807|51514;2|1239|91061|186826|33958|1578;2|200930|68337|191393|2945020|248038;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1077/1/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 1,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 3D,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|526524|526525|128827|174708;2|201174|1760|85004|31953|1678,Complete,NA
bsdb:1077/2/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3E,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|216572|244127;2|1239|186801|3082720|3030910;2|1239|186801|186802|31979|1485;2|976|200643|171549|2005473;2|1239|186801|186802|216572|119852;2|1239|526524|526525|2810281|191303,Complete,NA
bsdb:1077/2/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 2E,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|31979|49082;2|1239|186801|186802|31979;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|976|200643|171549|171550;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1077/3/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 3,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3B,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family level) in co-housed mice.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|186801|3082720|3030910;2|1239|526524|526525|2810281;2|74201|203494|48461|203557,Complete,NA
bsdb:1077/3/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 3,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3B,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family level) in co-housed mice.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
bsdb:1077/4/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 4,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3I,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|1239|186801|186802|186807|51514;2|1239|91061|186826|33958|1578;2|200930|68337|191393|2945020|248038;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1077/4/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 4,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3I,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|201174|84998|1643822|1643826|447020;2|1239|526524|526525|128827|174708;2|201174|1760|85004|31953|1678;2|976|200643|171549|2005473;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263,Complete,NA
bsdb:1077/5/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 5,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,unchanged,NA,increased,Signature 1,Figure 3J,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,2|1239|186801|3085636|186803|33042,Complete,NA
bsdb:1077/5/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 5,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,unchanged,NA,increased,Signature 2,Figure 3J,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1239|186801|186802|31979;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803,Complete,NA
bsdb:1077/6/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 6,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3G,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family level) in co-housed mice.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|186801|3082720|3030910;2|1239|186801|186802|216572;2|1239|526524|526525|2810281;2|74201|203494|48461|203557,Complete,NA
bsdb:1077/6/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 6,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 3G,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family level) in co-housed mice.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,2|976|200643|171549|171551,Complete,NA
bsdb:1077/7/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 7,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3N,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|1239|186801|186802|186807|51514;2|200930|68337|191393|2945020|248038;2|976|200643|171549|2005525|375288,Complete,NA
bsdb:1077/7/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 7,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3N,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|526524|526525|128827|174708;2|201174|1760|85004|31953|1678;2|976|200643|171549|2005473;2|976|200643|171549|171550;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1077/8/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 8,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3O,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,NA
bsdb:1077/8/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 8,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 3O,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,2|1224|1236,Complete,NA
bsdb:1077/9/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 9,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3L,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots showing differential taxa (family level) in co-housed mice.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|186801|186802|216572;2|1239|526524|526525|2810281;2|74201|203494|48461|203557,Complete,NA
bsdb:1077/10/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 10,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Gut microbiome measurement,EFO:0007874,JAX-CH colon group,JAX-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Jackson Laboratory (JAX-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|1239|186801|3085636|186803|207244;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979;2|1239|526524|526525|128827;2|1239|91061|186826|33958|1578;2|1224|28211|766;2|1239|526524|526525|2810281|191303,Complete,NA
bsdb:1077/10/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 10,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Gut microbiome measurement,EFO:0007874,JAX-CH colon group,JAX-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Jackson Laboratory (JAX-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).,decreased,"k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|544448|31969|186332|186333|2086;2|1239|186801|186802|216572|244127;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186807|51514;2|1239|91061|186826|81852|1350;2|1239|186801|186802;2|1239|186801|3085636|186803;2|200930|68337|191393|2945020|248038;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|41978,Complete,NA
bsdb:1077/11/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 11,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Gut microbiome measurement,EFO:0007874,TAC-CH colon group,TAC-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Taconic Farms (TAC-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales",2|201174|84998|1643822|1643826|447020;2|74201|203494|48461|1647988|239934;2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979;2|1239|526524|526525|128827;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005473;2|976|200643|171549|2005525|375288;2|1224|28211|766,Complete,NA
bsdb:1077/11/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 11,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Gut microbiome measurement,EFO:0007874,TAC-CH colon group,TAC-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Taconic Farms (TAC-CH).,16,16,None,16S,4,Illumina,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,15 April 2024,Aleru Divine,Aleru Divine,LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|186802;2|200930|68337|191393|2945020|248038;2|544448|31969|186332|186333|2086;2|1239|186801|186802|216572;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|41978;2|1239|186801|3085636|186803|33042,Complete,NA
bsdb:1077/12/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 12,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,P1 TAC group,P1 JAX group,Fecal pellet samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,None,16S,4,Illumina,"Kruskall-Wallis,Dunn's test",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|31979|1485;2|201174|84998|1643822|1643826|447020;2|1239|91061|186826|33958|1578,Complete,NA
bsdb:1077/12/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 12,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,P1 TAC group,P1 JAX group,Fecal pellet samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,None,16S,4,Illumina,"Kruskall-Wallis,Dunn's test",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 6 and S7,15 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|1239|186801|186802|31979|49082|49118;2|200930|68337|191393|2945020|248038;2|1239|186801|186802|216572,Complete,NA
bsdb:1077/13/NA,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 13,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,P1 JAX group,F1 mJAX group,Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,4,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1077/14/NA,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 14,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,P1 TAC group,F1 mTAC group,Fecal pellet samples from the maternal F1-generation of Taconic farms (mTAC) mice.,4,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1077/15/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 15,Canada,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,F1 mTAC group,F1 mJAX group,Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in F1 mJAX and mTAC mice,increased,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,NA
bsdb:1077/16/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 16,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,P1 TAC group,P1 JAX group,Colon samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|31979|1485;2|544448|31969|186332|186333|2086;2|201174|1760|85004|31953|1678;2|1224|1236|2887326|468|469;2|976|200643|171549|171550;2|976|200643|171549|2005473,Complete,NA
bsdb:1077/16/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 16,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,P1 TAC group,P1 JAX group,Colon samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 6 and S7,15 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|1239|186801|186802|31979|49082|49118;2|200930|68337|191393|2945020|248038;2|1239|186801|186802|186807|51514;2|1239|186801|3085636|186803|189330,Complete,NA
bsdb:1077/17/NA,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 17,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,P1 JAX group,F1 mJAX group,Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,4,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1077/18/NA,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 18,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,P1 TAC group,F1 mTAC group,Colon samples from the maternal F1-generation of Taconic farms (mTAC) mice.,4,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1077/19/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 19,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,F1 mTAC group,F1 mJAX group,Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|74201|203494|48461|1647988|239934;2|976|200643|171549|2005473,Complete,NA
bsdb:1077/19/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 19,Canada,Mus musculus,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,F1 mTAC group,F1 mJAX group,Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 6 and S7,15 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium",2|1239|186801|186802|31979|49082|49118;2|1239|186801|186802|186807|51514,Complete,NA
bsdb:1077/20/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 20,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,P1 TAC group,P1 JAX group,Ileum samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,16 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|31979|1485;2|201174|84998|1643822|1643826|447020;2|544448|31969|186332|186333|2086,Complete,NA
bsdb:1077/20/2,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 20,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,P1 TAC group,P1 JAX group,Ileum samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 6 and S7,16 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacteria|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium",2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|1239|186801|186802|31979|49082|49118;2|200930|68337|191393|2945020|248038;2|1239|186801|186802|186807|51514,Complete,NA
bsdb:1077/21/NA,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 21,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,P1 JAX group,F1 mJAX group,Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,4,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1077/22/NA,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 22,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,P1 TAC group,F1 mTAC group,Ileum samples from the maternal F1-generation of Taconic farms (mTAC) mice.,4,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1077/23/1,Study 1077,"cross-sectional observational, not case-control",31067473,https://doi.org/10.1016/j.celrep.2019.04.023,https://pubmed.ncbi.nlm.nih.gov/31067473/,"Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE , Philpott DJ",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 23,Canada,Mus musculus,Ileum,UBERON:0002116,Gut microbiome measurement,EFO:0007874,F1 mTAC group,F1 mJAX group,Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,None,16S,4,Illumina,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,16 April 2024,Aleru Divine,Aleru Divine,Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.,increased,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,NA
bsdb:1078/1/1,Study 1078,laboratory experiment,NA,10.1016/j.jff.2024.106106,https://www.sciencedirect.com/science/article/pii/S1756464624001087#s0125,"Haoyu Wang, Kaiwei Chen, Liang Xiao, Ningning He, Shangyong Li, Shengnan Yu, Xiaoqian Lin, Yuanqiang Zou, Zhinan Wu",Stachyose ameliorates obesity-related metabolic syndrome via improving intestinal barrier function and remodeling gut microbiota,Journal of Functional Foods,2024,"Butyrate-producing strains, Stachyose, gut microbiota, intestinal barrier, metabolic syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High-Fat Diet fed Mice (HFD),Stachyose-treated High-Fat Diet fed Mice (STA),"Male C57BL/6J mice (18–20g, 6 weeks old) which were fed a High-Fat Diet (D12492-HFD diet, #XTHF60-1) with 60% of energy from fat, for 12 weeks and treatment with stachyose in the last 8 weeks (200 mg/ kg/day).",7,7,None,WMS,NA,DNBSEQ-T7,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,2 May 2024,Joan Chuks,Joan Chuks,Bacterial taxa identified by Linear discriminant analysis effect size (LEfSe) as differentially abundant in mice fed with Stachyose-treated High-Fat Diet compared to mice fed with High-Fat Diet.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum|s__Allobaculum mucilyticum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Thermophilibacter|s__Thermophilibacter immobilis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella catena,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parafannyhessea|s__Parafannyhessea umbonata",2|201174|84998|84999|84107|102106|147206;2|1239|526524|526525|128827|174708|2834459;2|201174|84998|84999|1643824|2847307|2779519;2|201174|84998|84999|1643824|2082587|2003188;2|201174|84998|84999|1643824|2847312|604330,Complete,Svetlana up
bsdb:1078/1/2,Study 1078,laboratory experiment,NA,10.1016/j.jff.2024.106106,https://www.sciencedirect.com/science/article/pii/S1756464624001087#s0125,"Haoyu Wang, Kaiwei Chen, Liang Xiao, Ningning He, Shangyong Li, Shengnan Yu, Xiaoqian Lin, Yuanqiang Zou, Zhinan Wu",Stachyose ameliorates obesity-related metabolic syndrome via improving intestinal barrier function and remodeling gut microbiota,Journal of Functional Foods,2024,"Butyrate-producing strains, Stachyose, gut microbiota, intestinal barrier, metabolic syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High-Fat Diet fed Mice (HFD),Stachyose-treated High-Fat Diet fed Mice (STA),"Male C57BL/6J mice (18–20g, 6 weeks old) which were fed a High-Fat Diet (D12492-HFD diet, #XTHF60-1) with 60% of energy from fat, for 12 weeks and treatment with stachyose in the last 8 weeks (200 mg/ kg/day).",7,7,None,WMS,NA,DNBSEQ-T7,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,2 May 2024,Joan Chuks,Joan Chuks,Bacterial taxa identified by Linear discriminant analysis effect size (LEfSe) as differentially abundant in mice fed with Stachyose-treated High-Fat Diet compared to mice fed with High-Fat Diet.,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,2|1224|1236|91347|543|561|1499973,Complete,Svetlana up
bsdb:1079/1/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 1,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 2,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella.

This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).",NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Additional file 1, page 6",16 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.,increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales",2|1239|91061;2|1239|91061|186826;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|1385,Complete,NA
bsdb:1079/1/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 1,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 2,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella.

This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).",NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,"Additional file 1, page 6",25 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1079/2/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 2,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella.

This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, page 6",16 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|201174|84998|84999|1643824|1380;2|976|200643|171549;2|976|200643;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|32257;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1239|186801|3082720|3030910|86331;2|1239|909932;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|909929;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|91061|186826|186828;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977,Complete,NA
bsdb:1079/2/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 2,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella.

This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Additional file 1, page 6",25 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1079/3/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 3,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 2,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, page 6",16 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.	  ,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174;2|201174|84998|84999|1643824|1380;2|976|200643|171549;2|976|200643;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|32257;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1239|186801|3082720|3030910|86331;2|1239|909932;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|91061|186826|186828;2|1239|186801|3085636|186803;2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,NA
bsdb:1079/3/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 3,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 2,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Additional file 1, page 6",16 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales",2|1239|91061;2|1239|91061|186826;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|1385,Complete,NA
bsdb:1079/4/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 4,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 2,The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Additional file 1, page 7",25 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis. ,increased,k__Bacteria|p__Bacillota|c__Bacilli,2|1239|91061,Complete,NA
bsdb:1079/4/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 4,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 2,The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,"Additional file 1, page 7",29 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|201174|1760|2037;2|201174;2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743;2|1224|1236;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|201174|1760|85006|1268;2|1224|1236|135625|712;2|1224|1236|135625;2|1224;2759|33090|35493|3398|72025|3803|3814|508215;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|186828|117563,Complete,NA
bsdb:1079/5/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 5,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, page 7",29 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549;2|976|200643;2|1239|909932;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|838|28137;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1079/5/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 5,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Additional file 1, page 7",29 May 2024,Fiddyhamma,"Fiddyhamma,Victoria","The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.
		  ",decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|201174|1760|2037;2|201174;2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743;2|1224|1236;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|201174|1760|85006|1268;2|1224|1236|135625|712;2|1224|1236|135625;2|1224;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|186828|117563,Complete,NA
bsdb:1079/6/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 6,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 2,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, page 7",29 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549;2|976|200643;2|1239|909932;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|838|28137;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1079/6/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 6,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 2,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Additional file 1, page 7",29 May 2024,Fiddyhamma,"Fiddyhamma,Victoria",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.,decreased,k__Bacteria|p__Bacillota|c__Bacilli,2|1239|91061,Complete,NA
bsdb:1079/7/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 7,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease),This group consists of patients with Gastroesophageal reflux disease.,59,29,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 4",16 August 2024,Fiddyhamma,"Fiddyhamma,Victoria",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Acetoanaerobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",2|1239|186801|3082720|3118655|186831;2|1239|186801|3082720|3118655|44259;2|976|117743|200644|49546;2|29547|3031852|213849|72294|194,Complete,NA
bsdb:1079/7/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 7,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease),This group consists of patients with Gastroesophageal reflux disease.,59,29,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 4",17 August 2024,Victoria,"Victoria,Fiddyhamma",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|91061|186826|33958|1578;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|543|1940338,Complete,NA
bsdb:1079/8/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 8,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal,Gastroesophageal reflux disease GERD(within subjects classified as PPI NO),This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Acetoanaerobium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota",2759|33090|35493|3398|72025|3803|3814|508215;2|976|200643|171549|171552|838;2|976|117743|200644|49546;2|1239|91061|186826|1300|1301;2|1239|186801|3082720|3118655|44259;2|1239|186801|3082720|3118655|186831;2|1239|186801|186802;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|32067;2|1224|28216|206351;2|1224|28216|206351|481;2|29547|3031852|213849|72294|194;2|1224|1236|135615|868|2717;2|1224|1236|135625|712;2|1224,Complete,NA
bsdb:1079/8/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 8,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal,Gastroesophageal reflux disease GERD(within subjects classified as PPI NO),This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|201174|84998|1643822|1643826|84108;2|976|200643|171549|171552|838;2|1239|91061|186826|33958|1578;2|976|200643|171549;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|265975;2|1239|909932|909929|1843491|82202;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465;2|1224|1236|91347|543;2|1224|1236|91347|543|1940338;2|1224|1236|91347,Complete,NA
bsdb:1079/9/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 9,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Normal,Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,59,12,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|32066|203490|203491|1129771|32067;2|976|117743|200644|49546|1016,Complete,NA
bsdb:1079/10/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 10,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Gastroesophageal reflux disease (GERD),Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,29,12,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|1224|28216|80840;2|976|117743|200644|49546|1016,Complete,NA
bsdb:1079/10/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 10,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Gastroesophageal reflux disease (GERD),Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,29,12,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,2|976|200643|171549|171552|1283313,Complete,NA
bsdb:1079/11/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 11,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Gastroesophageal reflux disease (GERD),Glandular mucosa (GM),This group consists of patients with Glandular mucosa,29,14,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans",2|1224|1236|91347|543;2|1224|1236|91347;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1200657,Complete,NA
bsdb:1079/11/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 11,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Gastroesophageal reflux disease (GERD),Glandular mucosa (GM),This group consists of patients with Glandular mucosa,29,14,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Acetoanaerobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552|838;2|1239|186801|3082720|3118655|186831;2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,NA
bsdb:1079/12/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 12,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Normal,Glandular mucosa (GM),This group consists of patients with Glandular mucosa,59,14,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,NA
bsdb:1079/12/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 12,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Normal,Glandular mucosa (GM),This group consists of patients with Glandular mucosa,59,14,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 4",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,NA
bsdb:1079/13/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 13,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease),This group consists of patients with Gastroesophageal reflux disease.,59,29,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 5",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|189723;2|32066|203490;2|32066|203490|203491;2|1224|28216|206351|481|482|496;2|1224|28216|206351|481|482|487;2|1224|1236|135625|712|724|729;2|203691|203692|136|2845253|157|58231,Complete,NA
bsdb:1079/14/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 14,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO,This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 5",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,2|1224|28216|206351|481|482|487,Complete,NA
bsdb:1079/14/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 14,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO,This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 5",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens",2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838|60133,Complete,NA
bsdb:1079/15/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 15,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Normal,Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,59,12,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 5",18 August 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780",2|1239|91061|1385|539738|1378;2|1239|91061|186826|1300|1301|1305;2|1239|909932|1843489|31977|29465|671229,Complete,NA
bsdb:1079/16/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 16,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Normal,Glandular mucosa (GM),This group consists of patients with Glandular mucosa,59,14,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 5",24 September 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp. oral taxon 041,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multiformis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|46125;2|1239|91061|186826|186827;2|1239|909932|1843489|31977|156454;2|1239|909932|1843489|31977|156454|156456;2|1224|28216|80840|119060|32008;2|28221;2|200940|3024418|213118;2|200940|3031451|3024411|213121;2|200940|3031451|3024411|213121|893;2|200940|3031451|3024411|213121|893|712258;2|1239|526524|526525|2810280|1279384;2|1239|526524|526525|2810280|1279384|31973;2|32066|203490|203491|203492|848|859;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293|209|210;2|29547|3031852|213849|72293;2|976|200643|171549|171552|2974257|28134;2|1224|28216|206351|481|482|483;2|1224|28216|206351|481|482|484;2|976|200643|171549|171552|838|282402;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1302;2|203691|203692|136|2845253|157|53419;2|1224|28216|80840|119060|32008,Complete,NA
bsdb:1079/17/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 17,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,GERD(Gastroesophageal reflux disease),Glandular mucosa (GM),This group consists of patients with Glandular mucosa,29,14,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 5",24 September 2024,Fiddyhamma,Fiddyhamma,The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|46125;2|1239|91061|186826|186827;2|1224|1236|135625|712|416916|732;2|1239|526524|526525|2810280|1279384;2|1239|526524|526525|2810280|1279384|31973;2|32066|203490|203491|203492|848|859;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293|209|210;2|29547|3031852|213849|72293;2|976|200643|171549|171552|2974257|28134;2|1224|28216|206351|481|32257;2|1224|28216|206351|481|482|483;2|976|200643|171549|171551|836|837;2|1239|909932|909929|1843491|970|135083;2|1239|91061|186826|1300|1301|1302;2|1224|28216|206351|481|32257,Complete,NA
bsdb:1079/18/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 18,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 6",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|117743|200644|49546;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1079/18/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 18,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 6",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|1239|91061|186826|33958|1578;2|1224|1236|91347|543;2|1224|1236|91347,Complete,NA
bsdb:1079/19/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 19,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 6",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacillota",2|201174|1760|85007|1653|1716;2|201174|1760|2037;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|3118655|44259;2|1239|526524;2|1239|526524|526525;2|1239|526524|526525|128827;2|1239|526524|526525|128827|123375;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771;2|1224|28216|80840|80864|28219;2|1224|28216|206351|481|482;2|1224|1236|135625|712;2|1239,Complete,NA
bsdb:1079/19/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 19,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 6",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",2|976|200643|171549|171552|838;2|1224|1236;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|135625|712,Complete,NA
bsdb:1079/20/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 20,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 3),GERD(Gastroesophageal reflux disease) (Cluster 3),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 6",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Flavobacteriia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacillota",2|976|200643|171549|171552|838;2|976|117743;2|976|117743|200644;2|976|117743|200644|49546;2|976|117743|200644|49546|1016;2|976|117743|200644|49546;2|1224|1236|72274|135621;2|1239,Complete,NA
bsdb:1079/20/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 20,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 3),GERD(Gastroesophageal reflux disease) (Cluster 3),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 6",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,",2|1239|186801|3082720|186804;,Complete,NA
bsdb:1079/21/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 21,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 7",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|171552|1283313;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730,Complete,NA
bsdb:1079/21/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 21,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 7",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,2|976|200643|171549|171552|1283313,Complete,NA
bsdb:1079/22/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 22,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 7",24 September 2024,Fiddyhamma,Fiddyhamma,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|201174|1760|2037;2|201174;2;2|1239|186801|186802|543314;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771|32067|157687;2|32066|203490|203491|1129771;2|201174|1760|85006|1268;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28133;2|201174|1760|85006|1268|32207|43675;2|976|200643|171549|171552|2974251|28135;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1343;2|1239|186801|186802|543314|56774;2|32066|203490|203491|1129771|32067;2759|33090|35493|3398|72025|3803|3814|508215,Complete,NA
bsdb:1079/22/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 22,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 7",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,2|1224|1236|135625|712|724|735,Complete,NA
bsdb:1079/23/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 23,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 3),GERD(Gastroesophageal reflux disease) (Cluster 3),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, page 7",24 September 2024,Fiddyhamma,Fiddyhamma,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Pasteuriaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales",2|1239|91061|1385;2|1224|1236;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482;2|1224|28216|206351|481|482|496;2|1224|28216|206351|481|482|487;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|1236|135625;2|1239|91061|1385|538998;2|1224;2|203691|203692|136|2845253|157|58231;2|1239|91061|1385,Complete,NA
bsdb:1079/23/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 23,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 3),GERD(Gastroesophageal reflux disease) (Cluster 3),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, page 7",24 September 2024,NA,NA,Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula",2|976|200643|171549|171552;2|976|200643|171549;2|976|200643;2|201174|84998|84999|1643824|1380;2|201174|84998|84999|84107;2|976|200643|171549|171552|838;2|201174|84998|84999;2|201174|84998|84999|1643824|2767353|1382,Complete,NA
bsdb:1079/24/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 24,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with normal esophagus on PPI-No,Subjects with normal esophagus on PPI-Yes,This group consists of patients with normal esophagus,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional figure 3 A,24 September 2024,NA,NA,Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",2|976|200643|171549|171552|838|52227;2|1239|91061|186826|1300|1301|1343,Complete,NA
bsdb:1079/24/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 24,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with normal esophagus on PPI-No,Subjects with normal esophagus on PPI-Yes,This group consists of patients with normal esophagus,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional figure 3A,24 September 2024,NA,NA,Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae",2|1239|186801|3082720|186804|1257;2|1224|1236|135625|712|724|727;2|976|200643|171549|171552|2974251|228604,Complete,NA
bsdb:1079/25/1,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 25,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with GERD on PPI-No,Subjects with GERD on PPI-Yes,This group consists of patients with gastroesophageal reflux disease,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional figure 3A,24 September 2024,NA,NA,Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Bacillota|c__Negativicutes,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654|55565;2|201174|1760|85006|1268|32207;2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|2974251|228604;2|1239|91061|1385|539738|1378|29391;2|1239|91061|186826|1300|1301|76860;2|1239|186801|3085636|186803;2|1239|186801|3085636|186803|1213720;2|1239|186801|3085636|186803|1213720|796942;2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1079/25/2,Study 1079,"cross-sectional observational, not case-control",30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR , Kaakoush NO","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 25,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with GERD on PPI-No,Subjects with GERD on PPI-Yes,This group consists of patients with gastroesophageal reflux disease,NA,NA,2 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional figure 3A,24 September 2024,NA,NA,Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,decreased,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,2|1224|28216|206351|481|482|487,Complete,NA
bsdb:1080/1/1,Study 1080,"cross-sectional observational, not case-control",31637220,10.3389/fcimb.2019.00339,NA,"Kolbe AR, Castro-Nallar E, Preciado D , Pérez-Losada M",Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses,Frontiers in cellular and infection microbiology,2019,"amplicon sequence variants, asthma, bronchiolitis, middle ear microbiome, otitis media",Experiment 1,United States of America,Homo sapiens,Middle ear,UBERON:0001756,Lower respiratory tract disease,EFO:0009433,Chronic Otitis Media With Effusion (COME) without asthma or bronchiolitis,Chronic Otitis Media With Effusion (COME) with asthma or bronchiolitis,"Children from 3 to 176 months of age, with Chronic Otitis Media With Effusion (COME) with a history of lower airway disease (i.e., asthma or bronchiolitis),  defined by a history of pulmonary physician-diagnosed asthma; documented chronic wheezing being treated with a daily respiratory inhaler; or PCR (+) for rhinovirus bronchiolitis diagnosis.",37,13,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5,6 May 2024,Scholastica,Scholastica,"Differentially abundant genera/species (p-adjusted < 0.05) in middle ear fluid (MEF) of patients with lower airway disease diagnosis (i.e., asthma or bronchiolitis) compared to those without.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|1224|1236|135625|712|724;2|1239|91061|1385|90964|1279;2|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:1080/1/2,Study 1080,"cross-sectional observational, not case-control",31637220,10.3389/fcimb.2019.00339,NA,"Kolbe AR, Castro-Nallar E, Preciado D , Pérez-Losada M",Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses,Frontiers in cellular and infection microbiology,2019,"amplicon sequence variants, asthma, bronchiolitis, middle ear microbiome, otitis media",Experiment 1,United States of America,Homo sapiens,Middle ear,UBERON:0001756,Lower respiratory tract disease,EFO:0009433,Chronic Otitis Media With Effusion (COME) without asthma or bronchiolitis,Chronic Otitis Media With Effusion (COME) with asthma or bronchiolitis,"Children from 3 to 176 months of age, with Chronic Otitis Media With Effusion (COME) with a history of lower airway disease (i.e., asthma or bronchiolitis),  defined by a history of pulmonary physician-diagnosed asthma; documented chronic wheezing being treated with a daily respiratory inhaler; or PCR (+) for rhinovirus bronchiolitis diagnosis.",37,13,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 5,6 May 2024,Scholastica,Scholastica,"Differentially abundant genera/species (p-adjusted < 0.05) in middle ear fluid (MEF) of patients with lower airway disease diagnosis (i.e., asthma or bronchiolitis) compared to those without.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus|s__Alloiococcus otitis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium otitidis",2|1239|91061|186826|186828|1651|1652;2|201174|1760|85007|1653|1716|29321,Complete,Svetlana up
bsdb:1081/1/1,Study 1081,"cross-sectional observational, not case-control",35410125,10.1186/s12866-022-02502-4,https://link.springer.com/article/10.1186/s12866-022-02502-4,"Showering A, Martinez J, Benavente ED, Gezan SA, Jones RT, Oke C, Tytheridge S, Pretorius E, Scott D, Allen RL, D'Alessandro U, Lindsay SW, Armour JAL, Pickett J , Logan JG",Skin microbiome alters attractiveness to Anopheles mosquitoes,BMC microbiology,2022,"Anopheles coluzzii, Body odour, Diversity, Human attractiveness, Malaria, Mosquitoes, Repellents, Skin microbiome",Experiment 1,United Kingdom,Homo sapiens,Skin of sole of pes,UBERON:0013778,Taxonomic microbiome measurement,EFO:0007883,Poorly-attractive group,Highly-attractive group,"Post-menopausal females, aged between 50 and 90 years, whose skin/body odour were highly attractive to Anopheles mosquitoes.",28,27,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,18 May 2024,Aleru Divine,Aleru Divine,The differential abundance of bacterial genera between attractiveness groups tested using DESEQ2,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Methylococcales|f__Methylococcaceae|g__Methylocaldum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|1236|135618|403|73778;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:1081/1/2,Study 1081,"cross-sectional observational, not case-control",35410125,10.1186/s12866-022-02502-4,https://link.springer.com/article/10.1186/s12866-022-02502-4,"Showering A, Martinez J, Benavente ED, Gezan SA, Jones RT, Oke C, Tytheridge S, Pretorius E, Scott D, Allen RL, D'Alessandro U, Lindsay SW, Armour JAL, Pickett J , Logan JG",Skin microbiome alters attractiveness to Anopheles mosquitoes,BMC microbiology,2022,"Anopheles coluzzii, Body odour, Diversity, Human attractiveness, Malaria, Mosquitoes, Repellents, Skin microbiome",Experiment 1,United Kingdom,Homo sapiens,Skin of sole of pes,UBERON:0013778,Taxonomic microbiome measurement,EFO:0007883,Poorly-attractive group,Highly-attractive group,"Post-menopausal females, aged between 50 and 90 years, whose skin/body odour were highly attractive to Anopheles mosquitoes.",28,27,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,18 May 2024,Aleru Divine,Aleru Divine,The differential abundance of bacterial genera between attractiveness groups tested using DESEQ2,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae",2|1224|28211|204458|76892|41275;2|201174|1760|85007|1653|1716;2|1224|28216|80840|80864|665874;2|201174|1760|2037;2|201174|1760|85006|85021,Complete,Svetlana up
bsdb:1082/1/1,Study 1082,laboratory experiment,35787106,10.1080/19490976.2022.2085961,NA,"Rodriguez Paris V, Wong XYD, Solon-Biet SM, Edwards MC, Aflatounian A, Gilchrist RB, Simpson SJ, Handelsman DJ, Kaakoush NO , Walters KA",The interplay between PCOS pathology and diet on gut microbiota in a mouse model,Gut microbes,2022,"Microbiome, PCOS, animal model, diet, hyperandrogenism, polycystic ovary syndrome",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Controls,polycystic ovary syndrome (PCOS)-like mice,"Dihydrotestosterone (DHT)-induced PCOS- like mice exposed to diets that varied in protein (P), carbohydrate (C) and fat (F) content.",NA,NA,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3b,14 May 2024,Scholastica,Scholastica,Abundant OTU’s identified as being significantly different in control compared to polycystic ovary syndrome (PCOS)-like mice,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802;2|1224;2|1239|526524|526525|128827,Complete,Svetlana up
bsdb:1082/1/2,Study 1082,laboratory experiment,35787106,10.1080/19490976.2022.2085961,NA,"Rodriguez Paris V, Wong XYD, Solon-Biet SM, Edwards MC, Aflatounian A, Gilchrist RB, Simpson SJ, Handelsman DJ, Kaakoush NO , Walters KA",The interplay between PCOS pathology and diet on gut microbiota in a mouse model,Gut microbes,2022,"Microbiome, PCOS, animal model, diet, hyperandrogenism, polycystic ovary syndrome",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Controls,polycystic ovary syndrome (PCOS)-like mice,"Dihydrotestosterone (DHT)-induced PCOS- like mice exposed to diets that varied in protein (P), carbohydrate (C) and fat (F) content.",NA,NA,None,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3b,14 May 2024,Scholastica,Scholastica,Abundant OTU’s identified as being significantly different in control compared to polycystic ovary syndrome (PCOS)-like mice,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae|g__Aestuariispira",2|976|200643|171549|171551;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|1224|28211|204441|597359|1647175,Complete,Svetlana up
bsdb:1083/1/1,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 1,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B25.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 6a,21 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Actinomycetota|c__Acidimicrobiia,k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae,k__Bacteria|p__Chloroflexota|c__Anaerolineae,k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales,k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae,k__Bacteria|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae,k__Bacteria|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales,k__Bacteria|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Bacteria|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Actinomycetota|c__Thermoleophilia",2|201174|84992|84993;2|201174|84992;2|200795|292625|292629|292628;2|200795|292625;2|200795|292625|292629;2|1224|28216|80840|119060;2|1224|28211|204458|76892;2|1224|28211|204458;2|976|1853228|1853229|563835;2|976|768503|768507|89373;2|976|768503|768507;2|201174|1497346|1154584;2|142182|219685|219686|219687;2|142182|219685|219686;2|1224|28211|356|45401;2|1224|28211|356;2|1224|28216|32003|32011;2|2818505|32015|29;2|1224|28211|356|41294;2|1224|28216|32003|206379;2|1224|28216|32003;2|40117|203693|189778|189779|1234;2|40117|203693|189778;2|1224|28211|356|69277;2|1224|1236|72274|135621;2|1224|28211|356|82115;2|1224|28211|204441|41295;2|1224|28211|204441;2|976|117747|200666|84566;2|201174|1497346,Complete,NA
bsdb:1083/1/2,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 1,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B25.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 6a,22 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacillota|c__Negativicutes",2|976|200643|171549|171552;2|976|200643|171549;2|976|200643|171549;2|976|200643;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977;2|1239|909932|909929;2|1239|909932,Complete,NA
bsdb:1083/2/1,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 2,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2)),B-Group (B45.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 1,Figure 6b,22 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacteria|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales,k__Bacteria|p__Actinomycetota|c__Thermoleophilia",2|201174|1497346|1154584;2|201174|1497346,Complete,NA
bsdb:1083/2/2,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 2,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2)),B-Group (B45.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 2,Figure 6b,22 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|s__unidentified spirochete",2|1239|91061;2|28221;2|1224|1236|135619|28256;2|1239|91061|186826|33958;2|1239|91061|186826;2|1224|1236|135619;2|1224|1236|135622|267890;2|203691|203692|136|137;2|203691|203692|136;2|1239|909932|1843489|31977;2|203691|203692|136|56767,Complete,NA
bsdb:1083/3/1,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 3,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B75.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 1,Figure 6c,24 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes",2|1239|909932|1843488|909930;2|1224|28211|204457|41297;2|1224|1236|135624|83763;2|1224|1236|135624;2|1224|1236|91347|543;2|1224|1236|91347;2|544448|31969,Complete,NA
bsdb:1083/3/2,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 3,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B75.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 2,Figure 6c,24 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae,2|1239|91061|1385|186818,Complete,NA
bsdb:1083/4/1,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 4,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B25.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6d,24 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacteria|p__Lentisphaerota|c__Lentisphaeria,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales",2|256845|1313211;2|203691|203692|136|137;2|203691|203692|136;2|256845|1313211|278082|255528;2|256845|1313211|278082,Complete,NA
bsdb:1083/4/2,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 4,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B25.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6d,24 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|216572,Complete,NA
bsdb:1083/5/1,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 5,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B45.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,Figure 6e,27 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Mycoplasmatota|c__Mollicutes",2|1239|186801|3085636|186803;2|1239|909932|1843488|909930;2|1224|28216|80840|506;2|1224|28216|80840;2|1224|1236|135624|83763;2|1224|1236|135624;2|544448|31969,Complete,NA
bsdb:1083/5/2,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 5,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B45.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,Figure 6e,27 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae,k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales,k__Bacteria|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales",2|200795|292625|292629|292628;2|200795|292625|292629;2|200795|292625|292629|292628|233189;2|1239|91061|186826|33958;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|91061;2|1239|186801|3082720|186804;2|1224|28216|206351|481;2|1224|28216|206351,Complete,NA
bsdb:1083/6/1,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 6,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B75.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 1,Figure 6f,27 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",2|1239|909932|1843488|909930;2|1224|1236|135624;2|204428|204429|51291|809;2|204428|204429|51291;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1224|1236|135619|28256;2|1239|186801|3085636|186803;2|1224|1236|135619;2|203691|203692|136|137;2|203691|203692|136;2|1224|1236|135624|83763,Complete,NA
bsdb:1083/6/2,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 6,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B75.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 2,Figure 6f,27 May 2024,Victoria,Victoria,The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",2|1224|28216|206351|481;2|1224|28216|206351;2|1224|1236|135625|712;2|1224|1236|135625,Complete,NA
bsdb:1083/7/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 7,China,Capra hircus,Jejunum,UBERON:0002115,Diet,EFO:0002755,B-Group (B15.2),R-Group (R15.2),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Jejunum) were obtained on the 15th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,increased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1083/8/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 8,China,Capra hircus,Jejunum,UBERON:0002115,Diet,EFO:0002755,B-Group (B25.2),R-Group (R25.2),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Jejunum) were obtained on the 25th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1083/9/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 9,China,Capra hircus,Jejunum,UBERON:0002115,Diet,EFO:0002755,B-Group (B45.2),R-Group (R45.2),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Jejunum) were obtained on the 45th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1083/10/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 10,China,Capra hircus,Jejunum,UBERON:0002115,Diet,EFO:0002755,B-Group (B75.2),R-Group (R75.2),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Jejunum) were obtained on the 75th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1083/11/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 11,China,Capra hircus,Caecum,UBERON:0001153,Diet,EFO:0002755,B-Group (B15.4),R-Group (R15.4),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Cecum) were obtained on the 15th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1083/12/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 12,China,Capra hircus,Caecum,UBERON:0001153,Diet,EFO:0002755,B-Group (B25.4),R-Group (R25.4),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Cecum) were obtained on the 25th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1083/13/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 13,China,Capra hircus,Caecum,UBERON:0001153,Diet,EFO:0002755,B-Group (B45.4),R-Group (R45.4),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Cecum) were obtained on the 45th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1083/14/NA,Study 1083,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z , Li Y",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 14,China,Capra hircus,Caecum,UBERON:0001153,Diet,EFO:0002755,B-Group (B75.4),R-Group (R75.4),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Cecum) were obtained on the 75th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1085/1/1,Study 1085,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2357176,"Samarra A, Cabrera-Rubio R, Martínez-Costa C , Collado MC",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the seven (7) day-old infants.,57,42,NA,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,9 June 2024,Aleru Divine,Aleru Divine,"Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85004|31953|1678;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:1085/1/2,Study 1085,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2357176,"Samarra A, Cabrera-Rubio R, Martínez-Costa C , Collado MC",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the seven (7) day-old infants.,57,42,NA,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,9 June 2024,Aleru Divine,Aleru Divine,"Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|91061|1385|90964|1279;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:1085/2/1,Study 1085,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2357176,"Samarra A, Cabrera-Rubio R, Martínez-Costa C , Collado MC",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the one (1) month-old infants.,58,43,NA,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and 3,9 June 2024,Aleru Divine,Aleru Divine,"Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|201174|1760|85004|31953|1678|41200,Complete,Svetlana up
bsdb:1085/2/2,Study 1085,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2357176,"Samarra A, Cabrera-Rubio R, Martínez-Costa C , Collado MC",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the one (1) month-old infants.,58,43,NA,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and 3,9 June 2024,Aleru Divine,Aleru Divine,"Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678|1689;2|1239|186801|186802|31979|1485;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1224|1236|91347|543|570;2|976|200643|171549|2005525|375288|1869337,Complete,Svetlana up
bsdb:1086/1/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 1,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control (CTRL-S),Phenylketonuria (PKU-S),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,114,109,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,increased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Patients.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|29547|3031852|213849|72294|194;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1086/1/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 1,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control (CTRL-S),Phenylketonuria (PKU-S),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,114,109,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,increased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Patients.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|201174|1760|2037|2049|1654;2|201174|1760|85009|31957|2801844;2|1224|1236|135615|868|2717;2|1239|186801|3085636|186803|43996;2|508458|649775|649776|3029087|1434006;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186807|2740;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|1213720,Complete,NA
bsdb:1086/2/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 2,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Controls (CTRL-SP),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,113,96,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival Patients.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium",2|201174|1760|2037|2049|1654;2|508458|649775|649776|3029087|1434006,Complete,NA
bsdb:1086/2/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 2,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Controls (CTRL-SP),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,113,96,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival Patients.,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1224|1236|135625|712|416916;2|976|117743|200644|49546|1016;2|1239|91061|1385|539738|1378;2|32066|203490|203491|1129771|32067;2|1239|186801|3082720|186804|1257,Complete,NA
bsdb:1086/3/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 3,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Adults (CTRL-S),Phenylketonuria (PKU-S),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,52,50,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,decreased,NA,NA,NA,decreased,Signature 1,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Adult Patients.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella",2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1224|28216|206351|481|32257,Complete,NA
bsdb:1086/3/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 3,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Adults (CTRL-S),Phenylketonuria (PKU-S),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,52,50,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,decreased,NA,NA,NA,decreased,Signature 2,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Adult Patients.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|201174|1760|2037|2049|1654;2|201174|1760|85009|31957|2801844;2|1239|186801|3085636|186803|43996;2|508458|649775|649776|3029087|1434006;2|1239|186801|186802|186807|2740;2|1239|186801|3085636|186803|1213720,Complete,NA
bsdb:1086/4/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 4,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Adults (CTRL-SP),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,52,45,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival plaque Adults Patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella",2|201174|1760|2037|2049|1654;2|508458|649775|649776|3029087|1434006;2|1224|28216|206351|481|32257,Complete,NA
bsdb:1086/4/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 4,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Adults (CTRL-SP),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,52,45,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival plaque Adults Patients,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|1239|91061|1385|539738|1378;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|1213720,Complete,NA
bsdb:1086/5/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 5,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Children (CTRL-S),Phenylketonuria (PKU-S),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,62,59,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) Children and Control Children Saliva  Patients,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803|265975,Complete,NA
bsdb:1086/5/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 5,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Children (CTRL-S),Phenylketonuria (PKU-S),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,62,59,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) Children and Control Children Saliva  Patients,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|201174|1760|2037|2049|1654;2|201174|1760|85009|31957|2801844;2|508458|649775|649776|3029087|1434006;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186807|2740;2|1239|186801|3085636|186803|1213720;2|976|200643|171549|2005525|195950,Complete,NA
bsdb:1086/6/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 6,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Children (CTRL-SP),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,61,51,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria (PKU) Children and Control Children Subgingival plague Patients,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|508458|649775|649776|3029087|1434006;2|1224|28216|206351|481|32257;2|201174|84998|84999|1643824|133925;2|1239|186801|3085636|186803|265975;2|1239|909932|909929|1843491|970;2|1239|186801|3085636|186803|1213720,Complete,NA
bsdb:1086/6/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 6,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Children (CTRL-SP),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,61,51,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Phenylketonuria PKU Children and Control Children Subgingival plague  Patients,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1224|1236|135625|712|416916;2|976|117743|200644|49546|1016;2|1239|91061|1385|539738|1378;2|32066|203490|203491|1129771|32067;2|1239|186801|3082720|186804|1257,Complete,NA
bsdb:1086/7/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 7,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Ch-CTRL-rel (Healthy siblings of PKU patients),Ch-CTRL-unrel (unrelated control children),Control Children unrelated to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,12,26,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 1,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Ch-CTRL-related and Ch-CTRL-unrelated to Phenylketonuria  Patients.,increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1239|186801|3085636|186803|265975,Complete,NA
bsdb:1086/7/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 7,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Ch-CTRL-rel (Healthy siblings of PKU patients),Ch-CTRL-unrel (unrelated control children),Control Children unrelated to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,12,26,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 2,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Ch-CTRL-related and Ch-CTRL-unrelated to Phenylketonuria  Patients.,decreased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|508458|649775|649776|3029087|1434006;2|201174|1760|85009|31957|2801844;2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1224|28216|80840|119060|47670;2|1239|186801|3082720|186804|1257,Complete,NA
bsdb:1086/8/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 8,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Ch CTRL rel (Healthy siblings of PKU patients),Ch PKU (PKU children),Children diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,12,59,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Ch-CTRL-related and Phenylketonuria (PKU-Ch) Saliva Patients.,increased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",2|976|117743|200644|49546|1016;2|1239|186801|3082720|186804|1257;2|1239|186801|186802|186807|2740;2|32066|203490|203491|1129771|32067;2|1239|186801|3085636|186803|1164882;2|976|200643|171549|171551|836;2|1224|1236|135625|712|416916,Complete,NA
bsdb:1086/8/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 8,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Ch CTRL rel (Healthy siblings of PKU patients),Ch PKU (PKU children),Children diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,12,59,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2(D),13 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Ch-CTRL-related and Phenylketonuria (PKU-Ch) Saliva Patients.,decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium",2|201174|84998|84999|1643824|133925;2|1239|909932|909929|1843491|970;2|201174|84998|84999|1643824|1380;2|201174|1760|2037|2049|1654;2|508458|649775|649776|3029087|1434006,Complete,NA
bsdb:1086/9/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 9,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control (CTRL-S),Control (CTRL-SP),Healthy Controls who stimulated Subgingival plaque samples were gotten from.,114,113,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival Plague samples,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1213720;2|1239|186801|3082720|186804|1257;2|1224|1236|135625|712|724;2|1239|91061|1385|539738|1378;2|201174|84998|84999|1643824|1380;2|976|200643|171549|171552|1283313;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838,Complete,NA
bsdb:1086/9/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 9,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control (CTRL-S),Control (CTRL-SP),Healthy Controls who stimulated Subgingival plaque samples were gotten from.,114,113,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival plague,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|1224|1236|135625|712|416916;2|201174|1760|85009|31957|2801844;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|32257;2|32066|203490|203491|1129771|32067;2|201174|84998|84999|1643824|133925;2|1239|909932|909929|1843491|970;2|976|200643|171549|2005525|195950,Complete,NA
bsdb:1086/10/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 10,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Adults (CTRL-S),Control Adults (CTRL-SP),Healthy Control adults who stimulated Sub gingival plaque samples were gotten from,52,52,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival plague Adult samples,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1239|186801|3085636|186803|1213720;2|1239|186801|3082720|186804|1257;2|1224|1236|135625|712|724;2|1239|91061|1385|539738|1378;2|201174|84998|84999|1643824|1380;2|976|200643|171549|171552|1283313;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171552|838,Complete,NA
bsdb:1086/10/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 10,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Adults (CTRL-S),Control Adults (CTRL-SP),Healthy Control adults who stimulated Sub gingival plaque samples were gotten from,52,52,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival plague Adult samples,decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|1224|1236|135625|712|416916;2|201174|1760|85009|31957|2801844;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|32257;2|201174|84998|84999|1643824|133925;2|1239|909932|909929|1843491|970;2|976|200643|171549|2005525|195950,Complete,NA
bsdb:1086/11/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 11,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Children (CTRL Ch-S),Control Children (CTRL Ch-SP),Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival plague Children samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171551|836;2|1224|28216|206351|481|482;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1086/11/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 11,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Children (CTRL Ch-S),Control Children (CTRL Ch-SP),Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival plague Children samples,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium",2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|32257;2|201174|1760|85009|31957|2801844;2|1224|1236|135615|868|2717;2|201174|84998|84999|1643824|133925;2|976|200643|171549|2005525|195950;2|29547|3031852|213849|72294|194;2|508458|649775|649776|3029087|1434006,Complete,NA
bsdb:1086/12/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 12,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria (PKU-S),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Patient samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1086/12/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 12,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria (PKU-S),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Patients samples,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|416916;2|201174|1760|85009|31957|2801844;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|201174|1760|85007|1653|1716;2|508458|649775|649776|3029087|1434006;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|32257;2|1224|28216|80840|119060|47670;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186807|2740;2|1239|909932|909929|1843491|970;2|976|200643|171549|2005525|195950,Complete,NA
bsdb:1086/13/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 13,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults (PKU-S),Phenylketonuria Adults (PKU-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|3085636|186803|1164882;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1086/13/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 13,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults (PKU-S),Phenylketonuria Adults (PKU-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|29547|3031852|213849|72294|194;2|1239|186801|186802|186807|2740;2|201174|84998|84999|1643824|133925;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|970;2|201174|1760|85009|31957|2801844;2|508458|649775|649776|3029087|1434006;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|976|117743|200644|49546|1016,Complete,NA
bsdb:1086/14/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 14,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Ch (PKU-S),Phenylketonuria Ch (PKU-SP),Children diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,59,51,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Children samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1224|28216|206351|481|482;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
bsdb:1086/14/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 14,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Ch (PKU-S),Phenylketonuria Ch (PKU-SP),Children diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,59,51,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia",2|29547|3031852|213849|72294|194;2|976|200643|171549|2005525|195950;2|1239|186801|186802|186807|2740;2|201174|84998|84999|1643824|133925;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|970;2|1224|28216|206351|481|32257;2|508458|649775|649776|3029087|1434006;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|976|117743|200644|49546|1016;2|201174|1760|85009|31957|2801844,Complete,NA
bsdb:1086/15/NA,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 15,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control No period (CTRL-S),Phenylketonuria No Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) without suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1086/16/NA,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 16,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Period (CTRL-S),Phenylketonuria Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) with suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1086/17/NA,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 17,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria No Period (PKU-S),Phenylketonuria Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) with suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,N/A,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1087/1/4,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,control individuals without a psychiatric diagnosis (past or present),SCZ: individuals with a psychiatric diagnosis of schizophrenia,"Participants with a schizophrenia diagnosis categorized as follows:
1. AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine) with a total Positive and Negative Symptom Scale (PANSS) score of 60 or low.
2. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
3. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",25,72,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 4,Figure 3,29 June 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for control individuals and SCZ group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii",2|1239|186801|186802|216572|244127|169435;2|1239|186801|3085636|186803|572511|33035;2|201174|84998|1643822|1643826|84111|84112;2|1224|1236|91347|543|561|562;2|201174|84998|1643822|1643826|644652|1335613;2|1239|186801|3085636|186803|1649459|1096246,Complete,Svetlana up
bsdb:1087/1/5,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,control individuals without a psychiatric diagnosis (past or present),SCZ: individuals with a psychiatric diagnosis of schizophrenia,"Participants with a schizophrenia diagnosis categorized as follows:
1. AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine) with a total Positive and Negative Symptom Scale (PANSS) score of 60 or low.
2. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
3. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",25,72,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 5,Figure 3,29 June 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for control individuals and SCZ group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,2|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:1087/2/1,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Response to antipsychotic drug,GO:0097332,control individuals without a psychiatric diagnosis of schizophrenia,AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine),AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine) with a total Positive and Negative Symptom Scale (PANSS) score of 60 or low.,25,24,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for control individuals and AAP group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,NA,NA,Complete,Svetlana up
bsdb:1087/3/1,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine),TRS: individuals with treatment-resistant schizophrenia taking clozapine,"Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",24,48,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,1 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for AAP and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|1432051|1432052;2|1239|186801|3085636|186803|1649459|1096246;2|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:1087/3/2,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine),TRS: individuals with treatment-resistant schizophrenia taking clozapine,"Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",24,48,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,1 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for AAP and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,NA,NA,Complete,Svetlana up
bsdb:1087/4/1,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,TRS: individuals with treatment-resistant schizophrenia taking clozapine,Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60). 2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,48,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for control individuals and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",2|1239|186801|186802|216572|244127|169435;2|201174|84998|1643822|1643826|84111|84112;2|1224|1236|91347|543|561|562;2|201174|84998|1643822|1643826|644652|1335613;2|1239|186801|3085636|186803|1649459|1096246;2|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:1087/4/2,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,TRS: individuals with treatment-resistant schizophrenia taking clozapine,Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60). 2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,48,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,4 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for control individuals and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,2|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:1087/5/1,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 5,Australia,Homo sapiens,Feces,UBERON:0001988,Response to clozapine,GO:0097338,control individuals without a psychiatric diagnosis of schizophrenia,CR: individuals with treatment-resistant schizophrenia responsive to clozapine,CR: individuals with treatment-resistant schizophrenia who were clozapine responsive (total PANSS score ≤60).,25,26,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for control individuals and CR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii",2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|3085636|186803|1649459|1096246,Complete,Svetlana up
bsdb:1087/5/2,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 5,Australia,Homo sapiens,Feces,UBERON:0001988,Response to clozapine,GO:0097338,control individuals without a psychiatric diagnosis of schizophrenia,CR: individuals with treatment-resistant schizophrenia responsive to clozapine,CR: individuals with treatment-resistant schizophrenia who were clozapine responsive (total PANSS score ≤60).,25,26,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 3,4 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for control individuals and CR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,2|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:1087/6/1,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 6,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,CNR: individuals with treatment-resistant schizophrenia nonresponsive to clozapine,CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,22,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for CR and CNR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,2|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:1087/6/2,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 6,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,CNR: individuals with treatment-resistant schizophrenia nonresponsive to clozapine,CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,22,2 months,WMS,NA,Illumina,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,4 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,"Differentially abundant species identified for CR and CNR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,2|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:1088/1/1,Study 1088,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N, Ju M, Su X, Zhang Y, Huang Y, Rao X, Cui L, Lin Z , Dong Y",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HCF: healthy controls (no psychiatric diagnosis of schizophrenia),SCZF: patients with schizophrenia,antipsychotic-treated patients with schizophrenia,15,20,1 month,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2B,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",LEfSe comparison of gut microbiota in antipsychotic-treated patients with schizophrenia (SCZF group) versus healthy controls (HCF group),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|201174|1760|85006|1268|1663;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1224|28216|80840|119060|106589;2|1224|1236|91347|543;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1224|1236;2|1224|28216|80840|2975441|88;2|201174|1760|85006|1268;2|1224|28211|356|82115|13159;2|1224|28211|356|118882|354349;2|1224;2|1224|1236|72274|135621|286;2|1239|186801|186802|186806|113286;2|1224|1236|91347|543|620;2|201174;2|1224|1236|91347,Complete,Svetlana up
bsdb:1088/1/2,Study 1088,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N, Ju M, Su X, Zhang Y, Huang Y, Rao X, Cui L, Lin Z , Dong Y",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HCF: healthy controls (no psychiatric diagnosis of schizophrenia),SCZF: patients with schizophrenia,antipsychotic-treated patients with schizophrenia,15,20,1 month,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2B,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",LEfSe comparison of gut microbiota in antipsychotic-treated patients with schizophrenia (SCZF group) versus healthy controls (HCF group),decreased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|1224|28216|80840|92793;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|1239|186801;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|976|200643|171549|171551|1159323;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|46205;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|976;2|1239;2|1239|186801|186802;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:1088/2/1,Study 1088,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N, Ju M, Su X, Zhang Y, Huang Y, Rao X, Cui L, Lin Z , Dong Y",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: healthy control fecal microbiota-recipient mice,SCZ: schizophrenia fecal microbiota-recipient mice,Male C57BL/6 mice which transplanted fecal microbiota from a human patient with a schizophrenia psychiatric disorder.,5,5,NA,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4D,16 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Bacterial genera differentially expressed in mice transplanted with schizophrenia versus healthy control fecal microbiota,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|201174|1760|85007|1653|1716;2|29547|3031852|213849|72293|209;2|976|200643|171549|1853231|283168;2|976|200643|171549|171552|577309;2|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:1088/2/2,Study 1088,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N, Ju M, Su X, Zhang Y, Huang Y, Rao X, Cui L, Lin Z , Dong Y",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: healthy control fecal microbiota-recipient mice,SCZ: schizophrenia fecal microbiota-recipient mice,Male C57BL/6 mice which transplanted fecal microbiota from a human patient with a schizophrenia psychiatric disorder.,5,5,NA,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4D,16 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Bacterial genera differentially expressed in mice transplanted with schizophrenia versus healthy control fecal microbiota,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1239|186801|3082768|990719|990721;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|1239|526524|526525|2810280|1505663,Complete,Svetlana up
bsdb:1089/1/1,Study 1089,time series / longitudinal observational,35783418,https://doi.org/10.3389/fmicb.2022.909729,NA,"Xiang M, Zheng L, Pu D, Lin F, Ma X, Ye H, Pu D, Zhang Y, Wang D, Wang X, Zou K, Chen L, Zhang Y, Sun Z, Zhang T , Wu G",Intestinal Microbes in Patients With Schizophrenia Undergoing Short-Term Treatment: Core Species Identification Based on Co-Occurrence Networks and Regression Analysis,Frontiers in microbiology,2022,"16S rRNA sequencing, fecal microbiota transplantation, gut microbiota, gut-brain axis, schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Schizophrenia patients before treatment (BT),Schizophrenia patients after treatment (AT),Schizophrenia patients after antipsychotic treatment,25,25,14 days,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2A,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Bacterial taxa differentially abundant in patients before treatment (BT) compared to after treatment (AT),increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Acidobacteriota|c__Blastocatellia|g__Chloracidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549;2|976|200643;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|119852;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841;2|976;2|57723|1562566|458032;2|1239|186801|186802|216572,Complete,Svetlana up
bsdb:1089/1/2,Study 1089,time series / longitudinal observational,35783418,https://doi.org/10.3389/fmicb.2022.909729,NA,"Xiang M, Zheng L, Pu D, Lin F, Ma X, Ye H, Pu D, Zhang Y, Wang D, Wang X, Zou K, Chen L, Zhang Y, Sun Z, Zhang T , Wu G",Intestinal Microbes in Patients With Schizophrenia Undergoing Short-Term Treatment: Core Species Identification Based on Co-Occurrence Networks and Regression Analysis,Frontiers in microbiology,2022,"16S rRNA sequencing, fecal microbiota transplantation, gut microbiota, gut-brain axis, schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Schizophrenia patients before treatment (BT),Schizophrenia patients after treatment (AT),Schizophrenia patients after antipsychotic treatment,25,25,14 days,16S,34,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2A,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica",Bacterial taxa differentially abundant in patients before treatment (BT) compared to after treatment (AT),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:1090/1/1,Study 1090,"cross-sectional observational, not case-control",37576972,https://doi.org/10.3389/fendo.2023.1190954,https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1190954/full,"Xing M, Gao H, Yao L, Wang L, Zhang C, Zhu L , Cui D",Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome,Frontiers in endocrinology,2023,"16S rRNA, dyslipidemia, intestinal microbiota, metabolic syndrome, schizophrenia, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Metabolic syndrome,EFO:0000195,Schizophrenia patients with MetS,Schizophrenia patients without MetS,Schizophrenia patients with metabolic syndrome (MetS),58,57,3 Months,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 4A,12 July 2024,JoyceQ,"JoyceQ,Scholastica",A Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis of significant bacterial differences in the fecal microbiota of schizophrenia patients with versus without metabolic syndrome (MetS),increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Prochlorococcaceae|g__Prochlorococcus",2|74201|203494|48461|1647988|239934;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|186801|186802|186806|1730;2|1239|186801|3082720|186804;2|1239|186801|186802|31979|1266;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|74201|203494|48461|203557;2|1239|526524;2|74201|203494;2|74201|203494|48461;2|74201;2|1117|3028117|1890424|2881426|1218,Complete,Svetlana up
bsdb:1090/1/2,Study 1090,"cross-sectional observational, not case-control",37576972,https://doi.org/10.3389/fendo.2023.1190954,https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1190954/full,"Xing M, Gao H, Yao L, Wang L, Zhang C, Zhu L , Cui D",Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome,Frontiers in endocrinology,2023,"16S rRNA, dyslipidemia, intestinal microbiota, metabolic syndrome, schizophrenia, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Metabolic syndrome,EFO:0000195,Schizophrenia patients with MetS,Schizophrenia patients without MetS,Schizophrenia patients with metabolic syndrome (MetS),58,57,3 Months,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 4A,12 July 2024,JoyceQ,"JoyceQ,Scholastica",A Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis of significant bacterial differences in the fecal microbiota of schizophrenia patients with versus without metabolic syndrome (MetS),decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacteroidota",2|1224|28216|80840|506;2;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643;2|1224|28216;2|1224|28216|80840|119060|32008;2|1224|28216|80840|119060;2|1224|28216|80840;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|158846;2|1224|1236|2887326|468;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1224|1236|72274;2|1239|91061|1385|90964;2|1239|91061|186826|1300;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977;2|1239|91061|186826|33958;2|1224;2|976,Complete,Svetlana up
bsdb:1091/1/1,Study 1091,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S, Liao YT, Tsai MH, Wang YK, Wu IC, Liu CJ, Wu MS, Chan TS, Chen MY, Hu PJ, Kao WY, Liu HC, Tsai MJ, Liu CY, Chang CC, Wu DC , Hsu YH",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Chronic gastritis,Gastric cancer","EFO:0000337,MONDO:0001056",Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,"Mann-Whitney (Wilcoxon),LEfSe,edgeR",0.05,TRUE,4.27,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 1, 2, 3, Figure 2(a) and 5",21 July 2024,Shulamite,"Shulamite,Aleru Divine","Comparative analysis of differential abundance between chronic gastritis and gastric cancer at the phylum, genus, and species levels using the Wilcoxon Rank-Sum Test, EdgeR, and LEfSe.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Fusobacteriota,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",2|976|200643|171549|815|816|47678;2|201174|1760|85004|31953|1678|1689;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|116085;2|32066;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|97478;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|823;2|1239|909932|1843488|909930|33024;2|1239|91061|186826|1300|1301|1328;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|216572|459786;2|1224|28216|80840|995019,Complete,NA
bsdb:1091/1/2,Study 1091,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S, Liao YT, Tsai MH, Wang YK, Wu IC, Liu CJ, Wu MS, Chan TS, Chen MY, Hu PJ, Kao WY, Liu HC, Tsai MJ, Liu CY, Chang CC, Wu DC , Hsu YH",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Chronic gastritis,Gastric cancer","EFO:0000337,MONDO:0001056",Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,"Mann-Whitney (Wilcoxon),LEfSe,edgeR",0.05,TRUE,4.27,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 1, 2, 3, Figure 2(a) and 5",21 July 2024,Shulamite,"Shulamite,Aleru Divine","Comparative analysis of differential abundance between chronic gastritis and gastric cancer at the phylum, genus, and species levels using the Wilcoxon Rank-Sum Test, EdgeR, and LEfSe.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236|2887326|468|469;2|201174;2|201174|84998|1643822|1643826|447020;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|216816;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|1352;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803|1898203;2|1224|1236|91347|1903414|581;2|1224|1236|72274|135621|286,Complete,NA
bsdb:1091/2/1,Study 1091,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S, Liao YT, Tsai MH, Wang YK, Wu IC, Liu CJ, Wu MS, Chan TS, Chen MY, Hu PJ, Kao WY, Liu HC, Tsai MJ, Liu CY, Chang CC, Wu DC , Hsu YH",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Chronic gastritis,Gastric cancer","EFO:0000337,MONDO:0001056","Other sub-groups (NIM, IM and late-stage gastric cancer))",Early-stage gastric cancer,Participants diagnosed with early-stage gastric cancer (Phase I and II).,52,13,6 months,WMS,NA,Illumina,"LEfSe,edgeR",0.05,TRUE,4.27,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2(b) and 6",1 October 2024,Aleru Divine,Aleru Divine,"Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using EdgeR, and LEfSe.",increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",2|1239|91061|186826|81852|1350;2|976|200643|171549|1853231|283168;2|1239|909932|1843488|909930|33024;2|1239|909932|1843489|31977|29465;2|1224|28216|80840|995019,Complete,NA
bsdb:1091/3/1,Study 1091,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S, Liao YT, Tsai MH, Wang YK, Wu IC, Liu CJ, Wu MS, Chan TS, Chen MY, Hu PJ, Kao WY, Liu HC, Tsai MJ, Liu CY, Chang CC, Wu DC , Hsu YH",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Chronic gastritis,Gastric cancer","EFO:0000337,MONDO:0001056","Other sub-groups (NIM, IM and early-stage gastric cancer)",Late-stage gastric cancer,Participants diagnosed with late-stage gastric cancer (Phase III and IV).,46,19,6 months,WMS,NA,Illumina,"edgeR,LEfSe",0.05,TRUE,4.27,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2(b) and 6",1 October 2024,NA,NA,"Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using EdgeR, and LEfSe.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|459786;2|32066|203490|203491|203492|848;2|1224|28216|80840|995019|40544,Complete,NA
bsdb:1091/4/1,Study 1091,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S, Liao YT, Tsai MH, Wang YK, Wu IC, Liu CJ, Wu MS, Chan TS, Chen MY, Hu PJ, Kao WY, Liu HC, Tsai MJ, Liu CY, Chang CC, Wu DC , Hsu YH",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Chronic gastritis,Gastric cancer","EFO:0000337,MONDO:0001056","Other sub-groups (NIM, early-stage gastric cancer and late-stage gastric cancer))",Intestinal metaplasia,"Participants diagnosed with chronic gastritis with pre-cancer lesions (intestinal metaplasia, IM)",50,15,6 months,WMS,NA,Illumina,"edgeR,LEfSe",0.05,TRUE,4.27,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2(b) and 6",1 October 2024,Aleru Divine,Aleru Divine,"Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using EdgeR, and LEfSe.",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|201174|84998|1643822|1643826|447020;2|1239|186801|3085636|186803|1766253|39491;2|1239|186801|3085636|186803|207244;2|1239|186801|186802|186806|1730,Complete,NA
bsdb:1091/5/1,Study 1091,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S, Liao YT, Tsai MH, Wang YK, Wu IC, Liu CJ, Wu MS, Chan TS, Chen MY, Hu PJ, Kao WY, Liu HC, Tsai MJ, Liu CY, Chang CC, Wu DC , Hsu YH",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 5,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Chronic gastritis,Gastric cancer","EFO:0000337,MONDO:0001056","Other sub-groups (IM, early-stage gastric cancer and late-stage gastric cancer))",Non-intestinal metaplasia,"Participants diagnosed with chronic gastritis without pre-cancer lesions (non-intestinal metaplasia, IM)",47,18,6 months,WMS,NA,Illumina,"edgeR,LEfSe",0.05,TRUE,4.27,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2(b) and 6",1 October 2024,Aleru Divine,Aleru Divine,"Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using EdgeR, and LEfSe.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236|2887326|468|469;2|1239|909932|909929|1843491|158846;2|1224|1236|72274|135621|286,Complete,NA
bsdb:1092/1/1,Study 1092,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah MR, Bhatia U, Roach J, Gunstad J , Azcarate Peril MA","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive decline measurement,EFO:0007710,Placebo group,Probiotic group,Participants who received L. rhamnosus GG (LGG) supplementation,83,86,90,PCR,NA,Illumina,ANCOM,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3A and B,1 August 2024,JoyceQ,JoyceQ,"""Relative abundance and predicted functional pathways by cognitive status (A) Univariate comparison analysis showing a significant difference in the relative abundance of Prevotella between cognitively intact and impaired groups (KruskaleWallis Adj. p 1⁄4 0.0136). (B) Random Forest analysis between cognitive groups at the genus level (tree n 1⁄4 5000). Genera were ranked by their contributions to classification accuracy (Mean Decrease Accuracy). Extended error bar plot of PICRUSt2 predictions using Welch's test of C ECs and D KOs. All p values were corrected using Benjamin-Hochberg correction.""",increased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
bsdb:1092/1/2,Study 1092,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah MR, Bhatia U, Roach J, Gunstad J , Azcarate Peril MA","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive decline measurement,EFO:0007710,Placebo group,Probiotic group,Participants who received L. rhamnosus GG (LGG) supplementation,83,86,90,PCR,NA,Illumina,ANCOM,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Results 3.5,2 August 2024,JoyceQ,JoyceQ,NA,increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1224|28216|80840;2|1224|28216|80840|995019;2|1224|28216|80840|995019|577310;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|1239|186801|3085636|186803,Complete,NA
bsdb:1093/1/1,Study 1093,case-control,30775438,10.1126/sciadv.aau8317,NA,"Zheng P, Zeng B, Liu M, Chen J, Pan J, Han Y, Liu Y, Cheng K, Zhou C, Wang H, Zhou X, Gui S, Perry SW, Wong ML, Licinio J, Wei H , Xie P",The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice,Science advances,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: individuals without a psychiatric diagnosis of schizophrenia,SCZ: individuals with a psychiatric diagnosis of schizophrenia,"individuals with schizophrenia diagnosed by Structured Psychiatric Interview using Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV)",69,63,1 month,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Table S2A,23 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,Up-regulated relative abundance of operational taxonomic units in individuals with schizophrenia compared to normal controls.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__uncultured Acidaminococcus sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__uncultured Sarcina sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,s__metagenome,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium anhuiense,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__uncultured Alloprevotella sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,s__human gut metagenome,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|1239|909932|1843488|909930|904|352152;2|1224|28216|80840|995019|40544|40545;2|201174|1760|85004|31953|419014|419015;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816;2|1239|186801|186802|31979|1266|200448;2|201174|84998|84999|1643824|1380;256318;2|976|117743|200644|49546|237|459526;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|1283313|1283315;2|976|200643|171549|171552|838|159272;408170;2|1239|186801|186802|216572|946234|292800;2|1239|909932|1843489|31977|39948|278064;2|1239|909932|1843489|31977|906|907;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:1093/1/2,Study 1093,case-control,30775438,10.1126/sciadv.aau8317,NA,"Zheng P, Zeng B, Liu M, Chen J, Pan J, Han Y, Liu Y, Cheng K, Zhou C, Wang H, Zhou X, Gui S, Perry SW, Wong ML, Licinio J, Wei H , Xie P",The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice,Science advances,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: individuals without a psychiatric diagnosis of schizophrenia,SCZ: individuals with a psychiatric diagnosis of schizophrenia,"individuals with schizophrenia diagnosed by Structured Psychiatric Interview using Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV)",69,63,1 month,16S,34,Illumina,LEfSe,0.05,NA,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Table S2A,24 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,Down-regulated relative abundance of operational taxonomic units in individuals with schizophrenia compared to normal controls.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Candidatus Saccharibacteria|s__Candidatus Saccharibacteria bacterium UB2523,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral clone DR034,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral clone FR058,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__uncultured Citrobacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__uncultured Dorea sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__uncultured Granulicatella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__uncultured Hafnia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__uncultured Lachnoclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus RM2,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.",2|976|200643|171549|171550|239759|28117;2|976|200643|171549|815|816;2|976|200643|171549|815|816|28111;2|95818|1516129;2|201174|84998|84999|84107|102106|147206;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|39496;2|1239|91061|1385|539738|1378|84135;2|1224|1236|135625|712|724|729;2|1239|186801|3085636|186803|877420;2|976|200643|171549|1853231|283168|28118;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|204516;2|1224|1236|91347|543|160674|54291;2|1239|186801|186802|216572|3068309;2|1239|186801|186802|216572|1263|3062497;2|1239|91061|186826|1300|1301|1304;2|95818|163602;2|95818|175646;2|1239|186801|3085636|186803|2316020|33039;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|1239|186801|3085636|186803|572511;2|95818;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|1407607;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803;2|1224|28211|356|119045|407;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|544|200446;2|1239|186801|3085636|186803|189330|286138;2|1239|526524|526525|128827|331630;2|1239|91061|186826|186828|117563|316089;2|1224|1236|91347|1903412|568|374604;2|1239|186801|3085636|186803|1506553|1586779;2|1239|186801|3085636|186803|297314;2|544448|31969|220137;2|1239|186801|186802|216572|707003;2|1239|186801|186802|216572|1508657|1757166;2|1239|186801|186802|216572|1263|129703;2|1239|186801|186802|216572|1263|165186,Complete,Svetlana up
bsdb:1094/1/1,Study 1094,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y, Bi S, Li X, Zhong Y , Qi D",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",30,29,3 months,16S,34,Illumina,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3A, 3B",23 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,increased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales,k__Bacteria|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis|g__Sulfobacillus,k__Bacteria|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Leptospirillum",2|1239|909932|1843488|909930|904;2|1224|1807140|225057;2|1224|1807140|225057|225058|119977;2|1224|1236|135624;2|1239|186801|186802|216572|244127;2|1239|91061|1385;2|1239|526524|526525|128827|118747;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|201174|84998|84999;2|201174|84998|84999|84107|33870;2|201174|1760|85007|1653|1716;2|200940|3031449|213115|194924|872;2|200940|3031449|213115;2|1224|1236|91347|543|547;2|1224|1236|91347;2|1239|91061|1385|539738|1378;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|52225;2|1239|186801|3082720|3030910|86331;2|40117|203693|189778;2|1224|1236|91347|1903414|583;2|1239|186801|186802|31979|1266;2|1239|909932|909929|1843491|970;2|1224|1236|135624|83763|83770;2|1239|186801|186802|539000|28033;2|40117|203693|189778|189779|179,Complete,Svetlana up
bsdb:1094/1/2,Study 1094,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y, Bi S, Li X, Zhong Y , Qi D",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",30,29,3 months,16S,34,Illumina,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3A, 3B",24 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|3085642|580596;2|508458|649775|649776|649777|508459;2|1239|186801|3085636|186803|189330;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|91061|186826|1300|1357;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|482;2|1224|28216|206351;2|508458|649775|649776|3029088|638847;2|1239|909932|1843489|31977|29465;2|74201|203494|48461,Complete,Svetlana up
bsdb:1094/2/1,Study 1094,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y, Bi S, Li X, Zhong Y , Qi D",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",6,6,3 months,WMS,NA,Illumina,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3C, 3D",24 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:413,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus pontis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia|s__Massiliimalia timonensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|1470347;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1262803;2|1239|91061|186826|33958|2742598;2|1239|91061|186826|33958|2742598|35787;2|1239|186801|186802|216572|2895461;2|1239|186801|186802|216572|2895461|1987501;2|1239|909932|909929|1843491|158846;2|1239|909932|909929|1843491|158846|158847;2|1239|909932|909929|1843491|158846|491921;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|906|907;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|2049047;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|1262952;2|1239|909932|909929|1843491|970,Complete,Svetlana up
bsdb:1094/2/2,Study 1094,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y, Bi S, Li X, Zhong Y , Qi D",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",6,6,3 months,WMS,NA,Illumina,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3C, 3D",24 July 2024,Jacob A. De Jesus,Jacob A. De Jesus,Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides galacturonicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. TM05-53,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella porci,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. TF10-5,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Wujia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Wujia|s__Wujia chipingensis",2|976|200643|171549|815|816;2|976|200643|171549|815|816|384639;2|976|200643|171549|815|816|1262739;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|572511|1737424;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186806|1730|2292353;2|1239|526524|526525|128827|1573535;2|1239|526524|526525|128827|1573535|2652276;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|28050|28052;2|1239|186801|3085636|186803|28050|2049031;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|2293144;2|1239|186801|3085636|186803|2944152;2|1239|186801|3085636|186803|2944152|2763670,Complete,Svetlana up
bsdb:1095/1/1,Study 1095,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W, Zhao J, Wu J, Xu D, Meng X, Jiang P, Shi H, Ge X, Yang X, Hu M, Zhang P, Tang R, Nagaratnam N, Zheng K, Huang XF , Yu Y",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,HF+Veh (High fat and Vehicle treated mice),HF+DI (High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week.",12,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig. 5g,30 July 2024,Victoria,Victoria,A Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the HF+DI group compared to the HF+Veh group.,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|976|200643;2|976;2|976|200643|171549|171552;2|1239|526524|526525|128827|174708;2|976|200643|171549|171552|1283313;2|1239|91061;2|1224|28211|204441|2829815|191;2|1224|28211|204441|2829815;2|1224|1236|135624;2|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:1095/1/2,Study 1095,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W, Zhao J, Wu J, Xu D, Meng X, Jiang P, Shi H, Ge X, Yang X, Hu M, Zhang P, Tang R, Nagaratnam N, Zheng K, Huang XF , Yu Y",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,HF+Veh (High fat and Vehicle treated mice),HF+DI (High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week.",12,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig. 5g,30 July 2024,Victoria,Victoria,A Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the HF+DI group compared to the HF+Veh group.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Candidatus Actinomarinales,k__Bacteria|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Solibacteraceae|g__Candidatus Solibacter",2|1239;2|1239|186801;2|28221;2|200940|3031449|213115;2|1239|186801|186802;2|1239|186801|186802|1392389;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803;2|1224|1236|135614|32033|83618;2|1239|186801|186802|216572|1508657;2|201174|1760|1389450;2|57723|204432|332160|332161|332162,Complete,Svetlana up
bsdb:1095/2/1,Study 1095,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W, Zhao J, Wu J, Xu D, Meng X, Jiang P, Shi H, Ge X, Yang X, Hu M, Zhang P, Tang R, Nagaratnam N, Zheng K, Huang XF , Yu Y",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,FMT-HF+Veh (Fecal microbiome transplantation-High fat and Vehicle treated mice),FMT-HF+DI (Fecal microbiome transplantation-High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week. Afterward, they received fecal microbiome transplantation.",8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Supplemental Figure S5,2 August 2024,Victoria,Victoria,Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the FMT-HF+DI group compared to the FMT-HF+Veh group.,increased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Thermodesulfobacteriota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",2|201174;2|201174|84998|84999;2|201174|84998;2|200940|3031449|213115|194924|872;2|200940|3031449|213115;2|200940|3031449;2|201174|84998|1643822|1643826;2|201174|84998|1643822|1643826|580024;2|1239|186801|3085636|186803;2|544448|31969|2085|2092|2093;2|1239|186801|3085636|186803|841;2|200940;2|1239|186801|3085636|186803|1506577;2|200940|3031449|213115|194924,Complete,Svetlana up
bsdb:1095/2/2,Study 1095,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W, Zhao J, Wu J, Xu D, Meng X, Jiang P, Shi H, Ge X, Yang X, Hu M, Zhang P, Tang R, Nagaratnam N, Zheng K, Huang XF , Yu Y",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,FMT-HF+Veh (Fecal microbiome transplantation-High fat and Vehicle treated mice),FMT-HF+DI (Fecal microbiome transplantation-High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week. Afterward, they received fecal microbiome transplantation.",8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Supplemental Figure S5,2 August 2024,Victoria,Victoria,Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the FMT-HF+DI group compared to the FMT-HF+Veh group.,decreased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",2|1224|28211|356|118882|354349;2|1224|28211|356;2|1224|28211|356|82115;2|1239|526524|526525|128827|1937007;2|1239;2|1239|91061;2|1239|526524|526525|128827|1937008;2|1239|526524|526525|128827;2|1239|526524|526525,Complete,Svetlana up
bsdb:1096/1/1,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months prior to study recruitment,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental data 4 and 5,21 July 2024,Aleru Divine,Aleru Divine,Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to mothers.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria",2|1239|186801|186802|216572|258514;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|244127;2|1239|186801|3082720|3030910|109326;2|1239;2|976;2|976|200643|171549|2005519|397864;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|976|200643|171549|2005519|1348911;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|201174|84998|1643822|1643826|644652;2|1239|526524|526525|128827|61170;2|1239|186801|186802|1392389;2|1239|186801|3082720|3030910|86331;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|41978;2,Complete,Svetlana up
bsdb:1096/1/2,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months prior to study recruitment,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental data 4 and 5,21 July 2024,Aleru Divine,Aleru Divine,Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to mothers.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Eukaryota|p__Bacillariophyta,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Candidatus Parcubacteria,k__Bacteria|p__Cyanobacteriota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|201174;2|201174|84998|84999|1643824|1380;2759|2836;2|201174|1760|85004|31953|1678;2|221216;2|1117;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|526524|526525|128827;2|1224|1236|91347|543|1940338;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1224|28211|356|69277|68287;2|1224;2|201174|1760|85006|1268|32207;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279;2759|33090|35493;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1096/2/1,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months prior to study recruitment,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental data 4 and 5,21 July 2024,Aleru Divine,Aleru Divine,Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to grandmothers.,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae|g__Aestuariispira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria",2|1239|186801|186802|216572|258514;2|201174|84998|1643822|1643826|447020;2|1224|28211|204441|597359|1647175;2|976|200643|171549|171550|239759;2|1239;2|976;2|976|200643|171549|2005519|397864;2|200940|3031449|213115|194924|35832;2|1239|186801|3085636|186803|572511;2|1239|186801|186802|3085642|580596;2|1239|186801;2|976|200643|171549|2005519|1348911;2|1239|186801|3085636|186803|33042;2|201174|84998|84999|84107;2|1239|186801|186802;2157|28890;2|1239|186801|186802|216572|216851;2|1239|526524|526525|128827|1573536;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|526524|526525|128827|61170;2|1239|186801|186802|1392389;2157|28890|183925|2158|2159|2172;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1239|909932|1843488|909930|33024;2|1239|186801|3082720|186804|1501226;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239|526524|526525|2810281|191303;2,Complete,Svetlana up
bsdb:1096/2/2,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months prior to study recruitment,16S,34,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental data 4 and 5,21 July 2024,Aleru Divine,Aleru Divine,Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to grandmothers.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|201174;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|547;2|1224|1236|91347|543|1940338;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|539738|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1224|28211|356|69277|68287;2|1224;2|1224|28211|204457|41297|13687;2|1239|91061|1385|90964|1279;2|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1096/3/1,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months prior to study recruitment,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,Aleru Divine,"Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to mothers.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|s__Bacillota bacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Bittarella (ex Durand et al. 2017),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catenibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catenibacillus|s__Catenibacillus scindens,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Hydrogeniiclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia|s__Massiliimalia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota,k__Bacteria,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae",2|1239|186801|186802|3082771|1918385;2|201174|84998|1643822|1643826|447020;2|201174|84998|1643822|1643826|447020|446660;2|201174|84998|1643822|1643826|447020|446660|394340;2|1239|186801|186802|3085642|2048137;2|1239|186801|186802|3085642|2048137|1628085;2|1239|186801|186802|3085642|2048137|2048138;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|1288121;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|3082771|1924093;2|1239|186801|186802|3082771|1924093|1924094;2|1239|186801|3085636|3118652|2039240;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|216572|1935176|1871018;2|201174|84998|1643822|1643826|553372;2|1239;2|1239|1879010;2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|46506;2|976|200643|171549|2005519|397864;2|1239|186801|186802|216572|1929297;2|1239|186801|3085636|186803|572511|1737424;2|1239|186801|186802|3085642|580596;2|1239|186801|3085636|186803|2316203;2|1239|186801|3085636|186803|2316203|673271;2|200795;2|1239|186801|3082768|990719|990721;2|1239|186801|2044939;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|31979|1485|1650661;2|1239|186801|3085636|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|1955814;2|1239|526524|526525|128827|1472649;2|1239|526524|526525|128827|1472649|1034346;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|189330|88431;2|1239|186801|3085636|186803|189330|2040332;2|1239|186801|186802|216572|2591381;2|1239|186801|186802|543313;2|1239|186801|186802|186806|1730;2|1239|186801|186802|2211178;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|2005359;2|1239|186801|3085636|186803|2005359|290055;2|1239|186801|186802|216572|946234|2049025;2|1239|186801|186802|1918454;2|1239|186801|186802|1918454|1918624;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|201174|84998|1643822|1643826|644652;2|1239|526524|526525|128827|61170;2|1239|186801|186802|3082771|2764317;2|1239|186801|186802|1392389|1673721;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|1763508;2|1239|186801|186802|31979|420345;2|1239|186801|186802|216572|2172004;2|1239|186801|186802|216572|2895461;2|1239|186801|186802|216572|2895461|1987501;2|1239|186801|186802|216572|3028852;2|1239|186801|3082720|3030910|86331;2|976|200643|171549|1853231|283168;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|1945593;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|2485925;2|1239|91061|1385|186822|44249;2|1239|186801|186802|216572|1017280|106588;2|201174|84998|1643822|1643826|1926677;2|1239|186801|3085636|186803|841;2|1239|186801|3085636|186803|841|301302;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|841|2049040;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|3062497;2|1239|186801|186802|216572|1263|40519;2|203691;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|1306;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|292632|214851;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|1110546;2|1224|1236|135614|32033|338;2|1239|186801|3085636|186803|1506577|29361;2|1239;2;2|1239|186801;2|201174|84998;2|201174|84998|1643822|1643826;2|1239|186801|186802;2|1239|186801|3085636|186803;2|256845|1313211;2|1239|186801|186802|216572;2|1239|91061|1385|186822,Complete,Svetlana up
bsdb:1096/3/2,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months prior to study recruitment,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,Aleru Divine,"Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to mothers.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Bittarella (ex Liu et al. 2021)|s__Bittarella massiliensis (ex Liu et al. 2021),k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter butyricigenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium sp.,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|201174;2|976|200643|171549|171550|239759|2585118;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802|216572|3062447|3062437;2|1239|186801|3085636|186803|572511|536633;2|1239|186801|186802|1898207;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|186802|216572|2591381|2591382;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|186806|1730|142586;2|201174|1760|85004|31953|2701;2|1239|526524|526525|128827|61170|61171;2|1239|526524|526525|128827|61170|1468449;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|28050|39485;2|1239|186801|3085636|186803|1763508|2021453;2|1239|91061|186826|33958|1578;2|1239|186801|3085636|186803|2316020|2316025;2|1239|186801|3082720|3030910|86331|2049035;2|1224;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301|28037;2759|33090|35493;2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049;2|201174|1760|85004|31953;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|1300,Complete,Svetlana up
bsdb:1096/4/1,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months prior to study recruitment,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,Aleru Divine,"Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to grandmothers.",increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes dispar,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|s__Bacillota bacterium,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Chloroflexota,k__Bacteria|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacteria|p__Fibrobacterota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas gabonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium sp.,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|s__Porphyromonadaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Spirochaetota,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Eukaryota|k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichuridae|g__Trichuris,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] nexile,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota,k__Bacteria,k__Bacteria|p__Bacteroidota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae",2|1239|186801|186802|3082771|1918385;2|201174|84998|1643822|1643826|447020;2|201174|84998|1643822|1643826|447020|446660;2|201174|84998|1643822|1643826|447020|446660|394340;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|2585119;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171550|239759|1288121;2|976|200643|171549|171550|239759|328814;2|1239|186801|3085636|186803|2569097;2|1239|186801|186802|3082771|1924093;2|1239|186801|186802|3082771|1924093|1924094;2|1239|186801|3085636|3118652|2039240;2|1239|186801|186802|216572|1935176;2|1239|186801|186802|216572|1935176|1871018;2|201174|84998|1643822|1643826|553372;2|1239;2|1239|1879010;2|200940|3031449|213115|194924|35832;2|1239|186801|186802|3085642|580596;2|200795;2|1239|186801|2044939;2|1239|186801|186802|31979|1898204;2|1239|186801|186802|1898207;2|1239|186801|186802|31979|1485|1650661;2|1239|186801|3085636|186803|33042;2|1239|186801|3085636|186803|33042|410072;2|1239|186801|3085636|186803|189330;2|1239|186801|3085636|186803|189330|2040332;2|1239|186801|186802|216572|2591381;2|1239|186801|186802|186806|1730;2157|28890;2|1239|186801|186802|2211178;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|3085636|186803|2005359;2|1239|186801|3085636|186803|2005359|290055;2|65842;2|1239|186801|186802|216572|946234|2049025;2|1239|186801|186802|1918454;2|1239|186801|186802|1918454|1918624;2|1239|186801|3085636|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|186802|216572|1892380;2|1239|526524|526525|128827|61170;2|1239|186801|186802|1392389|1702285;2|1239|186801|3085636|186803|1506553;2|1239|186801|3085636|186803|1506553|2028282;2|1239|186801|3085636|186803|28050;2|1239|186801|3085636|186803|1763508;2|1239|186801|186802|216572|2172004;2|1239|186801|186802|216572|2895461;2|1239|186801|3082720|3030910|86331;2|1239|186801|3082720|3030910|86331|2049035;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|1945593;2|1239|186801|186802|216572;2|1239|91061|1385|186822|44249;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930|33024|33025;2|976|200643|171549|171551|2049046;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|3082720|186804|1501226;2|1239|186801|3082720|186804|1501226|1776391;2|1239|186801|3085636|186803|841|360807;2|1239|186801|3085636|186803|841|2049040;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263|40519;2|203691;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|1306;2|1239|186801|186802|216572|292632|214851;2759|33208|6231|119088|6329|119093|36086;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|1110546;2|1224|1236|135614|32033|338;2|1239|186801|3085636|186803|1506577|29361;2|1239|909932|1843488|909930;2|1239|91061;2|1239;2;2|976;2|1239|186801;2|201174|84998|84999;2|201174|84998;2|201174|84998|1643822|1643826;2|1239|186801|186802;2|1239|186801|3085636|186803;2|1239|186801|186802|216572;2|1239|91061|1385|186822,Complete,Svetlana up
bsdb:1096/4/2,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months prior to study recruitment,WMS,NA,Illumina,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,Aleru Divine,"Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to grandmothers.",decreased,"k__Bacteria|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter sp.,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__Eggerthellaceae bacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter butyricigenes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|201174;2|976|200643|171549|171550|239759|28117;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802|216572|2591381|2591382;2|201174|84998|1643822|1643826|1972561;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|186801|3085636|186803|1407607|1150298;2|201174|1760|85004|31953|2701;2|1224|1236|91347|543|570;2|1239|186801|3085636|186803|1763508|2021453;2|1239|91061|186826|33958|1578;2|256845|1313211|2053569;2|1239|186801|3085636|186803|2316020|2316025;2|976|200643|171549|1853231|283168|28118;2|1224;2|1224|1236|91347|543|620;2759|33090|35493;2|1239|186801|3085636|186803|1506577;2|1239|909932|1843489|31977|29465;2|201174|1760|85004|31953;2|201174|1760|85004;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|1300,Complete,Svetlana up
bsdb:1096/5/1,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Mothers and Grandmothers,Infants,Infants (0 - 12 months old),83,38,3 months before study recruitment,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7E,23 September 2024,Aleru Divine,Aleru Divine,Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Infants – compared to the other two groups (Mothers and Grandmothers),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:1096/6/1,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants and Grandmothers,Mothers,Mothers of the infants,78,43,3 months before study recruitment,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7E,23 September 2024,Aleru Divine,Aleru Divine,Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Mothers – compared to the other two groups (Infants and Grandmothers),increased,"k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801;2|1239|186801|186802;2|1239;2|1239|186801|3085636|186803|572511;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827|61170;2|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:1096/7/1,Study 1096,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,https://www.nature.com/articles/s41467-024-47182-y,"Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M , Villaseñor A",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Infants and Mothers,Grandmothers,Grandmothers of the infants.,81,40,3 months before study recruitment,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7E,23 September 2024,Aleru Divine,Aleru Divine,Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Grandmothers – compared to the other two groups (Infants and Mothers),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacteria|c__Deltaproteobacteria,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfobaculum,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Verrucomicrobiota",2|1239|186801|186802|216572|258514;2|74201|203494|48461|1647988|239934;2|200940|3031449|213115|194924|35832;2|201174|84998|84999|84107|33870;2|28221;2|200940|3031449|213115|194924|1433996;2|200940|3031449|213115|194924;2|200940|3031449|213115;2|201174|84998|84999|1643824|133925;2|201174|84998|84999|84107|1427376;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551;2|74201|203494|48461|203557;2|74201|203494|48461;2|74201|203494;2|74201,Complete,Svetlana up
bsdb:1097/1/NA,Study 1097,randomized controlled trial,34152099,10.1002/brb3.2259,NA,"Bharwani A, Szamosi JC, Taylor VH, Lee Y, Bala A, Mansur R, Subramaniapillai M, Surette M , McIntyre RS",Changes in the gut microbiome associated with infliximab in patients with bipolar disorder,Brain and behavior,2021,"16S rRNA sequencing, bipolar disorder, gut microbiota, inflammation, infliximab",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Placebo,Infliximab,"Participants who received infliximab, an antibody administered intravenously that is used for treating several chronic inflammatory diseases and works by blocking the effects of TNF-α",8,9,NA,16S,NA,Illumina,"PERMANOVA,ANCOM",0.05,FALSE,NA,bipolar disorder,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1099/1/1,Study 1099,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X, Wang Y, Li X, Jiang J, Kang Y, Pang L, Zhang P, Li A, Lv L, Andreassen OA, Fan X, Hu S , Song X","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,SCH patients,"first-episode, drug-naïve SCH patients",107,107,30,16S,34,Ion Torrent,Random Forest Analysis,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 4,29 July 2024,JoyceQ,JoyceQ,"""Dynamic changes of gut microbiota in SCH patients.""",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,2|1239|186801|3082720|186804|1501226,Complete,NA
bsdb:1099/1/2,Study 1099,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X, Wang Y, Li X, Jiang J, Kang Y, Pang L, Zhang P, Li A, Lv L, Andreassen OA, Fan X, Hu S , Song X","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,SCH patients,"first-episode, drug-naïve SCH patients",107,107,30,16S,34,Ion Torrent,Random Forest Analysis,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 4,3 August 2024,JoyceQ,JoyceQ,"""Dynamic changes of gut microbiota in SCH patients.""",increased,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,2|1239|186801|3085636|186803|1506553,Complete,NA
bsdb:1100/1/1,Study 1100,case-control,32830918,10.1002/aur.2358,NA,"Zou R, Xu F, Wang Y, Duan M, Guo M, Zhang Q, Zhao H , Zheng H",Changes in the Gut Microbiota of Children with Autism Spectrum Disorder,Autism research : official journal of the International Society for Autism Research,2020,"Akkermansia, Bacteroides, Prevotella, autism spectrum disorders, children, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Autistic,Diagnosis of autistic disorder defined by the Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition (DSM IV - TR) and confirmed using the Autism Diagnostic Interview-Revised (ADI-R),48,48,Use of probiotics or antibiotics prior to fecal sample collection,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Figure 3, Table 3, Table 4",19 September 2024,AlishaM,AlishaM,"Species, Families and Genera with significantly different abundances between ASD and control groups",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|3085636|186803|28050|39485;2|1239|909932|909929|1843491|158846;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|3085636|186803|841|301302;2|976|200643|171549|171552|2974251|165179,Complete,NA
bsdb:1100/1/2,Study 1100,case-control,32830918,10.1002/aur.2358,NA,"Zou R, Xu F, Wang Y, Duan M, Guo M, Zhang Q, Zhao H , Zheng H",Changes in the Gut Microbiota of Children with Autism Spectrum Disorder,Autism research : official journal of the International Society for Autism Research,2020,"Akkermansia, Bacteroides, Prevotella, autism spectrum disorders, children, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Autistic,Diagnosis of autistic disorder defined by the Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition (DSM IV - TR) and confirmed using the Autism Diagnostic Interview-Revised (ADI-R),48,48,Use of probiotics or antibiotics prior to fecal sample collection,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,"Figure 3, Table 3, Table 4",19 September 2024,AlishaM,AlishaM,"Species, Families and Genera with significantly different abundances between ASD and control groups",decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|817;2|1239|909932|1843489|31977|39948|218538;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|946234|292800;2|1224|1236|135625|712|724|729;2|1224|1236|91347|543;2|1224|1236|135625|712;2|74201|203494|48461|203557;2|1239|186801|3085636|186803|572511|1532;2|1239|186801|3085636|186803|1432051,Complete,NA
bsdb:1100/2/NA,Study 1100,case-control,32830918,10.1002/aur.2358,NA,"Zou R, Xu F, Wang Y, Duan M, Guo M, Zhang Q, Zhao H , Zheng H",Changes in the Gut Microbiota of Children with Autism Spectrum Disorder,Autism research : official journal of the International Society for Autism Research,2020,"Akkermansia, Bacteroides, Prevotella, autism spectrum disorders, children, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Autistic,Diagnosis of autistic disorder defined by the Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition (DSM IV-TR) and confirmed using the Autism Diagnostic Interview-Revised (ADI-R),48,48,Use of probiotics or antibiotics prior to fecal sample collection,16S,34,Illumina,ANOVA,0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1102/1/NA,Study 1102,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y, Fang L, Chen S, Zhou H, Fan Y, Lin L, Li J, Xu J, Chen Y, Ma Y , Chen Y",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,Alzheimer's Disease (AD) mouse model,97,121,NA,16S,34,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1103/1/1,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 1,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control,Mild Dry Eye,2s<TFBUT<5s (Tear Film Breakup Time between 2 and 5 sec),61,56,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,NA,Signature 1,Paragraph on page 1990,28 September 2024,Mary Bearkland,Mary Bearkland,Linear Discriminant Analysis Effect Size (Top 5 relatively abundant taxa in the family and genus level),increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Aphanizomenonaceae|g__Dolichospermum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae",2|201174|1760|85006|1268|1663;2|1224|28216|80840|80864;2|1117|3028117|1161|1892259|748770;2|201174|1760|85006|1268;2|201174|1760|85006|1268|57494;2|1224|1236|72274|135621;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1239|91061|1385|186818|1569;2|1117|3028117|1161|1162,Complete,NA
bsdb:1103/1/2,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 1,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control,Mild Dry Eye,2s<TFBUT<5s (Tear Film Breakup Time between 2 and 5 sec),61,56,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,NA,Signature 2,Paragraph on page 1990,28 September 2024,NA,NA,Linear Discriminant Analysis Effect Size (top 5 taxa at the family and genus levels),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|201174|1760|85007|1653;2|1239|91061|186826|33958|1578;2|1224|1236|2887326|468;2|1224|28211|356|118882;2|201174|1760|85009|31957;2|201174|1760|85007|1653|1716;2|1224|28211|356|212791;2|1224|28211|356|118882|528;2|201174|1760|85009|31957|1743,Complete,NA
bsdb:1103/2/1,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 2,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,61,82,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,decreased,decreased,decreased,unchanged,NA,decreased,Signature 1,Paragraph on page 1990,4 October 2024,Mary Bearkland,Mary Bearkland,Linear Discriminant Analysis Effect Size (top five taxa at the family and genus level),increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Chelativorans,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",2|1224|28211|204441|433;2|1239|526524|526525|128827|174708;2|1224|28211|356|45404;2|1224|28211|356|2036754|28209;2|1224|28216|80840|119060|106589;2|1224|28216|80840|75682;2|1297|188787|68933|188786;2|1297|188787|68933|188786|270;2|1224|28211|356|69277|449972;2|1224|1236|135614|32033,Complete,NA
bsdb:1103/2/2,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 2,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,61,82,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,decreased,decreased,decreased,unchanged,NA,decreased,Signature 2,Paragraph on page 1990,4 October 2024,NA,NA,Linear Discriminant Analysis Effect Size (Top 5 taxa at the family and genus levels),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|201174|1760|85007|1653;2|1239|91061|186826|33958|1578;2|1224|28211|356|212791;2|1224|28211|356|118882|528;2|1224|1236|2887326|468;2|1224|28211|356|118882;2|201174|1760|85009|31957;2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1743,Complete,NA
bsdb:1103/3/1,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 3,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,mild dry eye,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,56,82,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Paragraph on page 1990,4 October 2024,Mary Bearkland,Mary Bearkland,Linear Discriminant Analysis Effect Size (top five taxa at the family and genus levels),increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Chelativorans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus basilensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",2|1224|28211|204441|433;2|1239|526524|526525|128827|174708;2|1224|28211|356|45404;2|1224|28211|356|69277|449972;2|1224|28211|356|2036754|28209;2|1224|28216|80840|119060|106589|68895;2|1224|1236|135614|32033;2|1224|28216|80840|75682;2|1297|188787|68933|188786;2|1297|188787|68933|188786|270,Complete,NA
bsdb:1103/3/2,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 3,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,mild dry eye,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,56,82,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Paragraph on page 1990,4 October 2024,Mary Bearkland,Mary Bearkland,Linear Discriminant Analysis Effect Size (top five taxa at the family and genus levels),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Aphanizomenonaceae|g__Dolichospermum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae",2|201174|1760|85006|1268|1663;2|1224|28216|80840|80864;2|1117|3028117|1161|1892259|748770;2|201174|1760|85006|1268;2|201174|1760|85006|1268|57494;2|1224|1236|72274|135621;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1239|91061|1385|186818|1569;2|1117|3028117|1161|1162,Complete,NA
bsdb:1106/1/1,Study 1106,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM , Kuhn L",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 1,Bangladesh,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Exclusive Breast Feeding (EBF),Non_Exclusive Breast Feeding (Non-EBF),Infants who was feed breast milk with either formula or solid.,138,178,NA,16S,4,Illumina,Random Forest Analysis,0.001,FALSE,95,NA,"age,sex",NA,increased,unchanged,NA,NA,unchanged,Signature 1,Table 2,2 October 2024,Shulamite,Shulamite,Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|815|816;2|1239|186801|186802|186806|1730;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|31979|1485,Complete,NA
bsdb:1106/2/1,Study 1106,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM , Kuhn L",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,NA,NA,NA,NA,16S,4,Illumina,Random Forest Analysis,0.001,FALSE,95,NA,age,NA,increased,NA,NA,NA,NA,Signature 1,Table 3,3 October 2024,NA,NA,"Meta-analysis of five studies that included a non-breastfeeding group 
for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non
exclusive breastfeeding and non breastfeeding groups.",decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730;2|74201|203494|48461|1647988|239934;2|1239|91061|1385|90964|1279,Complete,NA
bsdb:1106/2/2,Study 1106,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM , Kuhn L",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,NA,NA,NA,NA,16S,4,Illumina,Random Forest Analysis,0.001,FALSE,95,NA,age,NA,increased,NA,NA,NA,NA,Signature 2,Table 3,3 October 2024,NA,NA,"Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, nonexclusive breastfeeding and non breastfeeding groups.",increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|74201|203494|48461|1647988|239934;2|1239|186801|3085636|186803|572511;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730,Complete,NA
bsdb:1106/3/1,Study 1106,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM , Kuhn L",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 3,Haiti,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,"Exclusively Breastfeeding (EBF), Vaginally Born and C-section Born","Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born",Infants fed with breast milk plus  solid or formula,74,22,NA,16S,4,Illumina,Random Forest Analysis,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,3 October 2024,Shulamite,Shulamite,Meta-analysis of six  studies without data from Haiti study for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age(sensitivity analysis).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|1239|186801|3085636|186803|33042;2|1239|186801|186802|186806|1730;2|1239|909932|1843489|31977|906,Complete,NA
bsdb:1106/4/NA,Study 1106,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM , Kuhn L",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Exclusive Breastfeeding (EBF),Non-Exclusive Breastfeeding (Non-EBF),Infants fed with breast milk plus solid or formula,87,57,NA,16S,4,Illumina,Random Forest Analysis,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1108/1/1,Study 1108,"prospective cohort,time series / longitudinal observational",NA,10.3389/fimmu.2023.1280262,https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1280262/full,NA,NA,NA,NA,NA,Experiment 1,Zimbabwe,Homo sapiens,Alimentary part of gastrointestinal system,UBERON:0005409,"HIV infection,Abnormal inflammatory response","EFO:0000764,HP:0012647",HIV-uninfected,HIV-infected,Group 1 refers to HIV-infected lactating women who are receiving combination antiretroviral therapy.,50,27,NA,16S,5,Ion Torrent,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon),Fisher's Exact Test,PERMANOVA",0.05,TRUE,2,"age,breastfeeding duration,socioeconomic status","age,breastfeeding duration,health,socioeconomic status",unchanged,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Microbial Signatures,2 October 2024,NA,NA,"Certain bacterial taxa were found to have increased abundance in HIV-infected women, such as Slackia and Collinsella.",increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|201174|84998|1643822|1643826|84108;2|201174|84998|84999|84107|102106,Complete,NA
bsdb:1108/1/2,Study 1108,"prospective cohort,time series / longitudinal observational",NA,10.3389/fimmu.2023.1280262,https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1280262/full,NA,NA,NA,NA,NA,Experiment 1,Zimbabwe,Homo sapiens,Alimentary part of gastrointestinal system,UBERON:0005409,"HIV infection,Abnormal inflammatory response","EFO:0000764,HP:0012647",HIV-uninfected,HIV-infected,Group 1 refers to HIV-infected lactating women who are receiving combination antiretroviral therapy.,50,27,NA,16S,5,Ion Torrent,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon),Fisher's Exact Test,PERMANOVA",0.05,TRUE,2,"age,breastfeeding duration,socioeconomic status","age,breastfeeding duration,health,socioeconomic status",unchanged,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Microbial Signatures,2 October 2024,NA,NA,"Other bacterial taxa, such as Clostridium sensu stricto 1, showed a decrease in relative abundance in the HIV-infected group compared to uninfected women",decreased,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,2|1239|186801|3082720|186804|1501226,Complete,NA
bsdb:1110/1/1,Study 1110,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 1,China,Mus musculus,"Feces,Blood","UBERON:0001988,UBERON:0000178",Acute pancreatitis,EFO:1000652,Control group,Acute Pancreatitis (AP),"Mouse models comprise of mild acute pancreatitis (MAP), moderately severe acute pancreatitis (MSAP) and severe acute pancreatitis (SAP).",3,3,No antibiotics exclusion was stated,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,3,"age,body weight,sex",NA,NA,decreased,decreased,increased,NA,NA,Signature 1,"Fig. 6D, Fig. 4A",2 October 2024,KateRasheed,KateRasheed,"Venn plots showed that Burkholderiales bacterium YL45 and Bifidobacterium pseudolongum differed significantly among the three model groups, and presented an increasing tendency in all AP mouse models. 

Also, analysis of the composition of microbiomes (ANCOM) revealed that Proteobacteria was upregulated in the three AP models along with an increase in Bacteroidetes in the Caerulein group and L-arginine group.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium YL45,k__Bacteria|p__Pseudomonadota",2|976|200643;2|201174|1760|85004|31953|1678|1694;2|1224|28216|80840|1834205;2|1224,Complete,NA
bsdb:1110/1/2,Study 1110,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 1,China,Mus musculus,"Feces,Blood","UBERON:0001988,UBERON:0000178",Acute pancreatitis,EFO:1000652,Control group,Acute Pancreatitis (AP),"Mouse models comprise of mild acute pancreatitis (MAP), moderately severe acute pancreatitis (MSAP) and severe acute pancreatitis (SAP).",3,3,No antibiotics exclusion was stated,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,3,"age,body weight,sex",NA,NA,decreased,decreased,increased,NA,NA,Signature 2,"Fig. S1, Table S1",2 October 2024,KateRasheed,KateRasheed,Supplementary table showing a significant downregulation in the Caerulein group.,decreased,"k__Bacteria|p__Bacillota,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|p__Mycoplasmatota,k__Archaea|p__Nitrososphaerota,k__Archaea|p__Thermoproteota",2|1239;2|363464;2|32066|203490;2|544448;2157|651137;2157|28889,Complete,NA
bsdb:1111/1/1,Study 1111,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J , Blaser MJ",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy Controls,Caucasian Americans (CA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were Caucasian Americans,15,15,Less than 3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D,3 October 2024,NA,NA,Differential abundance of taxa in Caucasian MS and control samples.,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobiota,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|74201|203494|48461;2|74201;2|74201|203494|48461|203557;2|74201|203494;2|1239|186801|186802|31979|1485;2|74201|203494|48461|1647988|239934,Complete,NA
bsdb:1111/2/1,Study 1111,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J , Blaser MJ",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy Controls,Hispanic Americans (HA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were Hispanic Americans by Ethnicity,15,16,Less than 3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,4 October 2024,NA,NA,Differential abundance of taxa's that were significantly enriched in Hispanic MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe),increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",2|1239|186801|3085636|186803|572511;2|1239|186801|186802|31979|1485;2|1239|91061;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827|61170;2|201174|84998|1643822|1643826|447020,Complete,NA
bsdb:1111/2/2,Study 1111,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J , Blaser MJ",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy Controls,Hispanic Americans (HA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were Hispanic Americans by Ethnicity,15,16,Less than 3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,4 October 2024,MyleeeA,MyleeeA,Differential abundance of taxa's that were significantly enriched in Hispanic MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe),decreased,"k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1239|909932|1843489|31977|39948;2|1239|186801|3085636|186803|28050;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|201174|84998|1643822|1643826|84108;2|976|200643|171549|2005473,Complete,NA
bsdb:1111/3/1,Study 1111,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J , Blaser MJ",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy Controls,African Americans (AA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were African Americans by Ethnicity,14,14,Less than 3 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2F,4 October 2024,MyleeeA,MyleeeA,Differential abundance of taxa's that were significantly enriched in African American MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe),increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Coriobacteriia",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998,Complete,NA
bsdb:1111/4/2,Study 1111,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J , Blaser MJ",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Relapsing-remitting multiple sclerosis,EFO:0003929,Healthy Controls,Multiple Sclerosis (MS),"All treatment-naïve Multiple Sclerosis subjects who were diagnosed within 6 months of the specimen collection. They subjects included Caucasian American, Hispanic American and African American.",24,24,Less than 3months,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,4 October 2024,NA,NA,Differential abundance of taxa in the Multiple Sclerosis and control subjects from Whole Genome Sequencing (WGS) analysis as determined by LDA effect size (LEfSe).,decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis",2|1224|28216|80840|469610;2|1224|1236|135625|712|724|729;2|976|200643|171549|171550|239759|1288121;2|976|200643|171549|815|816|371601;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005519|397864|487174,Complete,NA
bsdb:1115/1/NA,Study 1115,prospective cohort,37626573,https://doi.org/10.3390/brainsci13081217,NA,"Li Z, Gu M, Sun H, Chen X, Zhou J , Zhang Y",The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia,Brain sciences,2023,"gut microbiota, predictor, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Patients without stroke-associated pneumonia (SAP),Patients with stroke-associated pneumonia (SAP),"Patients who developed SAP, with significantly reduced SCFA-producing gut microbiota compared to those without SAP.",92,43,"1. Use of antibiotics, probiotics, corticosteroids, or immunosuppressants in the last 30 days before admission.
2. History of immune diseases, severe liver and kidney failure, or malignant tumors.
3. Acute hemorrhagic stroke.
4. Unavailable blood or stool samples.",16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1116/1/1,Study 1116,prospective cohort,36945124,10.1177/09564624231160806,NA,"Sabo MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN , McClelland RS",Next generation sequencing to examine associations between vaginal washing and vaginal microbiota: A cohort study,International journal of STD & AIDS,2023,"Africa, sex workers, sexual behaviour, women",Experiment 1,"United States of America,Kenya",Homo sapiens,"Wall of vagina,Anterior fornix of vagina,Posterior fornix of vagina","UBERON:0036523,UBERON:0016487,UBERON:0016486","Vulvovaginal candidiasis,Bacterial vaginosis","EFO:0007543,EFO:0003932",Vaginal washing,Vaginal microbiota,Participants who perform vaginal washing.,26,85,NA,16S,34,Illumina,"Wald Test,Linear Regression",0.1,NA,NA,NA,age,NA,increased,increased,NA,NA,increased,Signature 1,Table 1,3 October 2024,NA,NA,Baseline characteristic,NA,NA,NA,Complete,NA
bsdb:1116/1/2,Study 1116,prospective cohort,36945124,10.1177/09564624231160806,NA,"Sabo MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN , McClelland RS",Next generation sequencing to examine associations between vaginal washing and vaginal microbiota: A cohort study,International journal of STD & AIDS,2023,"Africa, sex workers, sexual behaviour, women",Experiment 1,"United States of America,Kenya",Homo sapiens,"Wall of vagina,Anterior fornix of vagina,Posterior fornix of vagina","UBERON:0036523,UBERON:0016487,UBERON:0016486","Vulvovaginal candidiasis,Bacterial vaginosis","EFO:0007543,EFO:0003932",Vaginal washing,Vaginal microbiota,Participants who perform vaginal washing.,26,85,NA,16S,34,Illumina,"Wald Test,Linear Regression",0.1,NA,NA,NA,age,NA,increased,increased,NA,NA,increased,Signature 2,Table 2,3 October 2024,Sproff,Sproff,Comparison of species diversity and richness at visits with and without vaginal washing.,increased,NA,NA,Complete,NA
bsdb:1116/1/3,Study 1116,prospective cohort,36945124,10.1177/09564624231160806,NA,"Sabo MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN , McClelland RS",Next generation sequencing to examine associations between vaginal washing and vaginal microbiota: A cohort study,International journal of STD & AIDS,2023,"Africa, sex workers, sexual behaviour, women",Experiment 1,"United States of America,Kenya",Homo sapiens,"Wall of vagina,Anterior fornix of vagina,Posterior fornix of vagina","UBERON:0036523,UBERON:0016487,UBERON:0016486","Vulvovaginal candidiasis,Bacterial vaginosis","EFO:0007543,EFO:0003932",Vaginal washing,Vaginal microbiota,Participants who perform vaginal washing.,26,85,NA,16S,34,Illumina,"Wald Test,Linear Regression",0.1,NA,NA,NA,age,NA,increased,increased,NA,NA,increased,Signature 3,Table 3,3 October 2024,Sproff,Sproff,Comparison of relative abundances of vaginal bacterial taxa selected by Wald score for analysis at visits with and without vaginal washing.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sp.",2|201174|1760|85007|1653|1716|169292;2|1239|91061|1385|539738|1378|1379;2|1239|91061|186826|33958|1578;2|1239|186801|3082720|186804|1257|1261;2|1239|91061|1385|90964|1279|29388;2|1239|91061|1385|90964|1279|1283;2|1239|91061|186826|1300|1301|1311;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1304;2|1224|28216|80840|995019|40544|1981025,Complete,NA
bsdb:1116/1/4,Study 1116,prospective cohort,36945124,10.1177/09564624231160806,NA,"Sabo MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN , McClelland RS",Next generation sequencing to examine associations between vaginal washing and vaginal microbiota: A cohort study,International journal of STD & AIDS,2023,"Africa, sex workers, sexual behaviour, women",Experiment 1,"United States of America,Kenya",Homo sapiens,"Wall of vagina,Anterior fornix of vagina,Posterior fornix of vagina","UBERON:0036523,UBERON:0016487,UBERON:0016486","Vulvovaginal candidiasis,Bacterial vaginosis","EFO:0007543,EFO:0003932",Vaginal washing,Vaginal microbiota,Participants who perform vaginal washing.,26,85,NA,16S,34,Illumina,"Wald Test,Linear Regression",0.1,NA,NA,NA,age,NA,increased,increased,NA,NA,increased,Signature 4,Table 4,3 October 2024,Sproff,Sproff,Comparison of relative abundances of vaginal bacterial taxa selected for analysis a priori at visits with and without vaginal washing.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera lornae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sp.",2|201174|84998|84999|1643824|2767327|82135;2|201174|1760|85004|31953|2701|2049026;2|1239|186801|186802|216572|1637257|884684;2|1239|909932|1843489|31977|906|699218;2|1239|909932|1843489|31977|906;2|32066|203490|203491|1129771|168808|187101;2|32066|203490|203491|1129771|168808|40543;2|32066|203490|203491|1129771|168808|2776143,Complete,NA
bsdb:1117/1/1,Study 1117,case-control,36154141,10.1128/msystems.00465-22,NA,"Zhu Q, Yang X, Zhang Y, Shan C , Shi Z",Role of the Gut Microbiota in the Increased Infant Body Mass Index Induced by Gestational Diabetes Mellitus,mSystems,2022,"16S rRNA, BMI, gestational diabetes mellitus, microbiota",Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Gestational diabetes,EFO:0004593,healthy controls,Gestational diabetes mellitus (GDM),"Women who had Gestational diabetes mellitus (GDM),",60,60,3 months,16S,3,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,FIG 2 (D),3 October 2024,Rahila,Rahila,Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in  Gestational diabetes mellitus (GDM) versus healthy controls,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Cytophaga,k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Xanthobacter,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lampyridae|s__Luciolinae|g__Serratia",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|976|768503|768507|89373|978;2|976|768503|768507|89373;2|1224|28211|356|335928;2|1224|1236|91347|1903411;2|1224|28211|356|335928|279;2759|33208|6656|50557|7041|7049|433515|2985502,Complete,NA
bsdb:1117/1/2,Study 1117,case-control,36154141,10.1128/msystems.00465-22,NA,"Zhu Q, Yang X, Zhang Y, Shan C , Shi Z",Role of the Gut Microbiota in the Increased Infant Body Mass Index Induced by Gestational Diabetes Mellitus,mSystems,2022,"16S rRNA, BMI, gestational diabetes mellitus, microbiota",Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Gestational diabetes,EFO:0004593,healthy controls,Gestational diabetes mellitus (GDM),"Women who had Gestational diabetes mellitus (GDM),",60,60,3 months,16S,3,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,FIG 2 (D),3 October 2024,Rahila,Rahila,Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in  Gestational diabetes mellitus (GDM) versus healthy controls,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles",2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375;2|1224|28216|80840|506;2|1224|28211|356|212791;2|1224|1236|91347|543;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1224|28216|80840|75682|963;2|1239|186801|186802|216572;2|1224|1236|2887326|468|497;2|1224|28216|80840|2975441|93681,Complete,NA
bsdb:1118/1/NA,Study 1118,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y, Sun J, Wei L, Jiang H, Hu C, Yang J, Huang Y, Ruan B , Zhu B",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 1,China,Homo sapiens,"Feces,Blood serum","UBERON:0001988,UBERON:0001977",HIV infection,EFO:0000764,Healthy HIV negative individual,HIV infected individual,"HIV infected individual included both 28 immunological responders
(IR), 30 immunological non-responders (INR), IR and INR were defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All
 HIV-positive subjects were on two nucleoside reverse
 transcriptase inhibitors (NRTIs) + nonnucleoside reverse
 transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil
 Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz
(EFV) or Lopinavir/ritonavir (LPV/r).",36,58,"6 months

Other exclusion criteria include: 
Candidates having age over 60 years old; having opportunistic infection; having hepatitis B or C infection; having used rectally administered
medications within 48 h before selection; BMI > 30; having
a history of inflammatory bowel disease (IBD); having active inflammation affecting the gastro intestines.",16S,34,Illumina,"LEfSe,Kruskall-Wallis",3,TRUE,0.05,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:1124/1/1,Study 1124,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford OSE, Alleyne AT , Nelson KE","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 1,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,Women without any specific microbiome conditions,Women with varying vaginal microbiome profiles based on their ancestry.,Women from different ancestries with varying vaginal microbiome compositions.,NA,151,30 days,16S,1234,Illumina,Kruskall-Wallis,0.05,TRUE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 1,3 October 2024,NA,NA,Taxonomic pattern and percentage relative abundance of the top seven phyla within the vaginal microbiomes of the five ethnic groups.,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. Marseille,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella sp.",2|1239|91061|1385|186817|1386|1409;2|976|200643|171549|171552|838|304215;2|201174|1760|85004|31953|2701|2049026,Complete,NA
bsdb:1124/1/2,Study 1124,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford OSE, Alleyne AT , Nelson KE","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 1,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,Women without any specific microbiome conditions,Women with varying vaginal microbiome profiles based on their ancestry.,Women from different ancestries with varying vaginal microbiome compositions.,NA,151,30 days,16S,1234,Illumina,Kruskall-Wallis,0.05,TRUE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 1,3 October 2024,NA,NA,Taxonomic pattern and percentage relative abundance of the top seven phyla within the vaginal microbiomes of the five ethnic groups.,decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis",2|1239|91061|1385|90964|1279;2|204428|204429|51291|809|810|813,Complete,NA
bsdb:1124/1/3,Study 1124,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford OSE, Alleyne AT , Nelson KE","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 1,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,Women without any specific microbiome conditions,Women with varying vaginal microbiome profiles based on their ancestry.,Women from different ancestries with varying vaginal microbiome compositions.,NA,151,30 days,16S,1234,Illumina,Kruskall-Wallis,0.05,TRUE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,NA,NA,NA,Signature 3,Figure 1,3 October 2024,NA,NA,increased abundance in Women with varying vaginal microbiome profiles based on their ancestry.,decreased,k__Bacteria|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,2|204428|204429|51291|809|810|813,Complete,NA
bsdb:1125/1/1,Study 1125,prospective cohort,36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P, Xu B, Liu L, Luo L, Liu T, Jiang M, Liu Z, Li C, Luo X , Lei M",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 1,China,Homo sapiens,"Feces,Venous blood","UBERON:0001988,UBERON:0013756","Gut microbiome measurement,Glucose metabolism measurement","EFO:0007874,EFO:0009367",Han-Chinese,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.8,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 1,3 October 2024,NA,NA,The diagram depicts the overlapping OTUs between Chinese and Africans,increased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. Marseille,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171552|838|304215;2|1239|909932|1843488|909930|33024|626940,Complete,NA
bsdb:1125/1/2,Study 1125,prospective cohort,36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P, Xu B, Liu L, Luo L, Liu T, Jiang M, Liu Z, Li C, Luo X , Lei M",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 1,China,Homo sapiens,"Feces,Venous blood","UBERON:0001988,UBERON:0013756","Gut microbiome measurement,Glucose metabolism measurement","EFO:0007874,EFO:0009367",Han-Chinese,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.8,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 1,3 October 2024,Balogun adekemi,Balogun adekemi,The diagram depicts the overlapping OTUs between Chinese and Africans,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",2|1239|186801|186802|31979|1485|1506;2|1224|28216|80840|995019|577310|487175;2|1239|909932|1843488|909930|33024|33025,Complete,NA
bsdb:1126/1/1,Study 1126,case-control,39198450,10.1038/s41522-024-00542-4,https://pubmed.ncbi.nlm.nih.gov/39198450/,"Licht P, Dominelli N, Kleemann J, Pastore S, Müller ES, Haist M, Hartmann KS, Stege H, Bros M, Meissner M, Grabbe S, Heermann R , Mailänder V",The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Germany,Homo sapiens,Skin epidermis,UBERON:0001003,Mycosis fungoides,EFO:1001051,healthy control( ΔSA-neutral subgroup),Mycosis fungoides( ΔSA-positive),"Patients with significant dysbiosis on MF lesions exhibiting S. aureus expansion. Antimicrobial peptides (AMPs) were probably less prevalent when the overgrowth occurred, and S. aureus was able to adapt to these peptides to become a more virulent strain on the lesions.",20,20,No account,16S,34,Illumina,"ANOVA,PERMANOVA",0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,fig 2a,3 October 2024,Jayybb,Jayybb,Differential abundance analysis of microbial species for N = 65 metagenomic samples.,increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus nagyae,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta",2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85009|31957|1912216|33010;2|1239|1737404|1737405|1570339|162289|54005;2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|1290;2|1239|1737404|1737405|1570339|165779|54007;2|1239|1737404|1737405|1570339|165779|1755241;2|1239|1737404|1737405|1570339|165779|33034;2|201174|1760|85007|1653|1716|38286;2|201174|1760|85007|1653|1716|161879;2|201174|1760|85007|1653|1716|38303;2|201174|1760|85007|1653|1716|38304;2|201174|1760|85009|31957|1912216|33011;2|1224|28211|356|212791|225324;2|1239|186801|186802|216572|216851|853;2759|4751|5204|1538075|162474|742845|55193|76775,Complete,NA
bsdb:1126/1/2,Study 1126,case-control,39198450,10.1038/s41522-024-00542-4,https://pubmed.ncbi.nlm.nih.gov/39198450/,"Licht P, Dominelli N, Kleemann J, Pastore S, Müller ES, Haist M, Hartmann KS, Stege H, Bros M, Meissner M, Grabbe S, Heermann R , Mailänder V",The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Germany,Homo sapiens,Skin epidermis,UBERON:0001003,Mycosis fungoides,EFO:1001051,healthy control( ΔSA-neutral subgroup),Mycosis fungoides( ΔSA-positive),"Patients with significant dysbiosis on MF lesions exhibiting S. aureus expansion. Antimicrobial peptides (AMPs) were probably less prevalent when the overgrowth occurred, and S. aureus was able to adapt to these peptides to become a more virulent strain on the lesions.",20,20,No account,16S,34,Illumina,"ANOVA,PERMANOVA",0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,fig 2a,3 October 2024,Jayybb,Jayybb,Differential abundance analysis of microbial species for N = 65 metagenomic samples.,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria rhizophila,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2|201174|1760|85006|1268|57493|72000;2|1239|91061|1385|90964|1279|1283;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|201174|1760|85007|1653|1716|38286;2|201174|1760|85007|1653|1716|43768;2|201174|1760|85006|1268|57493|71999;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1239|91061|1385|90964|1279|1282,Complete,NA